Starting phenix.real_space_refine on Wed Mar 20 21:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ser_40426/03_2024/8ser_40426_updated.pdb" } resolution = 3.42 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= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 960 5.16 5 C 90908 2.51 5 N 24684 2.21 5 O 26396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4196": "OE1" <-> "OE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3757": "OE1" <-> "OE2" Residue "B GLU 4196": "OE1" <-> "OE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3757": "OE1" <-> "OE2" Residue "C GLU 4196": "OE1" <-> "OE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4196": "OE1" <-> "OE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.40s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142952 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35546 Chain: "B" Number of atoms: 34900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35546 Chain: "C" Number of atoms: 34900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35546 Chain: "D" Number of atoms: 34900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 4376, 34837 Classifications: {'peptide': 4376} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4159} 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: 35546 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34226 SG CYS A4958 175.492 200.749 89.165 1.00169.88 S ATOM 34251 SG CYS A4961 178.065 202.050 91.713 1.00158.19 S ATOM 69126 SG CYS B4958 180.442 175.496 89.149 1.00169.88 S ATOM 69151 SG CYS B4961 179.145 178.068 91.700 1.00158.19 S ATOM A033U SG CYS C4958 205.751 180.441 89.150 1.00169.88 S ATOM A034J SG CYS C4961 203.179 179.144 91.701 1.00158.19 S ATOM A0U1A SG CYS D4958 200.807 205.750 89.151 1.00169.88 S ATOM A0U1Z SG CYS D4961 202.104 203.177 91.702 1.00158.19 S Time building chain proxies: 96.11, per 1000 atoms: 0.67 Number of scatterers: 142952 At special positions: 0 Unit cell: (382.536, 382.536, 216.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 960 16.00 O 26396 8.00 N 24684 7.00 C 90908 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: 40.18 Conformation dependent library (CDL) restraints added in 35.1 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 A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " 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 C4958 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " 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 D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " Number of angles added : 8 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33680 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: 688 helices and 80 sheets defined 58.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 41.10 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.063A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.949A 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 256 removed outlier: 4.707A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 308 through 313 removed outlier: 6.219A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 313' Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.424A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 423 removed outlier: 3.871A pdb=" N GLY A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.308A 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: 3.521A pdb=" N GLN A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 removed outlier: 3.981A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.931A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.576A pdb=" N ALA A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.716A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.564A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.645A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 4.257A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.935A 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 Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.902A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.584A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.532A 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: 3.875A pdb=" N PHE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.557A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.789A 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: 3.935A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1004 removed outlier: 3.535A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 removed outlier: 4.075A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 4.646A pdb=" N ARG A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 5.119A 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 1217 through 1222 removed outlier: 6.971A pdb=" N GLU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A1222 " --> pdb=" O GLY A1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1217 through 1222' Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.675A pdb=" N LEU A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 4.083A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.631A 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: 4.461A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 4.416A 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: 3.749A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1656 removed outlier: 4.515A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1675 removed outlier: 3.592A pdb=" N ARG A1668 " --> pdb=" O SER A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 4.162A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 removed outlier: 3.590A pdb=" N LEU A1694 " --> pdb=" O ASP A1690 " (cutoff:3.500A) removed outlier: 3.769A 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: 3.508A pdb=" N SER A1726 " --> pdb=" O SER A1722 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU A1733 " --> pdb=" O SER A1729 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.612A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.521A 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: 4.302A pdb=" N MET A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 5.745A 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: 3.725A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR A1985 " --> pdb=" O MET A1981 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2000 removed outlier: 4.384A pdb=" N ARG A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2011 removed outlier: 3.652A pdb=" N ILE A2006 " --> pdb=" O PRO A2002 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A2007 " --> pdb=" O GLN A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2022 removed outlier: 3.915A 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 removed outlier: 3.828A pdb=" N GLN A2036 " --> pdb=" O GLN A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.746A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.640A 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: 5.442A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2145 through 2169 removed outlier: 4.253A pdb=" N VAL A2149 " --> pdb=" O SER A2145 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A2150 " --> pdb=" O PRO A2146 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP A2151 " --> pdb=" O SER A2147 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A2165 " --> pdb=" O GLN A2161 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2189 removed outlier: 3.623A pdb=" N GLN A2180 " --> pdb=" O ASN A2176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2195 Proline residue: A2195 - end of helix Processing helix chain 'A' and resid 2196 through 2202 Processing helix chain 'A' and resid 2203 through 2219 removed outlier: 3.601A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY A2218 " --> pdb=" O VAL A2214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A2219 " --> pdb=" O LEU A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 3.655A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A2234 " --> pdb=" O THR A2230 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 4.072A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2265 removed outlier: 3.511A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.925A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2308 removed outlier: 3.698A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.695A pdb=" N LYS A2316 " --> pdb=" O MET A2312 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A2317 " --> pdb=" O LEU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.961A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A2337 " --> pdb=" O ASP A2333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.650A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (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 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: 3.983A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2525 removed outlier: 4.184A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2537 Processing helix chain 'A' and resid 2544 through 2566 removed outlier: 5.542A 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: 3.574A pdb=" N VAL A2579 " --> pdb=" O ARG A2575 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A2592 " --> pdb=" O ARG A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 3.588A pdb=" N VAL A2602 " --> pdb=" O ALA A2598 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 4.102A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A2620 " --> pdb=" O PRO A2616 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A2629 " --> pdb=" O ARG A2625 " (cutoff:3.500A) Processing helix chain 'A' and resid 2636 through 2652 Proline residue: A2640 - end of helix Processing helix chain 'A' and resid 2668 through 2689 removed outlier: 6.578A pdb=" N LEU A2672 " --> pdb=" O SER A2668 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A2673 " --> pdb=" O GLU A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2693 through 2711 removed outlier: 3.679A 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 2741 through 2746 removed outlier: 5.259A pdb=" N VAL A2745 " --> pdb=" O GLU A2741 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE A2746 " --> pdb=" O THR A2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2741 through 2746' Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 4.041A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A2774 " --> pdb=" O LYS A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2820 removed outlier: 4.192A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG A2806 " --> pdb=" O LYS A2802 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Proline residue: A2808 - end of helix removed outlier: 3.690A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU A2820 " --> pdb=" O MET A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 4.003A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2912 removed outlier: 3.581A pdb=" N LEU A2911 " --> pdb=" O PRO A2907 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR A2912 " --> pdb=" O TYR A2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2907 through 2912' Processing helix chain 'A' and resid 2913 through 2934 removed outlier: 3.587A pdb=" N ALA A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A2933 " --> pdb=" O PHE A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2983 removed outlier: 3.736A pdb=" N ARG A2954 " --> pdb=" O SER A2950 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE A2955 " --> pdb=" O ILE A2951 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA A2956 " --> pdb=" O GLU A2952 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE A2957 " --> pdb=" O LYS A2953 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A2976 " --> pdb=" O GLU A2972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3014 removed outlier: 5.070A 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 Processing helix chain 'A' and resid 3053 through 3058 removed outlier: 3.847A pdb=" N PHE A3057 " --> pdb=" O ARG A3053 " (cutoff:3.500A) removed outlier: 4.292A 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 3084 Processing helix chain 'A' and resid 3085 through 3112 removed outlier: 3.792A pdb=" N GLU A3108 " --> pdb=" O GLU A3104 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A3112 " --> pdb=" O GLU A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3151 removed outlier: 3.677A pdb=" N GLN A3127 " --> pdb=" O LYS A3123 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A3132 " --> pdb=" O ASN A3128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A3134 " --> pdb=" O THR A3130 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU A3137 " --> pdb=" O THR A3133 " (cutoff:3.500A) Proline residue: A3138 - end of helix Processing helix chain 'A' and resid 3159 through 3176 removed outlier: 4.220A pdb=" N VAL A3163 " --> pdb=" O ASP A3159 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A3175 " --> pdb=" O SER A3171 " (cutoff:3.500A) removed outlier: 4.926A 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 Processing helix chain 'A' and resid 3207 through 3215 removed outlier: 3.920A pdb=" N ASN A3211 " --> pdb=" O GLU A3207 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU A3212 " --> pdb=" O PRO A3208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A3213 " --> pdb=" O GLN A3209 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A3214 " --> pdb=" O LEU A3210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA A3215 " --> pdb=" O ASN A3211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3207 through 3215' Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3226 through 3231 removed outlier: 6.680A pdb=" N LEU A3230 " --> pdb=" O GLU A3226 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3226 through 3231' Processing helix chain 'A' and resid 3235 through 3241 removed outlier: 4.676A pdb=" N CYS A3240 " --> pdb=" O VAL A3236 " (cutoff:3.500A) Proline residue: A3241 - end of helix Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 3.610A 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 3285 removed outlier: 4.426A pdb=" N LEU A3274 " --> pdb=" O ILE A3270 " (cutoff:3.500A) Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3308 through 3327 removed outlier: 4.151A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) Processing helix chain 'A' and resid 3332 through 3350 removed outlier: 5.522A pdb=" N LYS A3336 " --> pdb=" O ALA A3332 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A3337 " --> pdb=" O THR A3333 " (cutoff:3.500A) Proline residue: A3344 - end of helix removed outlier: 4.094A pdb=" N SER A3347 " --> pdb=" O GLN A3343 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A3348 " --> pdb=" O PRO A3344 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA A3349 " --> pdb=" O ILE A3345 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG A3350 " --> pdb=" O VAL A3346 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3383 removed outlier: 4.357A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A3359 " --> pdb=" O HIS A3355 " (cutoff:3.500A) Proline residue: A3360 - end of helix removed outlier: 3.771A pdb=" N GLU A3382 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA A3383 " --> pdb=" O LEU A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3413 removed outlier: 6.612A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) Proline residue: A3410 - end of helix Processing helix chain 'A' and resid 3419 through 3427 Proline residue: A3427 - end of helix Processing helix chain 'A' and resid 3428 through 3449 removed outlier: 4.342A pdb=" N HIS A3449 " --> pdb=" O TRP A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3463 Processing helix chain 'A' and resid 3466 through 3478 removed outlier: 3.911A pdb=" N LEU A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP A3473 " --> pdb=" O PHE A3469 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER A3474 " --> pdb=" O LEU A3470 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET A3478 " --> pdb=" O SER A3474 " (cutoff:3.500A) Processing helix chain 'A' and resid 3508 through 3525 Proline residue: A3519 - end of helix removed outlier: 3.706A pdb=" N MET A3524 " --> pdb=" O ILE A3520 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) Processing helix chain 'A' and resid 3529 through 3543 removed outlier: 3.575A 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: 3.849A 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 3579 removed outlier: 4.230A pdb=" N GLY A3578 " --> pdb=" O ALA A3574 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A3579 " --> pdb=" O LEU A3575 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3612 removed outlier: 3.592A pdb=" N VAL A3593 " --> pdb=" O PRO A3589 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A3602 " --> pdb=" O GLU A3598 " (cutoff:3.500A) Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3628 through 3638 removed outlier: 4.245A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A3633 " --> pdb=" O ARG A3629 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3661 removed outlier: 3.642A pdb=" N MET A3652 " --> pdb=" O ARG A3648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A3659 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3679 removed outlier: 3.584A pdb=" N ILE A3674 " --> pdb=" O GLU A3670 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A3679 " --> pdb=" O ASP A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3682 through 3687 Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 3.808A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 3.574A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A3761 " --> pdb=" O GLU A3757 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A3765 " --> pdb=" O GLN A3761 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.201A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.721A pdb=" N THR A3797 " --> pdb=" O MET A3793 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3825 through 3839 removed outlier: 4.929A pdb=" N PHE A3829 " --> pdb=" O GLU A3825 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3857 Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.610A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.507A pdb=" N SER A3929 " --> pdb=" O ARG A3925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A3936 " --> pdb=" O ASP A3932 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.539A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4007 removed outlier: 3.675A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.712A pdb=" N ASP A4018 " --> pdb=" O LYS A4014 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A4020 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.040A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 5.345A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.973A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A4099 " --> pdb=" O LYS A4095 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN A4100 " --> pdb=" O ALA A4096 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 3.553A pdb=" N LEU A4112 " --> pdb=" O ILE A4108 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4155 removed outlier: 3.800A pdb=" N ALA A4129 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix removed outlier: 4.210A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 3.886A 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: 3.794A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 3.540A pdb=" N LYS A4230 " --> pdb=" O GLY A4226 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4543 through 4559 removed outlier: 3.608A pdb=" N GLN A4547 " --> pdb=" O GLU A4543 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 3.536A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4683 removed outlier: 4.117A 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: 4.304A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.489A 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 Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 4.538A pdb=" N LEU A4748 " --> pdb=" O ASP A4744 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4744 through 4749' Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.460A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4805 removed outlier: 3.765A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 5.172A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.621A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.364A pdb=" N TYR A4863 " --> pdb=" O PHE A4859 " (cutoff:3.500A) removed outlier: 5.043A 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: 4.051A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.209A 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: 4.666A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.955A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 3.910A 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 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.063A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.950A 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 256 removed outlier: 4.707A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 256' Processing helix chain 'B' and resid 308 through 313 removed outlier: 6.220A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.424A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 423 removed outlier: 3.870A pdb=" N GLY B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.308A 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: 3.522A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.981A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.930A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 removed outlier: 3.576A pdb=" N ALA B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 removed outlier: 3.716A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.563A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP B 552 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.645A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 4.258A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.934A 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 Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.903A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 Processing helix chain 'B' and resid 810 through 815 removed outlier: 4.584A pdb=" N ALA B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 4.532A 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: 3.875A pdb=" N PHE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.557A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU B 880 " --> pdb=" O GLU B 876 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 881 " --> pdb=" O ASN B 877 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.790A 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: 3.934A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1004 removed outlier: 3.535A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1048 removed outlier: 4.075A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1072 removed outlier: 4.647A pdb=" N ARG B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 5.119A 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 1217 through 1222 removed outlier: 6.972A pdb=" N GLU B1221 " --> pdb=" O CYS B1217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B1222 " --> pdb=" O GLY B1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1217 through 1222' Processing helix chain 'B' and resid 1423 through 1430 removed outlier: 3.675A pdb=" N LEU B1428 " --> pdb=" O PRO B1424 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN B1429 " --> pdb=" O GLU B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1449 removed outlier: 4.083A pdb=" N VAL B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) removed outlier: 5.631A 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: 4.461A pdb=" N PHE B1500 " --> pdb=" O TRP B1496 " (cutoff:3.500A) removed outlier: 4.417A 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: 3.748A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1656 removed outlier: 4.516A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1657 through 1675 removed outlier: 3.592A pdb=" N ARG B1668 " --> pdb=" O SER B1664 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 4.162A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.590A pdb=" N LEU B1694 " --> pdb=" O ASP B1690 " (cutoff:3.500A) removed outlier: 3.767A 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: 3.507A pdb=" N SER B1726 " --> pdb=" O SER B1722 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU B1733 " --> pdb=" O SER B1729 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR B1734 " --> pdb=" O MET B1730 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.612A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.520A 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: 4.302A pdb=" N MET B1929 " --> pdb=" O GLY B1925 " (cutoff:3.500A) removed outlier: 5.744A 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: 3.725A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B1982 " --> pdb=" O ALA B1978 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR B1985 " --> pdb=" O MET B1981 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2000 removed outlier: 4.385A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2011 removed outlier: 3.652A pdb=" N ILE B2006 " --> pdb=" O PRO B2002 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2022 removed outlier: 3.915A 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 removed outlier: 3.828A pdb=" N GLN B2036 " --> pdb=" O GLN B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.746A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.640A 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: 5.442A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2145 through 2169 removed outlier: 4.253A pdb=" N VAL B2149 " --> pdb=" O SER B2145 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU B2150 " --> pdb=" O PRO B2146 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP B2151 " --> pdb=" O SER B2147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B2165 " --> pdb=" O GLN B2161 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B2166 " --> pdb=" O ILE B2162 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2189 removed outlier: 3.622A pdb=" N GLN B2180 " --> pdb=" O ASN B2176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) removed outlier: 5.438A 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 2202 Processing helix chain 'B' and resid 2203 through 2219 removed outlier: 3.603A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY B2218 " --> pdb=" O VAL B2214 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B2219 " --> pdb=" O LEU B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2244 removed outlier: 3.655A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG B2234 " --> pdb=" O THR B2230 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 4.072A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2265 removed outlier: 3.511A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 3.925A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2290 Processing helix chain 'B' and resid 2291 through 2308 removed outlier: 3.698A pdb=" N LEU B2295 " --> pdb=" O GLN B2291 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.695A pdb=" N LYS B2316 " --> pdb=" O MET B2312 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY B2317 " --> pdb=" O LEU B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.961A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B2337 " --> pdb=" O ASP B2333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B2340 " --> pdb=" O ARG B2336 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.650A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (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 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: 3.982A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2525 removed outlier: 4.184A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2537 Processing helix chain 'B' and resid 2544 through 2566 removed outlier: 5.543A 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: 3.575A pdb=" N VAL B2579 " --> pdb=" O ARG B2575 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B2592 " --> pdb=" O ARG B2588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2596 through 2614 removed outlier: 3.588A pdb=" N VAL B2602 " --> pdb=" O ALA B2598 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR B2613 " --> pdb=" O ALA B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2630 removed outlier: 4.101A pdb=" N LEU B2619 " --> pdb=" O ARG B2615 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B2620 " --> pdb=" O PRO B2616 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS B2621 " --> pdb=" O SER B2617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B2622 " --> pdb=" O MET B2618 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B2628 " --> pdb=" O ARG B2624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B2629 " --> pdb=" O ARG B2625 " (cutoff:3.500A) Processing helix chain 'B' and resid 2636 through 2652 Proline residue: B2640 - end of helix Processing helix chain 'B' and resid 2668 through 2689 removed outlier: 6.577A pdb=" N LEU B2672 " --> pdb=" O SER B2668 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS B2673 " --> pdb=" O GLU B2669 " (cutoff:3.500A) Processing helix chain 'B' and resid 2693 through 2711 removed outlier: 3.679A 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 2741 through 2746 removed outlier: 5.260A pdb=" N VAL B2745 " --> pdb=" O GLU B2741 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE B2746 " --> pdb=" O THR B2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2741 through 2746' Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 4.040A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B2774 " --> pdb=" O LYS B2770 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2820 removed outlier: 4.191A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG B2806 " --> pdb=" O LYS B2802 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 3.691A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B2820 " --> pdb=" O MET B2816 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.003A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2907 through 2912 removed outlier: 3.581A pdb=" N LEU B2911 " --> pdb=" O PRO B2907 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR B2912 " --> pdb=" O TYR B2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2907 through 2912' Processing helix chain 'B' and resid 2913 through 2934 removed outlier: 3.588A pdb=" N ALA B2917 " --> pdb=" O ALA B2913 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS B2922 " --> pdb=" O ARG B2918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN B2933 " --> pdb=" O PHE B2929 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2983 removed outlier: 3.736A pdb=" N ARG B2954 " --> pdb=" O SER B2950 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE B2955 " --> pdb=" O ILE B2951 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B2956 " --> pdb=" O GLU B2952 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B2957 " --> pdb=" O LYS B2953 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B2975 " --> pdb=" O GLN B2971 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B2976 " --> pdb=" O GLU B2972 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3014 removed outlier: 5.070A 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 Processing helix chain 'B' and resid 3053 through 3058 removed outlier: 3.847A pdb=" N PHE B3057 " --> pdb=" O ARG B3053 " (cutoff:3.500A) removed outlier: 4.292A 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 3084 Processing helix chain 'B' and resid 3085 through 3112 removed outlier: 3.792A pdb=" N GLU B3108 " --> pdb=" O GLU B3104 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B3112 " --> pdb=" O GLU B3108 " (cutoff:3.500A) Processing helix chain 'B' and resid 3123 through 3151 removed outlier: 3.677A pdb=" N GLN B3127 " --> pdb=" O LYS B3123 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B3132 " --> pdb=" O ASN B3128 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR B3133 " --> pdb=" O LEU B3129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL B3134 " --> pdb=" O THR B3130 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B3137 " --> pdb=" O THR B3133 " (cutoff:3.500A) Proline residue: B3138 - end of helix Processing helix chain 'B' and resid 3159 through 3176 removed outlier: 4.219A pdb=" N VAL B3163 " --> pdb=" O ASP B3159 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B3175 " --> pdb=" O SER B3171 " (cutoff:3.500A) removed outlier: 4.926A 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 Processing helix chain 'B' and resid 3207 through 3215 removed outlier: 3.919A pdb=" N ASN B3211 " --> pdb=" O GLU B3207 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU B3212 " --> pdb=" O PRO B3208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B3213 " --> pdb=" O GLN B3209 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN B3214 " --> pdb=" O LEU B3210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA B3215 " --> pdb=" O ASN B3211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3207 through 3215' Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3226 through 3231 removed outlier: 6.679A pdb=" N LEU B3230 " --> pdb=" O GLU B3226 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3226 through 3231' Processing helix chain 'B' and resid 3235 through 3241 removed outlier: 4.676A pdb=" N CYS B3240 " --> pdb=" O VAL B3236 " (cutoff:3.500A) Proline residue: B3241 - end of helix Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 3.612A 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 3285 removed outlier: 4.427A pdb=" N LEU B3274 " --> pdb=" O ILE B3270 " (cutoff:3.500A) Proline residue: B3275 - end of helix Proline residue: B3282 - end of helix Processing helix chain 'B' and resid 3308 through 3327 removed outlier: 4.152A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) Processing helix chain 'B' and resid 3332 through 3350 removed outlier: 5.522A pdb=" N LYS B3336 " --> pdb=" O ALA B3332 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B3337 " --> pdb=" O THR B3333 " (cutoff:3.500A) Proline residue: B3344 - end of helix removed outlier: 4.095A pdb=" N SER B3347 " --> pdb=" O GLN B3343 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG B3348 " --> pdb=" O PRO B3344 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA B3349 " --> pdb=" O ILE B3345 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B3350 " --> pdb=" O VAL B3346 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3383 removed outlier: 4.357A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B3359 " --> pdb=" O HIS B3355 " (cutoff:3.500A) Proline residue: B3360 - end of helix removed outlier: 3.771A pdb=" N GLU B3382 " --> pdb=" O GLN B3378 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA B3383 " --> pdb=" O LEU B3379 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3413 removed outlier: 6.613A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) Proline residue: B3410 - end of helix Processing helix chain 'B' and resid 3419 through 3427 Proline residue: B3427 - end of helix Processing helix chain 'B' and resid 3428 through 3449 removed outlier: 4.342A pdb=" N HIS B3449 " --> pdb=" O TRP B3445 " (cutoff:3.500A) Processing helix chain 'B' and resid 3450 through 3463 Processing helix chain 'B' and resid 3466 through 3478 removed outlier: 3.911A pdb=" N LEU B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP B3473 " --> pdb=" O PHE B3469 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B3474 " --> pdb=" O LEU B3470 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B3478 " --> pdb=" O SER B3474 " (cutoff:3.500A) Processing helix chain 'B' and resid 3508 through 3525 Proline residue: B3519 - end of helix removed outlier: 3.706A pdb=" N MET B3524 " --> pdb=" O ILE B3520 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS B3525 " --> pdb=" O GLY B3521 " (cutoff:3.500A) Processing helix chain 'B' and resid 3529 through 3543 removed outlier: 3.577A 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: 3.849A 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 3579 removed outlier: 4.230A pdb=" N GLY B3578 " --> pdb=" O ALA B3574 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B3579 " --> pdb=" O LEU B3575 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3612 removed outlier: 3.592A pdb=" N VAL B3593 " --> pdb=" O PRO B3589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B3602 " --> pdb=" O GLU B3598 " (cutoff:3.500A) Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3628 through 3638 removed outlier: 4.245A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B3633 " --> pdb=" O ARG B3629 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3661 removed outlier: 3.642A pdb=" N MET B3652 " --> pdb=" O ARG B3648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B3659 " --> pdb=" O GLU B3655 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3679 removed outlier: 3.584A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B3676 " --> pdb=" O ARG B3672 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B3679 " --> pdb=" O ASP B3675 " (cutoff:3.500A) Processing helix chain 'B' and resid 3682 through 3687 Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 3.809A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 3.573A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B3761 " --> pdb=" O GLU B3757 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B3765 " --> pdb=" O GLN B3761 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.201A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.721A pdb=" N THR B3797 " --> pdb=" O MET B3793 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3825 through 3839 removed outlier: 4.929A pdb=" N PHE B3829 " --> pdb=" O GLU B3825 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3857 Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.611A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.508A pdb=" N SER B3929 " --> pdb=" O ARG B3925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.539A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4007 removed outlier: 3.674A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER B4007 " --> pdb=" O LEU B4003 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.712A pdb=" N ASP B4018 " --> pdb=" O LYS B4014 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.041A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 5.345A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.972A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B4099 " --> pdb=" O LYS B4095 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 3.554A pdb=" N LEU B4112 " --> pdb=" O ILE B4108 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4155 removed outlier: 3.799A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 4.210A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.885A 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: 3.794A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 3.540A pdb=" N LYS B4230 " --> pdb=" O GLY B4226 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4543 through 4559 removed outlier: 3.608A pdb=" N GLN B4547 " --> pdb=" O GLU B4543 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 3.537A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4683 removed outlier: 4.117A 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: 4.303A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.488A 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 Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 4.538A pdb=" N LEU B4748 " --> pdb=" O ASP B4744 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4744 through 4749' Processing helix chain 'B' and resid 4772 through 4787 removed outlier: 5.461A pdb=" N ASN B4787 " --> pdb=" O ILE B4783 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4805 removed outlier: 3.764A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 5.172A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.621A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.364A pdb=" N TYR B4863 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 5.042A 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: 4.050A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.209A 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: 4.666A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.954A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.910A 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 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5033 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.063A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.949A 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 256 removed outlier: 4.707A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 256' Processing helix chain 'C' and resid 308 through 313 removed outlier: 6.219A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.424A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 423 removed outlier: 3.871A pdb=" N GLY C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.308A 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: 3.522A pdb=" N GLN C 465 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 497 removed outlier: 3.982A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR C 497 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.930A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 531 removed outlier: 3.575A pdb=" N ALA C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.716A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 552 removed outlier: 3.564A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP C 552 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.645A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 579 removed outlier: 4.258A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 5.934A 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 Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.902A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 Processing helix chain 'C' and resid 810 through 815 removed outlier: 4.584A pdb=" N ALA C 814 " --> pdb=" O PRO C 810 " (cutoff:3.500A) removed outlier: 4.532A 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: 3.875A pdb=" N PHE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.557A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU C 880 " --> pdb=" O GLU C 876 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.790A 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: 3.935A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1004 removed outlier: 3.534A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1048 removed outlier: 4.075A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1072 removed outlier: 4.646A pdb=" N ARG C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) removed outlier: 5.119A 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 1217 through 1222 removed outlier: 6.970A pdb=" N GLU C1221 " --> pdb=" O CYS C1217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C1222 " --> pdb=" O GLY C1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1222' Processing helix chain 'C' and resid 1423 through 1430 removed outlier: 3.675A pdb=" N LEU C1428 " --> pdb=" O PRO C1424 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN C1429 " --> pdb=" O GLU C1425 " (cutoff:3.500A) Processing helix chain 'C' and resid 1444 through 1449 removed outlier: 4.083A pdb=" N VAL C1448 " --> pdb=" O GLU C1444 " (cutoff:3.500A) removed outlier: 5.630A 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: 4.460A pdb=" N PHE C1500 " --> pdb=" O TRP C1496 " (cutoff:3.500A) removed outlier: 4.416A 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: 3.748A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1656 removed outlier: 4.515A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) Processing helix chain 'C' and resid 1657 through 1675 removed outlier: 3.591A pdb=" N ARG C1668 " --> pdb=" O SER C1664 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 4.161A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 removed outlier: 3.590A pdb=" N LEU C1694 " --> pdb=" O ASP C1690 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.507A pdb=" N SER C1726 " --> pdb=" O SER C1722 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU C1733 " --> pdb=" O SER C1729 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.612A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.519A 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: 4.303A pdb=" N MET C1929 " --> pdb=" O GLY C1925 " (cutoff:3.500A) removed outlier: 5.744A 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: 3.725A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C1982 " --> pdb=" O ALA C1978 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR C1985 " --> pdb=" O MET C1981 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1990 through 2000 removed outlier: 4.384A pdb=" N ARG C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2011 removed outlier: 3.652A pdb=" N ILE C2006 " --> pdb=" O PRO C2002 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN C2007 " --> pdb=" O GLN C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2017 through 2022 removed outlier: 3.915A 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 removed outlier: 3.828A pdb=" N GLN C2036 " --> pdb=" O GLN C2032 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.746A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.640A 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: 5.443A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2145 through 2169 removed outlier: 4.253A pdb=" N VAL C2149 " --> pdb=" O SER C2145 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU C2150 " --> pdb=" O PRO C2146 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP C2151 " --> pdb=" O SER C2147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C2165 " --> pdb=" O GLN C2161 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C2166 " --> pdb=" O ILE C2162 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2189 removed outlier: 3.622A pdb=" N GLN C2180 " --> pdb=" O ASN C2176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) removed outlier: 5.438A 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 2202 Processing helix chain 'C' and resid 2203 through 2219 removed outlier: 3.602A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY C2218 " --> pdb=" O VAL C2214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C2219 " --> pdb=" O LEU C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2244 removed outlier: 3.656A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C2234 " --> pdb=" O THR C2230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 4.072A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2265 removed outlier: 3.511A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 3.926A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2308 removed outlier: 3.698A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.695A pdb=" N LYS C2316 " --> pdb=" O MET C2312 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C2317 " --> pdb=" O LEU C2313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.961A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C2337 " --> pdb=" O ASP C2333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C2340 " --> pdb=" O ARG C2336 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.651A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (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 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: 3.982A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2525 removed outlier: 4.185A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2537 Processing helix chain 'C' and resid 2544 through 2566 removed outlier: 5.543A 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: 3.575A pdb=" N VAL C2579 " --> pdb=" O ARG C2575 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C2592 " --> pdb=" O ARG C2588 " (cutoff:3.500A) Processing helix chain 'C' and resid 2596 through 2614 removed outlier: 3.589A pdb=" N VAL C2602 " --> pdb=" O ALA C2598 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C2613 " --> pdb=" O ALA C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2630 removed outlier: 4.101A pdb=" N LEU C2619 " --> pdb=" O ARG C2615 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN C2620 " --> pdb=" O PRO C2616 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C2621 " --> pdb=" O SER C2617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C2622 " --> pdb=" O MET C2618 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C2628 " --> pdb=" O ARG C2624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C2629 " --> pdb=" O ARG C2625 " (cutoff:3.500A) Processing helix chain 'C' and resid 2636 through 2652 Proline residue: C2640 - end of helix Processing helix chain 'C' and resid 2668 through 2689 removed outlier: 6.578A pdb=" N LEU C2672 " --> pdb=" O SER C2668 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C2673 " --> pdb=" O GLU C2669 " (cutoff:3.500A) Processing helix chain 'C' and resid 2693 through 2711 removed outlier: 3.678A 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 2741 through 2746 removed outlier: 5.260A pdb=" N VAL C2745 " --> pdb=" O GLU C2741 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE C2746 " --> pdb=" O THR C2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2741 through 2746' Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 4.040A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C2774 " --> pdb=" O LYS C2770 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2820 removed outlier: 4.191A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Proline residue: C2808 - end of helix removed outlier: 3.691A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU C2820 " --> pdb=" O MET C2816 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 4.003A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2907 through 2912 removed outlier: 3.581A pdb=" N LEU C2911 " --> pdb=" O PRO C2907 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR C2912 " --> pdb=" O TYR C2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2907 through 2912' Processing helix chain 'C' and resid 2913 through 2934 removed outlier: 3.587A pdb=" N ALA C2917 " --> pdb=" O ALA C2913 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C2933 " --> pdb=" O PHE C2929 " (cutoff:3.500A) Processing helix chain 'C' and resid 2949 through 2983 removed outlier: 3.736A pdb=" N ARG C2954 " --> pdb=" O SER C2950 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE C2955 " --> pdb=" O ILE C2951 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA C2956 " --> pdb=" O GLU C2952 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE C2957 " --> pdb=" O LYS C2953 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C2975 " --> pdb=" O GLN C2971 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS C2976 " --> pdb=" O GLU C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3014 removed outlier: 5.070A 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 Processing helix chain 'C' and resid 3053 through 3058 removed outlier: 3.847A pdb=" N PHE C3057 " --> pdb=" O ARG C3053 " (cutoff:3.500A) removed outlier: 4.293A 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 3084 Processing helix chain 'C' and resid 3085 through 3112 removed outlier: 3.792A pdb=" N GLU C3108 " --> pdb=" O GLU C3104 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C3112 " --> pdb=" O GLU C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3123 through 3151 removed outlier: 3.677A pdb=" N GLN C3127 " --> pdb=" O LYS C3123 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C3132 " --> pdb=" O ASN C3128 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C3133 " --> pdb=" O LEU C3129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL C3134 " --> pdb=" O THR C3130 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C3137 " --> pdb=" O THR C3133 " (cutoff:3.500A) Proline residue: C3138 - end of helix Processing helix chain 'C' and resid 3159 through 3176 removed outlier: 4.220A pdb=" N VAL C3163 " --> pdb=" O ASP C3159 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C3175 " --> pdb=" O SER C3171 " (cutoff:3.500A) removed outlier: 4.926A 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 Processing helix chain 'C' and resid 3207 through 3215 removed outlier: 3.919A pdb=" N ASN C3211 " --> pdb=" O GLU C3207 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU C3212 " --> pdb=" O PRO C3208 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR C3213 " --> pdb=" O GLN C3209 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN C3214 " --> pdb=" O LEU C3210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA C3215 " --> pdb=" O ASN C3211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3207 through 3215' Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3226 through 3231 removed outlier: 6.679A pdb=" N LEU C3230 " --> pdb=" O GLU C3226 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3226 through 3231' Processing helix chain 'C' and resid 3235 through 3241 removed outlier: 4.675A pdb=" N CYS C3240 " --> pdb=" O VAL C3236 " (cutoff:3.500A) Proline residue: C3241 - end of helix Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 3.611A 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 3285 removed outlier: 4.426A pdb=" N LEU C3274 " --> pdb=" O ILE C3270 " (cutoff:3.500A) Proline residue: C3275 - end of helix Proline residue: C3282 - end of helix Processing helix chain 'C' and resid 3308 through 3327 removed outlier: 4.152A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) Processing helix chain 'C' and resid 3332 through 3350 removed outlier: 5.522A pdb=" N LYS C3336 " --> pdb=" O ALA C3332 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C3337 " --> pdb=" O THR C3333 " (cutoff:3.500A) Proline residue: C3344 - end of helix removed outlier: 4.095A pdb=" N SER C3347 " --> pdb=" O GLN C3343 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG C3348 " --> pdb=" O PRO C3344 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA C3349 " --> pdb=" O ILE C3345 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG C3350 " --> pdb=" O VAL C3346 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3383 removed outlier: 4.357A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE C3359 " --> pdb=" O HIS C3355 " (cutoff:3.500A) Proline residue: C3360 - end of helix removed outlier: 3.771A pdb=" N GLU C3382 " --> pdb=" O GLN C3378 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA C3383 " --> pdb=" O LEU C3379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3389 through 3413 removed outlier: 6.612A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) Proline residue: C3410 - end of helix Processing helix chain 'C' and resid 3419 through 3427 Proline residue: C3427 - end of helix Processing helix chain 'C' and resid 3428 through 3449 removed outlier: 4.342A pdb=" N HIS C3449 " --> pdb=" O TRP C3445 " (cutoff:3.500A) Processing helix chain 'C' and resid 3450 through 3463 Processing helix chain 'C' and resid 3466 through 3478 removed outlier: 3.911A pdb=" N LEU C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ASP C3473 " --> pdb=" O PHE C3469 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C3474 " --> pdb=" O LEU C3470 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET C3478 " --> pdb=" O SER C3474 " (cutoff:3.500A) Processing helix chain 'C' and resid 3508 through 3525 Proline residue: C3519 - end of helix removed outlier: 3.705A pdb=" N MET C3524 " --> pdb=" O ILE C3520 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS C3525 " --> pdb=" O GLY C3521 " (cutoff:3.500A) Processing helix chain 'C' and resid 3529 through 3543 removed outlier: 3.576A 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: 3.849A 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 3579 removed outlier: 4.231A pdb=" N GLY C3578 " --> pdb=" O ALA C3574 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C3579 " --> pdb=" O LEU C3575 " (cutoff:3.500A) Processing helix chain 'C' and resid 3588 through 3612 removed outlier: 3.592A pdb=" N VAL C3593 " --> pdb=" O PRO C3589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C3602 " --> pdb=" O GLU C3598 " (cutoff:3.500A) Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3628 through 3638 removed outlier: 4.245A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL C3633 " --> pdb=" O ARG C3629 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3661 removed outlier: 3.643A pdb=" N MET C3652 " --> pdb=" O ARG C3648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C3659 " --> pdb=" O GLU C3655 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3679 removed outlier: 3.584A pdb=" N ILE C3674 " --> pdb=" O GLU C3670 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C3676 " --> pdb=" O ARG C3672 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS C3679 " --> pdb=" O ASP C3675 " (cutoff:3.500A) Processing helix chain 'C' and resid 3682 through 3687 Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 3.809A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU C3735 " --> pdb=" O LYS C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 3.573A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C3761 " --> pdb=" O GLU C3757 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C3765 " --> pdb=" O GLN C3761 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.201A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.722A pdb=" N THR C3797 " --> pdb=" O MET C3793 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3825 through 3839 removed outlier: 4.929A pdb=" N PHE C3829 " --> pdb=" O GLU C3825 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3857 Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.611A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.507A pdb=" N SER C3929 " --> pdb=" O ARG C3925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C3936 " --> pdb=" O ASP C3932 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.540A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4007 removed outlier: 3.675A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER C4007 " --> pdb=" O LEU C4003 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.712A pdb=" N ASP C4018 " --> pdb=" O LYS C4014 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.040A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 5.345A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.973A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C4099 " --> pdb=" O LYS C4095 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN C4100 " --> pdb=" O ALA C4096 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 3.554A pdb=" N LEU C4112 " --> pdb=" O ILE C4108 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4155 removed outlier: 3.800A pdb=" N ALA C4129 " --> pdb=" O PHE C4125 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 4.210A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 3.886A 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: 3.794A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 3.540A pdb=" N LYS C4230 " --> pdb=" O GLY C4226 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4543 through 4559 removed outlier: 3.608A pdb=" N GLN C4547 " --> pdb=" O GLU C4543 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 3.536A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4639 through 4683 removed outlier: 4.118A 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: 4.304A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.489A 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 Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 4.538A pdb=" N LEU C4748 " --> pdb=" O ASP C4744 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4744 through 4749' Processing helix chain 'C' and resid 4772 through 4787 removed outlier: 5.461A pdb=" N ASN C4787 " --> pdb=" O ILE C4783 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4805 removed outlier: 3.765A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 5.171A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE C4816 " --> pdb=" O HIS C4812 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA C4817 " --> pdb=" O LEU C4813 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.621A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.363A pdb=" N TYR C4863 " --> pdb=" O PHE C4859 " (cutoff:3.500A) removed outlier: 5.042A 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: 4.051A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.208A 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: 4.666A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.956A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.911A 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 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5033 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.063A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.950A 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 256 removed outlier: 4.707A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 256' Processing helix chain 'D' and resid 308 through 313 removed outlier: 6.219A pdb=" N THR D 312 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.424A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 423 removed outlier: 3.870A pdb=" N GLY D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.523A pdb=" N GLN D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 497 removed outlier: 3.981A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.931A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 531 removed outlier: 3.576A pdb=" N ALA D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.716A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.564A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.645A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 removed outlier: 4.258A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 5.935A 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 Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.903A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.583A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 4.532A 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: 3.875A pdb=" N PHE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.557A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLU D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU D 881 " --> pdb=" O ASN D 877 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.790A 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: 3.935A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1004 removed outlier: 3.534A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1048 removed outlier: 4.076A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1072 removed outlier: 4.646A pdb=" N ARG D1071 " --> pdb=" O SER D1067 " (cutoff:3.500A) removed outlier: 5.119A 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 1217 through 1222 removed outlier: 6.972A pdb=" N GLU D1221 " --> pdb=" O CYS D1217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY D1222 " --> pdb=" O GLY D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1217 through 1222' Processing helix chain 'D' and resid 1423 through 1430 removed outlier: 3.675A pdb=" N LEU D1428 " --> pdb=" O PRO D1424 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN D1429 " --> pdb=" O GLU D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1444 through 1449 removed outlier: 4.083A pdb=" N VAL D1448 " --> pdb=" O GLU D1444 " (cutoff:3.500A) removed outlier: 5.630A 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: 4.460A pdb=" N PHE D1500 " --> pdb=" O TRP D1496 " (cutoff:3.500A) removed outlier: 4.416A 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: 3.748A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1656 removed outlier: 4.514A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) Processing helix chain 'D' and resid 1657 through 1675 removed outlier: 3.592A pdb=" N ARG D1668 " --> pdb=" O SER D1664 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 4.162A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.590A pdb=" N LEU D1694 " --> pdb=" O ASP D1690 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.508A pdb=" N SER D1726 " --> pdb=" O SER D1722 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU D1733 " --> pdb=" O SER D1729 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TYR D1734 " --> pdb=" O MET D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.612A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.520A 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: 4.302A pdb=" N MET D1929 " --> pdb=" O GLY D1925 " (cutoff:3.500A) removed outlier: 5.745A 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: 3.725A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D1982 " --> pdb=" O ALA D1978 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR D1985 " --> pdb=" O MET D1981 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 2000 removed outlier: 4.384A pdb=" N ARG D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2011 removed outlier: 3.652A pdb=" N ILE D2006 " --> pdb=" O PRO D2002 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN D2007 " --> pdb=" O GLN D2003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2017 through 2022 removed outlier: 3.915A 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 removed outlier: 3.828A pdb=" N GLN D2036 " --> pdb=" O GLN D2032 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.746A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.640A 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: 5.442A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2145 through 2169 removed outlier: 4.253A pdb=" N VAL D2149 " --> pdb=" O SER D2145 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU D2150 " --> pdb=" O PRO D2146 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP D2151 " --> pdb=" O SER D2147 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D2165 " --> pdb=" O GLN D2161 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D2166 " --> pdb=" O ILE D2162 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2189 removed outlier: 3.623A pdb=" N GLN D2180 " --> pdb=" O ASN D2176 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS D2189 " --> pdb=" O ILE D2185 " (cutoff:3.500A) Processing helix chain 'D' and resid 2190 through 2195 Proline residue: D2195 - end of helix Processing helix chain 'D' and resid 2196 through 2202 Processing helix chain 'D' and resid 2203 through 2219 removed outlier: 3.601A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY D2218 " --> pdb=" O VAL D2214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D2219 " --> pdb=" O LEU D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.656A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D2234 " --> pdb=" O THR D2230 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 4.073A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2265 removed outlier: 3.511A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.925A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2308 removed outlier: 3.699A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.695A pdb=" N LYS D2316 " --> pdb=" O MET D2312 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY D2317 " --> pdb=" O LEU D2313 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.961A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D2337 " --> pdb=" O ASP D2333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D2340 " --> pdb=" O ARG D2336 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.651A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (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 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: 3.982A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 removed outlier: 4.184A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2537 Processing helix chain 'D' and resid 2544 through 2566 removed outlier: 5.542A 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: 3.575A pdb=" N VAL D2579 " --> pdb=" O ARG D2575 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY D2592 " --> pdb=" O ARG D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 3.588A pdb=" N VAL D2602 " --> pdb=" O ALA D2598 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2630 removed outlier: 4.101A pdb=" N LEU D2619 " --> pdb=" O ARG D2615 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN D2620 " --> pdb=" O PRO D2616 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU D2622 " --> pdb=" O MET D2618 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D2629 " --> pdb=" O ARG D2625 " (cutoff:3.500A) Processing helix chain 'D' and resid 2636 through 2652 Proline residue: D2640 - end of helix Processing helix chain 'D' and resid 2668 through 2689 removed outlier: 6.578A pdb=" N LEU D2672 " --> pdb=" O SER D2668 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS D2673 " --> pdb=" O GLU D2669 " (cutoff:3.500A) Processing helix chain 'D' and resid 2693 through 2711 removed outlier: 3.679A 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 2741 through 2746 removed outlier: 5.259A pdb=" N VAL D2745 " --> pdb=" O GLU D2741 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE D2746 " --> pdb=" O THR D2742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2741 through 2746' Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 4.041A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN D2774 " --> pdb=" O LYS D2770 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2820 removed outlier: 4.191A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG D2806 " --> pdb=" O LYS D2802 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 3.691A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU D2820 " --> pdb=" O MET D2816 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 4.003A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2907 through 2912 removed outlier: 3.580A pdb=" N LEU D2911 " --> pdb=" O PRO D2907 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR D2912 " --> pdb=" O TYR D2908 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2907 through 2912' Processing helix chain 'D' and resid 2913 through 2934 removed outlier: 3.587A pdb=" N ALA D2917 " --> pdb=" O ALA D2913 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D2922 " --> pdb=" O ARG D2918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D2933 " --> pdb=" O PHE D2929 " (cutoff:3.500A) Processing helix chain 'D' and resid 2949 through 2983 removed outlier: 3.736A pdb=" N ARG D2954 " --> pdb=" O SER D2950 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE D2955 " --> pdb=" O ILE D2951 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA D2956 " --> pdb=" O GLU D2952 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D2957 " --> pdb=" O LYS D2953 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D2975 " --> pdb=" O GLN D2971 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D2976 " --> pdb=" O GLU D2972 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3014 removed outlier: 5.070A 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 Processing helix chain 'D' and resid 3053 through 3058 removed outlier: 3.847A pdb=" N PHE D3057 " --> pdb=" O ARG D3053 " (cutoff:3.500A) removed outlier: 4.292A 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 3084 Processing helix chain 'D' and resid 3085 through 3112 removed outlier: 3.792A pdb=" N GLU D3108 " --> pdb=" O GLU D3104 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D3112 " --> pdb=" O GLU D3108 " (cutoff:3.500A) Processing helix chain 'D' and resid 3123 through 3151 removed outlier: 3.676A pdb=" N GLN D3127 " --> pdb=" O LYS D3123 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D3132 " --> pdb=" O ASN D3128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR D3133 " --> pdb=" O LEU D3129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL D3134 " --> pdb=" O THR D3130 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU D3137 " --> pdb=" O THR D3133 " (cutoff:3.500A) Proline residue: D3138 - end of helix Processing helix chain 'D' and resid 3159 through 3176 removed outlier: 4.220A pdb=" N VAL D3163 " --> pdb=" O ASP D3159 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU D3175 " --> pdb=" O SER D3171 " (cutoff:3.500A) removed outlier: 4.927A 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 Processing helix chain 'D' and resid 3207 through 3215 removed outlier: 3.919A pdb=" N ASN D3211 " --> pdb=" O GLU D3207 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU D3212 " --> pdb=" O PRO D3208 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR D3213 " --> pdb=" O GLN D3209 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D3214 " --> pdb=" O LEU D3210 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA D3215 " --> pdb=" O ASN D3211 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3207 through 3215' Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3226 through 3231 removed outlier: 6.679A pdb=" N LEU D3230 " --> pdb=" O GLU D3226 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3226 through 3231' Processing helix chain 'D' and resid 3235 through 3241 removed outlier: 4.677A pdb=" N CYS D3240 " --> pdb=" O VAL D3236 " (cutoff:3.500A) Proline residue: D3241 - end of helix Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 3.611A 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 3285 removed outlier: 4.427A pdb=" N LEU D3274 " --> pdb=" O ILE D3270 " (cutoff:3.500A) Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix Processing helix chain 'D' and resid 3308 through 3327 removed outlier: 4.151A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) Processing helix chain 'D' and resid 3332 through 3350 removed outlier: 5.522A pdb=" N LYS D3336 " --> pdb=" O ALA D3332 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG D3337 " --> pdb=" O THR D3333 " (cutoff:3.500A) Proline residue: D3344 - end of helix removed outlier: 4.095A pdb=" N SER D3347 " --> pdb=" O GLN D3343 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG D3348 " --> pdb=" O PRO D3344 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA D3349 " --> pdb=" O ILE D3345 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG D3350 " --> pdb=" O VAL D3346 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3383 removed outlier: 4.356A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE D3359 " --> pdb=" O HIS D3355 " (cutoff:3.500A) Proline residue: D3360 - end of helix removed outlier: 3.772A pdb=" N GLU D3382 " --> pdb=" O GLN D3378 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA D3383 " --> pdb=" O LEU D3379 " (cutoff:3.500A) Processing helix chain 'D' and resid 3389 through 3413 removed outlier: 6.613A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) Proline residue: D3410 - end of helix Processing helix chain 'D' and resid 3419 through 3427 Proline residue: D3427 - end of helix Processing helix chain 'D' and resid 3428 through 3449 removed outlier: 4.343A pdb=" N HIS D3449 " --> pdb=" O TRP D3445 " (cutoff:3.500A) Processing helix chain 'D' and resid 3450 through 3463 Processing helix chain 'D' and resid 3466 through 3478 removed outlier: 3.911A pdb=" N LEU D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP D3473 " --> pdb=" O PHE D3469 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER D3474 " --> pdb=" O LEU D3470 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET D3478 " --> pdb=" O SER D3474 " (cutoff:3.500A) Processing helix chain 'D' and resid 3508 through 3525 Proline residue: D3519 - end of helix removed outlier: 3.706A pdb=" N MET D3524 " --> pdb=" O ILE D3520 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) Processing helix chain 'D' and resid 3529 through 3543 removed outlier: 3.577A 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: 3.849A 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 3579 removed outlier: 4.230A pdb=" N GLY D3578 " --> pdb=" O ALA D3574 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D3579 " --> pdb=" O LEU D3575 " (cutoff:3.500A) Processing helix chain 'D' and resid 3588 through 3612 removed outlier: 3.593A pdb=" N VAL D3593 " --> pdb=" O PRO D3589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D3602 " --> pdb=" O GLU D3598 " (cutoff:3.500A) Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3628 through 3638 removed outlier: 4.245A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D3633 " --> pdb=" O ARG D3629 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3661 removed outlier: 3.641A pdb=" N MET D3652 " --> pdb=" O ARG D3648 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D3659 " --> pdb=" O GLU D3655 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 removed outlier: 3.583A pdb=" N ILE D3674 " --> pdb=" O GLU D3670 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D3676 " --> pdb=" O ARG D3672 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS D3679 " --> pdb=" O ASP D3675 " (cutoff:3.500A) Processing helix chain 'D' and resid 3682 through 3687 Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.807A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.573A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN D3761 " --> pdb=" O GLU D3757 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR D3765 " --> pdb=" O GLN D3761 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.201A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.722A pdb=" N THR D3797 " --> pdb=" O MET D3793 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3825 through 3839 removed outlier: 4.929A pdb=" N PHE D3829 " --> pdb=" O GLU D3825 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3857 Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.611A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.507A pdb=" N SER D3929 " --> pdb=" O ARG D3925 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR D3936 " --> pdb=" O ASP D3932 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.540A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4007 removed outlier: 3.675A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.712A pdb=" N ASP D4018 " --> pdb=" O LYS D4014 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.040A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 5.345A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.973A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D4099 " --> pdb=" O LYS D4095 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN D4100 " --> pdb=" O ALA D4096 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 3.554A pdb=" N LEU D4112 " --> pdb=" O ILE D4108 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4155 removed outlier: 3.800A pdb=" N ALA D4129 " --> pdb=" O PHE D4125 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 4.210A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 3.886A 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: 3.795A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 3.540A pdb=" N LYS D4230 " --> pdb=" O GLY D4226 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4543 through 4559 removed outlier: 3.608A pdb=" N GLN D4547 " --> pdb=" O GLU D4543 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 3.537A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4683 removed outlier: 4.117A 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: 4.304A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.489A 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 Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 4.538A pdb=" N LEU D4748 " --> pdb=" O ASP D4744 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4744 through 4749' Processing helix chain 'D' and resid 4772 through 4787 removed outlier: 5.461A pdb=" N ASN D4787 " --> pdb=" O ILE D4783 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4805 removed outlier: 3.764A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 5.172A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.621A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.824A 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: 4.364A pdb=" N TYR D4863 " --> pdb=" O PHE D4859 " (cutoff:3.500A) removed outlier: 5.042A 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: 4.050A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.208A 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: 4.666A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.955A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.910A 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 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 Processing helix chain 'E' and resid 38 through 43 removed outlier: 4.501A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 removed outlier: 3.559A pdb=" N MET E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 4.354A pdb=" N TYR E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 removed outlier: 4.502A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 67 removed outlier: 3.559A pdb=" N MET F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 4.354A pdb=" N TYR F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 removed outlier: 4.502A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 67 removed outlier: 3.559A pdb=" N MET G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 removed outlier: 4.354A pdb=" N TYR G 82 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 4.501A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 3.559A pdb=" N MET H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 4.354A pdb=" N TYR H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.515A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.783A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 147 through 153 removed outlier: 7.752A pdb=" N TRP A 147 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 153 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP A 168 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 15.178A pdb=" N LEU A 169 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N LEU A 182 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 171 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 178 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 220 through 224 Processing sheet with id= 5, first strand: chain 'A' and resid 229 through 233 removed outlier: 5.531A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 260 through 264 removed outlier: 3.590A pdb=" N GLU A 263 " --> pdb=" O ARG A 281 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 290 through 293 Processing sheet with id= 8, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 9, first strand: chain 'A' and resid 664 through 669 removed outlier: 6.800A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 681 through 686 removed outlier: 5.835A pdb=" N HIS A 681 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A1646 " --> pdb=" O ILE A1641 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 744 through 750 Processing sheet with id= 12, first strand: chain 'A' and resid 766 through 769 Processing sheet with id= 13, first strand: chain 'A' and resid 830 through 833 removed outlier: 3.707A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLY A1086 " --> pdb=" O LEU A1155 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A1161 " --> pdb=" O MET A1152 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 937 through 941 No H-bonds generated for sheet with id= 14 Processing sheet with id= 15, first strand: chain 'A' and resid 1134 through 1138 removed outlier: 3.759A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR A1235 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR A1236 " --> pdb=" O MET A1608 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 6.567A pdb=" N GLU A1596 " --> pdb=" O SER A1292 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) removed outlier: 13.980A pdb=" N MET A1286 " --> pdb=" O PRO A1602 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR A1546 " --> pdb=" O PHE A1297 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1267 through 1273 removed outlier: 3.753A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A1561 " --> pdb=" O PHE A1440 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY A1567 " --> pdb=" O TYR A1434 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A1434 " --> pdb=" O GLY A1567 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR A1431 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1526 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY A1525 " --> pdb=" O VAL A1542 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 5.528A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 4581 through 4584 Processing sheet with id= 20, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.514A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.016A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.757A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.783A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 147 through 153 removed outlier: 7.751A pdb=" N TRP B 147 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 153 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP B 168 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 15.179A pdb=" N LEU B 169 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N LEU B 182 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 171 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 178 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 220 through 224 Processing sheet with id= 24, first strand: chain 'B' and resid 229 through 233 removed outlier: 5.530A pdb=" N VAL B 245 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 260 through 264 removed outlier: 3.590A pdb=" N GLU B 263 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 290 through 293 Processing sheet with id= 27, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 28, first strand: chain 'B' and resid 664 through 669 removed outlier: 6.799A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY B1625 " --> pdb=" O ALA B1620 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 681 through 686 removed outlier: 5.836A pdb=" N HIS B 681 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 744 through 750 Processing sheet with id= 31, first strand: chain 'B' and resid 766 through 769 Processing sheet with id= 32, first strand: chain 'B' and resid 830 through 833 removed outlier: 3.707A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY B1086 " --> pdb=" O LEU B1155 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B1161 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 937 through 941 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'B' and resid 1134 through 1138 removed outlier: 3.758A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B1235 " --> pdb=" O GLU B1078 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR B1236 " --> pdb=" O MET B1608 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1243 through 1247 removed outlier: 6.568A pdb=" N GLU B1596 " --> pdb=" O SER B1292 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 13.981A pdb=" N MET B1286 " --> pdb=" O PRO B1602 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR B1546 " --> pdb=" O PHE B1297 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1267 through 1273 removed outlier: 3.753A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL B1561 " --> pdb=" O PHE B1440 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY B1567 " --> pdb=" O TYR B1434 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR B1434 " --> pdb=" O GLY B1567 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR B1431 " --> pdb=" O LEU B1522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1526 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY B1525 " --> pdb=" O VAL B1542 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 5.528A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 4581 through 4584 Processing sheet with id= 39, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.514A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.784A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 147 through 153 removed outlier: 7.751A pdb=" N TRP C 147 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 153 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 15.179A pdb=" N LEU C 169 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N LEU C 182 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU C 171 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 178 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 220 through 224 Processing sheet with id= 43, first strand: chain 'C' and resid 229 through 233 removed outlier: 5.531A pdb=" N VAL C 245 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 260 through 264 removed outlier: 3.590A pdb=" N GLU C 263 " --> pdb=" O ARG C 281 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 290 through 293 Processing sheet with id= 46, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 47, first strand: chain 'C' and resid 664 through 669 removed outlier: 6.800A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C1625 " --> pdb=" O ALA C1620 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 681 through 686 removed outlier: 5.836A pdb=" N HIS C 681 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C1646 " --> pdb=" O ILE C1641 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 744 through 750 Processing sheet with id= 50, first strand: chain 'C' and resid 766 through 769 Processing sheet with id= 51, first strand: chain 'C' and resid 830 through 833 removed outlier: 3.707A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY C1086 " --> pdb=" O LEU C1155 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE C1161 " --> pdb=" O MET C1152 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 937 through 941 No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, first strand: chain 'C' and resid 1134 through 1138 removed outlier: 3.759A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C1235 " --> pdb=" O GLU C1078 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR C1236 " --> pdb=" O MET C1608 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 1243 through 1247 removed outlier: 6.567A pdb=" N GLU C1596 " --> pdb=" O SER C1292 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 13.980A pdb=" N MET C1286 " --> pdb=" O PRO C1602 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR C1546 " --> pdb=" O PHE C1297 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 1267 through 1273 removed outlier: 3.753A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL C1561 " --> pdb=" O PHE C1440 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLY C1567 " --> pdb=" O TYR C1434 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR C1434 " --> pdb=" O GLY C1567 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR C1431 " --> pdb=" O LEU C1522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C1526 " --> pdb=" O ASP C1521 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY C1525 " --> pdb=" O VAL C1542 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 5.528A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 4581 through 4584 Processing sheet with id= 58, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.515A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 11.017A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.783A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 147 through 153 removed outlier: 7.752A pdb=" N TRP D 147 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 153 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 15.179A pdb=" N LEU D 169 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 10.904A pdb=" N LEU D 182 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU D 171 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 178 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 220 through 224 Processing sheet with id= 62, first strand: chain 'D' and resid 229 through 233 removed outlier: 5.531A pdb=" N VAL D 245 " --> pdb=" O ALA D 376 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 260 through 264 removed outlier: 3.590A pdb=" N GLU D 263 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 290 through 293 Processing sheet with id= 65, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 66, first strand: chain 'D' and resid 664 through 669 removed outlier: 6.800A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY D1625 " --> pdb=" O ALA D1620 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 681 through 686 removed outlier: 5.835A pdb=" N HIS D 681 " --> pdb=" O SER D 784 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D1646 " --> pdb=" O ILE D1641 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 744 through 750 Processing sheet with id= 69, first strand: chain 'D' and resid 766 through 769 Processing sheet with id= 70, first strand: chain 'D' and resid 830 through 833 removed outlier: 3.707A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY D1086 " --> pdb=" O LEU D1155 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D1161 " --> pdb=" O MET D1152 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 937 through 941 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 3.758A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR D1235 " --> pdb=" O GLU D1078 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR D1236 " --> pdb=" O MET D1608 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 1243 through 1247 removed outlier: 6.567A pdb=" N GLU D1596 " --> pdb=" O SER D1292 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 13.980A pdb=" N MET D1286 " --> pdb=" O PRO D1602 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR D1546 " --> pdb=" O PHE D1297 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 1267 through 1273 removed outlier: 3.753A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL D1561 " --> pdb=" O PHE D1440 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY D1567 " --> pdb=" O TYR D1434 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR D1434 " --> pdb=" O GLY D1567 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR D1431 " --> pdb=" O LEU D1522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.528A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 4581 through 4584 Processing sheet with id= 77, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.729A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 70 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE E 99 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR E 27 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 2 through 7 removed outlier: 6.729A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 70 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'G' and resid 2 through 7 removed outlier: 6.729A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 70 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE G 99 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR G 27 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 2 through 7 removed outlier: 6.729A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN H 70 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 27 " --> pdb=" O ASP H 100 " (cutoff:3.500A) 6888 hydrogen bonds defined for protein. 20588 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: 107.84 Time building geometry restraints manager: 44.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 46040 1.34 - 1.46: 32742 1.46 - 1.58: 65906 1.58 - 1.71: 4 1.71 - 1.83: 1512 Bond restraints: 146204 Sorted by residual: bond pdb=" C HIS A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.334 1.425 -0.091 2.34e-02 1.83e+03 1.51e+01 bond pdb=" C HIS D 904 " pdb=" N PRO D 905 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.48e+01 bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.48e+01 bond pdb=" C HIS C 904 " pdb=" N PRO C 905 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.48e+01 bond pdb=" C VAL C4666 " pdb=" N PRO C4667 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.36e-02 5.41e+03 6.96e+00 ... (remaining 146199 not shown) Histogram of bond angle deviations from ideal: 96.12 - 103.78: 2329 103.78 - 111.45: 58814 111.45 - 119.11: 60131 119.11 - 126.78: 74540 126.78 - 134.44: 2226 Bond angle restraints: 198040 Sorted by residual: angle pdb=" C LEU A4178 " pdb=" N GLY A4179 " pdb=" CA GLY A4179 " ideal model delta sigma weight residual 122.18 116.13 6.05 6.90e-01 2.10e+00 7.69e+01 angle pdb=" C LEU C4178 " pdb=" N GLY C4179 " pdb=" CA GLY C4179 " ideal model delta sigma weight residual 122.18 116.14 6.04 6.90e-01 2.10e+00 7.66e+01 angle pdb=" C LEU D4178 " pdb=" N GLY D4179 " pdb=" CA GLY D4179 " ideal model delta sigma weight residual 122.18 116.16 6.02 6.90e-01 2.10e+00 7.61e+01 angle pdb=" C LEU B4178 " pdb=" N GLY B4179 " pdb=" CA GLY B4179 " ideal model delta sigma weight residual 122.18 116.16 6.02 6.90e-01 2.10e+00 7.61e+01 angle pdb=" C SER C3615 " pdb=" N LYS C3616 " pdb=" CA LYS C3616 " ideal model delta sigma weight residual 121.54 131.72 -10.18 1.91e+00 2.74e-01 2.84e+01 ... (remaining 198035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 79781 18.00 - 36.00: 6726 36.00 - 53.99: 1401 53.99 - 71.99: 320 71.99 - 89.99: 144 Dihedral angle restraints: 88372 sinusoidal: 36196 harmonic: 52176 Sorted by residual: dihedral pdb=" CA HIS A 904 " pdb=" C HIS A 904 " pdb=" N PRO A 905 " pdb=" CA PRO A 905 " ideal model delta harmonic sigma weight residual -180.00 -151.60 -28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA HIS D 904 " pdb=" C HIS D 904 " pdb=" N PRO D 905 " pdb=" CA PRO D 905 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA HIS C 904 " pdb=" C HIS C 904 " pdb=" N PRO C 905 " pdb=" CA PRO C 905 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 88369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 19107 0.087 - 0.175: 2484 0.175 - 0.262: 153 0.262 - 0.349: 24 0.349 - 0.437: 16 Chirality restraints: 21784 Sorted by residual: chirality pdb=" CB ILE A2223 " pdb=" CA ILE A2223 " pdb=" CG1 ILE A2223 " pdb=" CG2 ILE A2223 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CB ILE B2223 " pdb=" CA ILE B2223 " pdb=" CG1 ILE B2223 " pdb=" CG2 ILE B2223 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB ILE D2223 " pdb=" CA ILE D2223 " pdb=" CG1 ILE D2223 " pdb=" CG2 ILE D2223 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 21781 not shown) Planarity restraints: 25752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1143 " -0.023 2.00e-02 2.50e+03 2.73e-02 1.87e+01 pdb=" CG TRP A1143 " 0.068 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 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A1143 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1143 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A1143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D1143 " 0.023 2.00e-02 2.50e+03 2.73e-02 1.87e+01 pdb=" CG TRP D1143 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP D1143 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP D1143 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D1143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D1143 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D1143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1143 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP D1143 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1143 " 0.022 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP C1143 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP C1143 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP C1143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1143 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C1143 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C1143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1143 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP C1143 " 0.001 2.00e-02 2.50e+03 ... (remaining 25749 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 5942 2.72 - 3.27: 142895 3.27 - 3.81: 236929 3.81 - 4.36: 292575 4.36 - 4.90: 486822 Nonbonded interactions: 1165163 Sorted by model distance: nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.179 2.440 nonbonded pdb=" OD2 ASP A4917 " pdb=" OH TYR D4888 " model vdw 2.182 2.440 ... (remaining 1165158 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.140 Extract box with map and model: 18.200 Check model and map are aligned: 1.510 Set scattering table: 1.010 Process input model: 453.590 Find NCS groups from input model: 8.530 Set up NCS constraints: 1.020 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 490.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.005 0.091 146204 Z= 0.352 Angle : 0.987 14.242 198040 Z= 0.548 Chirality : 0.058 0.437 21784 Planarity : 0.008 0.093 25752 Dihedral : 14.465 89.990 54656 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 2.55 % Allowed : 2.25 % Favored : 95.20 % Cbeta Deviations : 0.02 % 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: -0.36 (0.06), residues: 17832 helix: 0.30 (0.06), residues: 8716 sheet: -0.70 (0.13), residues: 1776 loop : -0.64 (0.07), residues: 7340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A1143 HIS 0.020 0.002 HIS A3771 PHE 0.059 0.003 PHE D2973 TYR 0.046 0.002 TYR B1712 ARG 0.019 0.001 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 913 time to evaluate : 11.912 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: A 213 TYR cc_start: 0.7924 (m-80) cc_final: 0.7021 (m-80) REVERT: A 227 MET cc_start: 0.8936 (tpp) cc_final: 0.8651 (mmm) REVERT: A 340 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8859 (mtpp) REVERT: A 343 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8685 (mp0) REVERT: A 384 MET cc_start: 0.7376 (tmm) cc_final: 0.7153 (tmm) REVERT: A 960 MET cc_start: -0.0822 (mmm) cc_final: -0.2260 (ptp) REVERT: A 961 MET cc_start: 0.7468 (pmm) cc_final: 0.7104 (pmm) REVERT: A 1108 GLU cc_start: 0.8921 (pm20) cc_final: 0.8675 (pm20) REVERT: A 1152 MET cc_start: 0.9303 (mmp) cc_final: 0.8900 (mmp) REVERT: A 1186 ASP cc_start: 0.9557 (m-30) cc_final: 0.9292 (m-30) REVERT: A 1494 MET cc_start: 0.8916 (mtm) cc_final: 0.8635 (mtp) REVERT: A 1579 MET cc_start: 0.9271 (mtm) cc_final: 0.8883 (mtm) REVERT: A 1601 MET cc_start: 0.9179 (mmm) cc_final: 0.8936 (mmm) REVERT: A 1636 MET cc_start: 0.9162 (ppp) cc_final: 0.8934 (ppp) REVERT: A 1984 PHE cc_start: 0.7231 (m-10) cc_final: 0.6852 (p90) REVERT: A 2008 MET cc_start: 0.9543 (mpp) cc_final: 0.8781 (tmm) REVERT: A 2259 GLU cc_start: 0.9508 (tt0) cc_final: 0.9199 (tp30) REVERT: A 2297 LYS cc_start: 0.9787 (tptt) cc_final: 0.9514 (tptp) REVERT: A 2582 MET cc_start: 0.9242 (mtm) cc_final: 0.8738 (mtt) REVERT: A 2700 MET cc_start: 0.9224 (tmm) cc_final: 0.8976 (tmm) REVERT: A 2932 MET cc_start: 0.6845 (pmm) cc_final: 0.6492 (pmm) REVERT: A 3517 MET cc_start: 0.9494 (mmm) cc_final: 0.9015 (mmm) REVERT: A 3524 MET cc_start: 0.9426 (mmt) cc_final: 0.9132 (mmp) REVERT: A 3534 MET cc_start: 0.9685 (mmp) cc_final: 0.9467 (mmt) REVERT: A 3638 MET cc_start: 0.6038 (ptt) cc_final: 0.5122 (ppp) REVERT: A 3782 MET cc_start: 0.9500 (mmm) cc_final: 0.9092 (mmm) REVERT: A 3932 ASP cc_start: 0.9327 (m-30) cc_final: 0.8727 (p0) REVERT: A 4000 MET cc_start: 0.9119 (mtt) cc_final: 0.8915 (mtp) REVERT: A 4044 MET cc_start: 0.9198 (ttt) cc_final: 0.8908 (tpp) REVERT: A 4047 MET cc_start: 0.9557 (tmm) cc_final: 0.8876 (tmm) REVERT: A 4056 GLU cc_start: 0.9492 (tt0) cc_final: 0.9194 (tp30) REVERT: A 4165 GLU cc_start: 0.9523 (mt-10) cc_final: 0.9220 (pt0) REVERT: A 4184 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8577 (tpp) REVERT: A 4187 SER cc_start: 0.9718 (OUTLIER) cc_final: 0.9408 (p) REVERT: A 4189 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8695 (mtm110) REVERT: A 4191 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: A 4192 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8627 (ttm170) REVERT: A 4548 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8504 (mmp-170) REVERT: A 4565 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 4580 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: A 4581 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8980 (mtpp) REVERT: A 4639 MET cc_start: 0.8511 (mtt) cc_final: 0.8131 (mmp) REVERT: A 4730 ASP cc_start: 0.9399 (OUTLIER) cc_final: 0.8849 (p0) REVERT: A 4797 VAL cc_start: 0.9768 (OUTLIER) cc_final: 0.9561 (p) REVERT: A 4822 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8848 (t) REVERT: A 4839 MET cc_start: 0.9402 (mmm) cc_final: 0.9099 (mtp) REVERT: A 4874 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9084 (mmm) REVERT: A 4951 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8611 (ttmm) REVERT: A 4966 ASP cc_start: 0.9602 (m-30) cc_final: 0.9276 (p0) REVERT: A 4971 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9327 (p) REVERT: A 4989 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8973 (tmm) REVERT: A 5004 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 5008 SER cc_start: 0.9699 (OUTLIER) cc_final: 0.9195 (p) REVERT: A 5012 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9270 (mmtm) REVERT: A 5035 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9049 (mp10) REVERT: B 213 TYR cc_start: 0.7928 (m-80) cc_final: 0.7051 (m-80) REVERT: B 340 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8830 (mtpp) REVERT: B 343 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8585 (mp0) REVERT: B 384 MET cc_start: 0.7416 (tmm) cc_final: 0.7186 (tmm) REVERT: B 960 MET cc_start: -0.1380 (mmm) cc_final: -0.2558 (ptp) REVERT: B 961 MET cc_start: 0.7755 (pmm) cc_final: 0.7480 (pmm) REVERT: B 1108 GLU cc_start: 0.9031 (pm20) cc_final: 0.8780 (pm20) REVERT: B 1152 MET cc_start: 0.9221 (mmp) cc_final: 0.8682 (mmp) REVERT: B 1186 ASP cc_start: 0.9538 (m-30) cc_final: 0.9285 (m-30) REVERT: B 1601 MET cc_start: 0.9101 (mmm) cc_final: 0.8861 (mmm) REVERT: B 1984 PHE cc_start: 0.7116 (m-10) cc_final: 0.6784 (p90) REVERT: B 2198 MET cc_start: 0.9456 (mmp) cc_final: 0.9198 (mpp) REVERT: B 2259 GLU cc_start: 0.9507 (tt0) cc_final: 0.9197 (tp30) REVERT: B 2297 LYS cc_start: 0.9785 (tptt) cc_final: 0.9518 (tptp) REVERT: B 2530 MET cc_start: 0.9577 (mtp) cc_final: 0.9334 (mpp) REVERT: B 2582 MET cc_start: 0.9243 (mtm) cc_final: 0.8787 (mtt) REVERT: B 2700 MET cc_start: 0.9217 (tmm) cc_final: 0.8970 (tmm) REVERT: B 2932 MET cc_start: 0.6916 (pmm) cc_final: 0.6595 (pmm) REVERT: B 3517 MET cc_start: 0.9483 (mmm) cc_final: 0.9015 (mmm) REVERT: B 3524 MET cc_start: 0.9439 (mmt) cc_final: 0.9102 (mmp) REVERT: B 3638 MET cc_start: 0.5887 (ptt) cc_final: 0.4881 (ppp) REVERT: B 3782 MET cc_start: 0.9525 (mmm) cc_final: 0.9134 (mmm) REVERT: B 3932 ASP cc_start: 0.9330 (m-30) cc_final: 0.8728 (p0) REVERT: B 4044 MET cc_start: 0.9203 (ttt) cc_final: 0.8907 (tpp) REVERT: B 4047 MET cc_start: 0.9534 (tmm) cc_final: 0.8780 (tmm) REVERT: B 4056 GLU cc_start: 0.9484 (tt0) cc_final: 0.9205 (tp30) REVERT: B 4059 LEU cc_start: 0.9671 (mt) cc_final: 0.9465 (pp) REVERT: B 4165 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9234 (pt0) REVERT: B 4184 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: B 4187 SER cc_start: 0.9726 (OUTLIER) cc_final: 0.9413 (p) REVERT: B 4189 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8699 (mtm110) REVERT: B 4191 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 4192 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8579 (ttm170) REVERT: B 4548 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8525 (mmp-170) REVERT: B 4565 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 4580 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: B 4581 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8941 (mtpp) REVERT: B 4633 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (tp30) REVERT: B 4636 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 4639 MET cc_start: 0.8481 (mtt) cc_final: 0.8108 (mmp) REVERT: B 4730 ASP cc_start: 0.9382 (OUTLIER) cc_final: 0.8818 (p0) REVERT: B 4874 MET cc_start: 0.9487 (OUTLIER) cc_final: 0.9287 (mmm) REVERT: B 4879 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8648 (tpt) REVERT: B 4951 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8607 (ttmm) REVERT: B 4966 ASP cc_start: 0.9603 (m-30) cc_final: 0.9280 (p0) REVERT: B 4989 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8877 (tmm) REVERT: B 5004 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8690 (t) REVERT: B 5008 SER cc_start: 0.9696 (OUTLIER) cc_final: 0.9176 (p) REVERT: B 5012 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9273 (mmtm) REVERT: B 5020 ASP cc_start: 0.9504 (m-30) cc_final: 0.9299 (m-30) REVERT: B 5035 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9048 (mp10) REVERT: C 213 TYR cc_start: 0.7926 (m-80) cc_final: 0.7050 (m-80) REVERT: C 340 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8832 (mtpp) REVERT: C 343 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8586 (mp0) REVERT: C 384 MET cc_start: 0.7416 (tmm) cc_final: 0.7186 (tmm) REVERT: C 403 MET cc_start: 0.9203 (mtp) cc_final: 0.8869 (mtp) REVERT: C 960 MET cc_start: -0.1384 (mmm) cc_final: -0.2558 (ptp) REVERT: C 961 MET cc_start: 0.7750 (pmm) cc_final: 0.7477 (pmm) REVERT: C 1108 GLU cc_start: 0.9033 (pm20) cc_final: 0.8781 (pm20) REVERT: C 1152 MET cc_start: 0.9208 (mmp) cc_final: 0.8663 (mmp) REVERT: C 1186 ASP cc_start: 0.9538 (m-30) cc_final: 0.9285 (m-30) REVERT: C 1601 MET cc_start: 0.9102 (mmm) cc_final: 0.8863 (mmm) REVERT: C 1984 PHE cc_start: 0.7116 (m-10) cc_final: 0.6783 (p90) REVERT: C 2198 MET cc_start: 0.9456 (mmp) cc_final: 0.9198 (mpp) REVERT: C 2259 GLU cc_start: 0.9507 (tt0) cc_final: 0.9196 (tp30) REVERT: C 2297 LYS cc_start: 0.9785 (tptt) cc_final: 0.9519 (tptp) REVERT: C 2530 MET cc_start: 0.9577 (mtp) cc_final: 0.9367 (mpp) REVERT: C 2582 MET cc_start: 0.9243 (mtm) cc_final: 0.8785 (mtt) REVERT: C 2700 MET cc_start: 0.9217 (tmm) cc_final: 0.8969 (tmm) REVERT: C 2932 MET cc_start: 0.6916 (pmm) cc_final: 0.6597 (pmm) REVERT: C 3517 MET cc_start: 0.9483 (mmm) cc_final: 0.9016 (mmm) REVERT: C 3524 MET cc_start: 0.9439 (mmt) cc_final: 0.9101 (mmp) REVERT: C 3638 MET cc_start: 0.5888 (ptt) cc_final: 0.4883 (ppp) REVERT: C 3782 MET cc_start: 0.9526 (mmm) cc_final: 0.9135 (mmm) REVERT: C 3932 ASP cc_start: 0.9329 (m-30) cc_final: 0.8726 (p0) REVERT: C 4044 MET cc_start: 0.9203 (ttt) cc_final: 0.8909 (tpp) REVERT: C 4047 MET cc_start: 0.9535 (tmm) cc_final: 0.8781 (tmm) REVERT: C 4056 GLU cc_start: 0.9483 (tt0) cc_final: 0.9204 (tp30) REVERT: C 4059 LEU cc_start: 0.9670 (mt) cc_final: 0.9464 (pp) REVERT: C 4165 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9235 (pt0) REVERT: C 4184 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: C 4187 SER cc_start: 0.9726 (OUTLIER) cc_final: 0.9416 (p) REVERT: C 4189 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8688 (mtm110) REVERT: C 4191 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: C 4192 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8575 (ttm170) REVERT: C 4548 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8526 (mmp-170) REVERT: C 4565 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9088 (tp) REVERT: C 4580 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: C 4581 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8952 (mtpp) REVERT: C 4633 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8580 (tp30) REVERT: C 4636 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.8907 (p) REVERT: C 4639 MET cc_start: 0.8478 (mtt) cc_final: 0.8106 (mmp) REVERT: C 4730 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.8822 (p0) REVERT: C 4839 MET cc_start: 0.9354 (mmm) cc_final: 0.9054 (mtm) REVERT: C 4879 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8716 (tpt) REVERT: C 4951 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8609 (ttmm) REVERT: C 4966 ASP cc_start: 0.9602 (m-30) cc_final: 0.9279 (p0) REVERT: C 4989 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8877 (tmm) REVERT: C 5004 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8689 (t) REVERT: C 5008 SER cc_start: 0.9697 (OUTLIER) cc_final: 0.9174 (p) REVERT: C 5012 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.8962 (mmtm) REVERT: C 5020 ASP cc_start: 0.9504 (m-30) cc_final: 0.9298 (m-30) REVERT: C 5035 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.9032 (mp10) REVERT: D 213 TYR cc_start: 0.7930 (m-80) cc_final: 0.7053 (m-80) REVERT: D 340 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8832 (mtpp) REVERT: D 343 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8586 (mp0) REVERT: D 384 MET cc_start: 0.7408 (tmm) cc_final: 0.7180 (tmm) REVERT: D 403 MET cc_start: 0.9202 (mtp) cc_final: 0.8867 (mtp) REVERT: D 960 MET cc_start: -0.1397 (mmm) cc_final: -0.2566 (ptp) REVERT: D 961 MET cc_start: 0.7749 (pmm) cc_final: 0.7474 (pmm) REVERT: D 1108 GLU cc_start: 0.9032 (pm20) cc_final: 0.8782 (pm20) REVERT: D 1152 MET cc_start: 0.9208 (mmp) cc_final: 0.8664 (mmp) REVERT: D 1186 ASP cc_start: 0.9539 (m-30) cc_final: 0.9286 (m-30) REVERT: D 1601 MET cc_start: 0.9101 (mmm) cc_final: 0.8861 (mmm) REVERT: D 1984 PHE cc_start: 0.7116 (m-10) cc_final: 0.6783 (p90) REVERT: D 2198 MET cc_start: 0.9457 (mmp) cc_final: 0.9200 (mpp) REVERT: D 2259 GLU cc_start: 0.9507 (tt0) cc_final: 0.9196 (tp30) REVERT: D 2297 LYS cc_start: 0.9785 (tptt) cc_final: 0.9519 (tptp) REVERT: D 2530 MET cc_start: 0.9577 (mtp) cc_final: 0.9333 (mpp) REVERT: D 2582 MET cc_start: 0.9243 (mtm) cc_final: 0.8786 (mtt) REVERT: D 2700 MET cc_start: 0.9217 (tmm) cc_final: 0.8969 (tmm) REVERT: D 2932 MET cc_start: 0.6911 (pmm) cc_final: 0.6594 (pmm) REVERT: D 3517 MET cc_start: 0.9485 (mmm) cc_final: 0.9016 (mmm) REVERT: D 3524 MET cc_start: 0.9440 (mmt) cc_final: 0.9104 (mmp) REVERT: D 3638 MET cc_start: 0.5885 (ptt) cc_final: 0.4882 (ppp) REVERT: D 3782 MET cc_start: 0.9526 (mmm) cc_final: 0.9134 (mmm) REVERT: D 3932 ASP cc_start: 0.9328 (m-30) cc_final: 0.8725 (p0) REVERT: D 4044 MET cc_start: 0.9201 (ttt) cc_final: 0.8909 (tpp) REVERT: D 4047 MET cc_start: 0.9536 (tmm) cc_final: 0.8781 (tmm) REVERT: D 4056 GLU cc_start: 0.9484 (tt0) cc_final: 0.9204 (tp30) REVERT: D 4059 LEU cc_start: 0.9670 (mt) cc_final: 0.9464 (pp) REVERT: D 4165 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9235 (pt0) REVERT: D 4184 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: D 4187 SER cc_start: 0.9726 (OUTLIER) cc_final: 0.9413 (p) REVERT: D 4189 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8690 (mtm110) REVERT: D 4191 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: D 4192 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8579 (ttm170) REVERT: D 4548 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8524 (mmp-170) REVERT: D 4565 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9088 (tp) REVERT: D 4580 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: D 4581 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8946 (mtpp) REVERT: D 4633 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8578 (tp30) REVERT: D 4636 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.8903 (p) REVERT: D 4639 MET cc_start: 0.8474 (mtt) cc_final: 0.8105 (mmp) REVERT: D 4730 ASP cc_start: 0.9384 (OUTLIER) cc_final: 0.8822 (p0) REVERT: D 4839 MET cc_start: 0.9352 (mmm) cc_final: 0.9052 (mtm) REVERT: D 4879 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8700 (tpt) REVERT: D 4951 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8609 (ttmm) REVERT: D 4966 ASP cc_start: 0.9602 (m-30) cc_final: 0.9278 (p0) REVERT: D 4989 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8877 (tmm) REVERT: D 5004 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8685 (t) REVERT: D 5008 SER cc_start: 0.9696 (OUTLIER) cc_final: 0.9174 (p) REVERT: D 5012 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9285 (mmtm) REVERT: D 5020 ASP cc_start: 0.9503 (m-30) cc_final: 0.9298 (m-30) REVERT: D 5035 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.9017 (mp10) REVERT: E 18 LYS cc_start: 0.9159 (mppt) cc_final: 0.8937 (mmtm) REVERT: E 29 MET cc_start: 0.8856 (mtp) cc_final: 0.8495 (ttm) REVERT: F 18 LYS cc_start: 0.9159 (mppt) cc_final: 0.8937 (mmtm) REVERT: F 29 MET cc_start: 0.8858 (mtp) cc_final: 0.8495 (ttm) REVERT: G 18 LYS cc_start: 0.9159 (mppt) cc_final: 0.8938 (mmtm) REVERT: G 29 MET cc_start: 0.8857 (mtp) cc_final: 0.8493 (ttm) REVERT: H 18 LYS cc_start: 0.9159 (mppt) cc_final: 0.8937 (mmtm) REVERT: H 29 MET cc_start: 0.8858 (mtp) cc_final: 0.8494 (ttm) outliers start: 385 outliers final: 85 residues processed: 1226 average time/residue: 1.2027 time to fit residues: 2599.0671 Evaluate side-chains 936 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 773 time to evaluate : 11.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3611 HIS Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4189 ARG Chi-restraints excluded: chain A residue 4191 GLU Chi-restraints excluded: chain A residue 4192 ARG Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4548 ARG Chi-restraints excluded: chain A residue 4565 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4628 VAL Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4710 SER Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4747 SER Chi-restraints excluded: chain A residue 4750 ILE Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4874 MET Chi-restraints excluded: chain A residue 4876 CYS Chi-restraints excluded: chain A residue 4879 MET Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4995 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5008 SER Chi-restraints excluded: chain A residue 5012 LYS Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain A residue 5035 GLN Chi-restraints excluded: chain B residue 3611 HIS Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4187 SER Chi-restraints excluded: chain B residue 4189 ARG Chi-restraints excluded: chain B residue 4191 GLU Chi-restraints excluded: chain B residue 4192 ARG Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4548 ARG Chi-restraints excluded: chain B residue 4565 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4628 VAL Chi-restraints excluded: chain B residue 4633 GLU Chi-restraints excluded: chain B residue 4636 THR Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4710 SER Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4736 ARG Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4747 SER Chi-restraints excluded: chain B residue 4750 ILE Chi-restraints excluded: chain B residue 4874 MET Chi-restraints excluded: chain B residue 4876 CYS Chi-restraints excluded: chain B residue 4879 MET Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4981 GLU Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4995 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5008 SER Chi-restraints excluded: chain B residue 5012 LYS Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain B residue 5035 GLN Chi-restraints excluded: chain C residue 3611 HIS Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4187 SER Chi-restraints excluded: chain C residue 4189 ARG Chi-restraints excluded: chain C residue 4191 GLU Chi-restraints excluded: chain C residue 4192 ARG Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4548 ARG Chi-restraints excluded: chain C residue 4565 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4628 VAL Chi-restraints excluded: chain C residue 4633 GLU Chi-restraints excluded: chain C residue 4636 THR Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4710 SER Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4736 ARG Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4747 SER Chi-restraints excluded: chain C residue 4750 ILE Chi-restraints excluded: chain C residue 4876 CYS Chi-restraints excluded: chain C residue 4879 MET Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4981 GLU Chi-restraints excluded: chain C residue 4989 MET Chi-restraints excluded: chain C residue 4995 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5008 SER Chi-restraints excluded: chain C residue 5012 LYS Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain C residue 5035 GLN Chi-restraints excluded: chain D residue 3611 HIS Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4187 SER Chi-restraints excluded: chain D residue 4189 ARG Chi-restraints excluded: chain D residue 4191 GLU Chi-restraints excluded: chain D residue 4192 ARG Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4548 ARG Chi-restraints excluded: chain D residue 4565 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4628 VAL Chi-restraints excluded: chain D residue 4633 GLU Chi-restraints excluded: chain D residue 4636 THR Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4710 SER Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4736 ARG Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4747 SER Chi-restraints excluded: chain D residue 4750 ILE Chi-restraints excluded: chain D residue 4876 CYS Chi-restraints excluded: chain D residue 4879 MET Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4981 GLU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4995 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5008 SER Chi-restraints excluded: chain D residue 5012 LYS Chi-restraints excluded: chain D residue 5034 ASP Chi-restraints excluded: chain D residue 5035 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 5.9990 chunk 1355 optimal weight: 8.9990 chunk 751 optimal weight: 9.9990 chunk 462 optimal weight: 20.0000 chunk 914 optimal weight: 0.0040 chunk 724 optimal weight: 50.0000 chunk 1401 optimal weight: 8.9990 chunk 542 optimal weight: 4.9990 chunk 852 optimal weight: 4.9990 chunk 1043 optimal weight: 5.9990 chunk 1623 optimal weight: 20.0000 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2127 GLN ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2872 GLN ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3052 HIS ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3766 GLN A3895 HIS ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 ASN A4626 ASN A4700 GLN A4805 ASN A4812 HIS A5035 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 634 GLN ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B2127 GLN ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2872 GLN ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3214 ASN B3766 GLN B3895 HIS ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4201 ASN B4626 ASN B4700 GLN B4805 ASN B4812 HIS B5035 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS C2127 GLN ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2872 GLN ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3766 GLN C3895 HIS ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4201 ASN C4626 ASN C4700 GLN C4805 ASN C4812 HIS C5035 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2872 GLN ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3766 GLN D3895 HIS ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4201 ASN D4626 ASN D4700 GLN D4805 ASN D4812 HIS D5035 GLN E 65 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN G 65 GLN ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 146204 Z= 0.259 Angle : 0.613 11.923 198040 Z= 0.314 Chirality : 0.041 0.179 21784 Planarity : 0.004 0.074 25752 Dihedral : 6.891 78.679 20016 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.16 % Allowed : 6.57 % Favored : 92.27 % 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: 0.48 (0.06), residues: 17832 helix: 1.25 (0.06), residues: 8748 sheet: -0.49 (0.13), residues: 1792 loop : -0.54 (0.08), residues: 7292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1143 HIS 0.013 0.001 HIS C2498 PHE 0.026 0.001 PHE A2973 TYR 0.018 0.001 TYR A4080 ARG 0.010 0.000 ARG B1180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 794 time to evaluate : 12.063 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 81 MET cc_start: 0.9119 (tmm) cc_final: 0.8507 (ppp) REVERT: A 213 TYR cc_start: 0.7429 (m-80) cc_final: 0.7111 (m-80) REVERT: A 227 MET cc_start: 0.8753 (tpp) cc_final: 0.8542 (mmp) REVERT: A 340 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8964 (mtpp) REVERT: A 343 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8479 (mp0) REVERT: A 384 MET cc_start: 0.7506 (tmm) cc_final: 0.7233 (tmm) REVERT: A 403 MET cc_start: 0.9545 (ttm) cc_final: 0.8932 (mtp) REVERT: A 960 MET cc_start: -0.1338 (mmm) cc_final: -0.1572 (mmt) REVERT: A 1108 GLU cc_start: 0.8869 (pm20) cc_final: 0.8650 (pm20) REVERT: A 1152 MET cc_start: 0.9255 (mmp) cc_final: 0.8737 (mmp) REVERT: A 1170 MET cc_start: 0.9128 (tpp) cc_final: 0.8775 (tpp) REVERT: A 1186 ASP cc_start: 0.9618 (m-30) cc_final: 0.9347 (m-30) REVERT: A 1636 MET cc_start: 0.9136 (ppp) cc_final: 0.8775 (ppp) REVERT: A 1984 PHE cc_start: 0.7283 (m-10) cc_final: 0.6965 (p90) REVERT: A 2198 MET cc_start: 0.9488 (mpp) cc_final: 0.9259 (mpp) REVERT: A 2297 LYS cc_start: 0.9767 (tptt) cc_final: 0.9556 (tptm) REVERT: A 2312 MET cc_start: 0.9229 (tmm) cc_final: 0.8913 (tmm) REVERT: A 2578 MET cc_start: 0.9312 (ppp) cc_final: 0.8996 (ppp) REVERT: A 3517 MET cc_start: 0.9456 (mmm) cc_final: 0.9000 (mmm) REVERT: A 3524 MET cc_start: 0.9316 (mmt) cc_final: 0.9101 (mmp) REVERT: A 3638 MET cc_start: 0.6183 (ptt) cc_final: 0.4939 (ppp) REVERT: A 3673 MET cc_start: 0.9534 (mtt) cc_final: 0.9170 (tpp) REVERT: A 3693 LYS cc_start: 0.9462 (tmtt) cc_final: 0.9163 (mmtm) REVERT: A 3932 ASP cc_start: 0.9362 (m-30) cc_final: 0.8784 (p0) REVERT: A 4047 MET cc_start: 0.9519 (tmm) cc_final: 0.9289 (tmm) REVERT: A 4056 GLU cc_start: 0.9645 (tt0) cc_final: 0.9352 (tp30) REVERT: A 4165 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9198 (pt0) REVERT: A 4184 MET cc_start: 0.9073 (tpt) cc_final: 0.8786 (tpp) REVERT: A 4187 SER cc_start: 0.9740 (OUTLIER) cc_final: 0.9368 (p) REVERT: A 4191 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: A 4548 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8464 (mmp80) REVERT: A 4580 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: A 4730 ASP cc_start: 0.9406 (OUTLIER) cc_final: 0.8825 (p0) REVERT: A 4796 MET cc_start: 0.9313 (tpt) cc_final: 0.8901 (tpt) REVERT: A 4822 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8681 (t) REVERT: A 4874 MET cc_start: 0.9395 (mmm) cc_final: 0.9067 (mmm) REVERT: A 4966 ASP cc_start: 0.9643 (m-30) cc_final: 0.9338 (p0) REVERT: A 4967 TYR cc_start: 0.9281 (t80) cc_final: 0.9076 (t80) REVERT: A 4989 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9068 (tmm) REVERT: A 5013 MET cc_start: 0.9306 (mtt) cc_final: 0.9036 (mtm) REVERT: A 5035 GLN cc_start: 0.9311 (mp10) cc_final: 0.9046 (mp10) REVERT: B 213 TYR cc_start: 0.7430 (m-80) cc_final: 0.7184 (m-80) REVERT: B 227 MET cc_start: 0.8681 (tpp) cc_final: 0.8456 (mmp) REVERT: B 340 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8948 (mtpp) REVERT: B 343 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8490 (mp0) REVERT: B 384 MET cc_start: 0.7534 (tmm) cc_final: 0.7259 (tmm) REVERT: B 1108 GLU cc_start: 0.8983 (pm20) cc_final: 0.8754 (pm20) REVERT: B 1152 MET cc_start: 0.9213 (mmp) cc_final: 0.8590 (mmp) REVERT: B 1170 MET cc_start: 0.9125 (tpp) cc_final: 0.8713 (tpp) REVERT: B 1186 ASP cc_start: 0.9605 (m-30) cc_final: 0.9335 (m-30) REVERT: B 1601 MET cc_start: 0.9061 (mmm) cc_final: 0.8855 (mmm) REVERT: B 1984 PHE cc_start: 0.7287 (m-10) cc_final: 0.6977 (p90) REVERT: B 2008 MET cc_start: 0.9457 (ptp) cc_final: 0.8638 (tmm) REVERT: B 2297 LYS cc_start: 0.9763 (tptt) cc_final: 0.9562 (tptm) REVERT: B 2578 MET cc_start: 0.9301 (ppp) cc_final: 0.9007 (ppp) REVERT: B 3517 MET cc_start: 0.9479 (mmm) cc_final: 0.9062 (mmm) REVERT: B 3524 MET cc_start: 0.9306 (mmt) cc_final: 0.9055 (mmp) REVERT: B 3638 MET cc_start: 0.6057 (ptt) cc_final: 0.4895 (ppp) REVERT: B 3673 MET cc_start: 0.9527 (mtt) cc_final: 0.9171 (tpp) REVERT: B 3932 ASP cc_start: 0.9365 (m-30) cc_final: 0.8784 (p0) REVERT: B 4047 MET cc_start: 0.9512 (tmm) cc_final: 0.9283 (tmm) REVERT: B 4056 GLU cc_start: 0.9546 (tt0) cc_final: 0.9289 (tp30) REVERT: B 4059 LEU cc_start: 0.9644 (mt) cc_final: 0.9414 (pp) REVERT: B 4165 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9234 (pt0) REVERT: B 4184 MET cc_start: 0.9059 (tpt) cc_final: 0.8783 (tpp) REVERT: B 4187 SER cc_start: 0.9747 (OUTLIER) cc_final: 0.9406 (p) REVERT: B 4191 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: B 4548 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8427 (mmp80) REVERT: B 4580 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: B 4730 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.8696 (p0) REVERT: B 4796 MET cc_start: 0.9291 (tpt) cc_final: 0.8667 (tpt) REVERT: B 4874 MET cc_start: 0.9469 (mmm) cc_final: 0.9156 (mmm) REVERT: B 4966 ASP cc_start: 0.9632 (m-30) cc_final: 0.9322 (p0) REVERT: B 4989 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9044 (tmm) REVERT: B 5013 MET cc_start: 0.9339 (mtt) cc_final: 0.9066 (mtm) REVERT: B 5020 ASP cc_start: 0.9479 (m-30) cc_final: 0.9272 (m-30) REVERT: B 5035 GLN cc_start: 0.9243 (mp10) cc_final: 0.8989 (mp10) REVERT: C 213 TYR cc_start: 0.7428 (m-80) cc_final: 0.7183 (m-80) REVERT: C 227 MET cc_start: 0.8680 (tpp) cc_final: 0.8456 (mmp) REVERT: C 340 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8950 (mtpp) REVERT: C 343 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8493 (mp0) REVERT: C 384 MET cc_start: 0.7533 (tmm) cc_final: 0.7258 (tmm) REVERT: C 1108 GLU cc_start: 0.8986 (pm20) cc_final: 0.8758 (pm20) REVERT: C 1152 MET cc_start: 0.9214 (mmp) cc_final: 0.8591 (mmp) REVERT: C 1170 MET cc_start: 0.9130 (tpp) cc_final: 0.8720 (tpp) REVERT: C 1186 ASP cc_start: 0.9604 (m-30) cc_final: 0.9337 (m-30) REVERT: C 1601 MET cc_start: 0.9062 (mmm) cc_final: 0.8857 (mmm) REVERT: C 1984 PHE cc_start: 0.7288 (m-10) cc_final: 0.6978 (p90) REVERT: C 2008 MET cc_start: 0.9454 (ptp) cc_final: 0.8636 (tmm) REVERT: C 2578 MET cc_start: 0.9302 (ppp) cc_final: 0.9007 (ppp) REVERT: C 3517 MET cc_start: 0.9480 (mmm) cc_final: 0.9065 (mmm) REVERT: C 3524 MET cc_start: 0.9308 (mmt) cc_final: 0.9057 (mmp) REVERT: C 3638 MET cc_start: 0.6052 (ptt) cc_final: 0.4879 (ppp) REVERT: C 3673 MET cc_start: 0.9527 (mtt) cc_final: 0.9171 (tpp) REVERT: C 3932 ASP cc_start: 0.9364 (m-30) cc_final: 0.8784 (p0) REVERT: C 4047 MET cc_start: 0.9515 (tmm) cc_final: 0.9285 (tmm) REVERT: C 4056 GLU cc_start: 0.9545 (tt0) cc_final: 0.9289 (tp30) REVERT: C 4059 LEU cc_start: 0.9644 (mt) cc_final: 0.9414 (pp) REVERT: C 4165 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9238 (pt0) REVERT: C 4184 MET cc_start: 0.9061 (tpt) cc_final: 0.8783 (tpp) REVERT: C 4187 SER cc_start: 0.9746 (OUTLIER) cc_final: 0.9415 (p) REVERT: C 4191 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: C 4548 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8427 (mmp80) REVERT: C 4580 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: C 4730 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.8710 (p0) REVERT: C 4796 MET cc_start: 0.9293 (tpt) cc_final: 0.8668 (tpt) REVERT: C 4966 ASP cc_start: 0.9632 (m-30) cc_final: 0.9321 (p0) REVERT: C 4967 TYR cc_start: 0.9329 (t80) cc_final: 0.9113 (t80) REVERT: C 4989 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9034 (tmm) REVERT: C 5013 MET cc_start: 0.9418 (mtt) cc_final: 0.9097 (mtm) REVERT: C 5020 ASP cc_start: 0.9473 (m-30) cc_final: 0.9267 (m-30) REVERT: C 5035 GLN cc_start: 0.9238 (mp10) cc_final: 0.8970 (mp10) REVERT: D 213 TYR cc_start: 0.7433 (m-80) cc_final: 0.7187 (m-80) REVERT: D 227 MET cc_start: 0.8681 (tpp) cc_final: 0.8456 (mmp) REVERT: D 340 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8960 (mtpp) REVERT: D 343 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8490 (mp0) REVERT: D 384 MET cc_start: 0.7537 (tmm) cc_final: 0.7260 (tmm) REVERT: D 1108 GLU cc_start: 0.8983 (pm20) cc_final: 0.8755 (pm20) REVERT: D 1152 MET cc_start: 0.9212 (mmp) cc_final: 0.8599 (mmp) REVERT: D 1170 MET cc_start: 0.9125 (tpp) cc_final: 0.8716 (tpp) REVERT: D 1186 ASP cc_start: 0.9604 (m-30) cc_final: 0.9334 (m-30) REVERT: D 1601 MET cc_start: 0.9062 (mmm) cc_final: 0.8857 (mmm) REVERT: D 1984 PHE cc_start: 0.7289 (m-10) cc_final: 0.6978 (p90) REVERT: D 2008 MET cc_start: 0.9455 (ptp) cc_final: 0.8636 (tmm) REVERT: D 2297 LYS cc_start: 0.9763 (tptt) cc_final: 0.9562 (tptm) REVERT: D 2578 MET cc_start: 0.9301 (ppp) cc_final: 0.9007 (ppp) REVERT: D 3517 MET cc_start: 0.9463 (mmm) cc_final: 0.9055 (mmm) REVERT: D 3524 MET cc_start: 0.9308 (mmt) cc_final: 0.9057 (mmp) REVERT: D 3638 MET cc_start: 0.6059 (ptt) cc_final: 0.4896 (ppp) REVERT: D 3673 MET cc_start: 0.9527 (mtt) cc_final: 0.9172 (tpp) REVERT: D 3932 ASP cc_start: 0.9365 (m-30) cc_final: 0.8782 (p0) REVERT: D 4047 MET cc_start: 0.9514 (tmm) cc_final: 0.9285 (tmm) REVERT: D 4056 GLU cc_start: 0.9546 (tt0) cc_final: 0.9289 (tp30) REVERT: D 4059 LEU cc_start: 0.9643 (mt) cc_final: 0.9414 (pp) REVERT: D 4165 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9239 (pt0) REVERT: D 4184 MET cc_start: 0.9060 (tpt) cc_final: 0.8783 (tpp) REVERT: D 4187 SER cc_start: 0.9747 (OUTLIER) cc_final: 0.9408 (p) REVERT: D 4191 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: D 4548 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8426 (mmp80) REVERT: D 4580 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: D 4730 ASP cc_start: 0.9367 (OUTLIER) cc_final: 0.8707 (p0) REVERT: D 4796 MET cc_start: 0.9292 (tpt) cc_final: 0.8666 (tpt) REVERT: D 4966 ASP cc_start: 0.9633 (m-30) cc_final: 0.9322 (p0) REVERT: D 4967 TYR cc_start: 0.9329 (t80) cc_final: 0.9113 (t80) REVERT: D 4989 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9042 (tmm) REVERT: D 5013 MET cc_start: 0.9342 (mtt) cc_final: 0.9068 (mtm) REVERT: D 5020 ASP cc_start: 0.9477 (m-30) cc_final: 0.9270 (m-30) REVERT: D 5035 GLN cc_start: 0.9239 (mp10) cc_final: 0.8970 (mp10) REVERT: E 18 LYS cc_start: 0.9167 (mppt) cc_final: 0.8885 (mmtm) REVERT: E 29 MET cc_start: 0.8891 (mtp) cc_final: 0.8607 (ttm) REVERT: F 18 LYS cc_start: 0.9167 (mppt) cc_final: 0.8886 (mmtm) REVERT: F 29 MET cc_start: 0.8889 (mtp) cc_final: 0.8603 (ttm) REVERT: G 18 LYS cc_start: 0.9167 (mppt) cc_final: 0.8885 (mmtm) REVERT: G 29 MET cc_start: 0.8890 (mtp) cc_final: 0.8602 (ttm) REVERT: H 18 LYS cc_start: 0.9166 (mppt) cc_final: 0.8884 (mmtm) REVERT: H 29 MET cc_start: 0.8890 (mtp) cc_final: 0.8602 (ttm) outliers start: 165 outliers final: 73 residues processed: 922 average time/residue: 1.2401 time to fit residues: 2028.1293 Evaluate side-chains 845 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 747 time to evaluate : 11.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1511 HIS Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 4187 SER Chi-restraints excluded: chain A residue 4191 GLU Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4548 ARG Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4695 ASP Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 4187 SER Chi-restraints excluded: chain B residue 4191 GLU Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4214 LYS Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4548 ARG Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4695 ASP Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4736 ARG Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 4187 SER Chi-restraints excluded: chain C residue 4191 GLU Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4214 LYS Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4548 ARG Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4695 ASP Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4736 ARG Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4989 MET Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 4187 SER Chi-restraints excluded: chain D residue 4191 GLU Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4548 ARG Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4695 ASP Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4736 ARG Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 10.0000 chunk 503 optimal weight: 0.9980 chunk 1351 optimal weight: 20.0000 chunk 1105 optimal weight: 9.9990 chunk 447 optimal weight: 0.7980 chunk 1626 optimal weight: 40.0000 chunk 1757 optimal weight: 6.9990 chunk 1448 optimal weight: 5.9990 chunk 1613 optimal weight: 7.9990 chunk 554 optimal weight: 20.0000 chunk 1304 optimal weight: 0.0870 overall best weight: 2.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3052 HIS B3325 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3052 HIS ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3052 HIS ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 146204 Z= 0.199 Angle : 0.567 11.005 198040 Z= 0.287 Chirality : 0.039 0.202 21784 Planarity : 0.004 0.063 25752 Dihedral : 5.759 73.519 19780 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.80 % Allowed : 8.03 % Favored : 91.17 % 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: 0.76 (0.07), residues: 17832 helix: 1.55 (0.06), residues: 8812 sheet: -0.45 (0.13), residues: 1872 loop : -0.48 (0.08), residues: 7148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2886 HIS 0.009 0.001 HIS A3771 PHE 0.027 0.001 PHE D2973 TYR 0.036 0.001 TYR A4080 ARG 0.009 0.000 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 756 time to evaluate : 12.050 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 340 LYS cc_start: 0.9246 (mtpt) cc_final: 0.8976 (mtpp) REVERT: A 343 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8348 (mp0) REVERT: A 384 MET cc_start: 0.7512 (tmm) cc_final: 0.7233 (tmm) REVERT: A 403 MET cc_start: 0.9518 (ttm) cc_final: 0.9004 (mtp) REVERT: A 483 MET cc_start: 0.9319 (mmm) cc_final: 0.9091 (mmt) REVERT: A 941 MET cc_start: 0.6769 (tpt) cc_final: 0.5245 (mtm) REVERT: A 1108 GLU cc_start: 0.8875 (pm20) cc_final: 0.8652 (pm20) REVERT: A 1152 MET cc_start: 0.9236 (mmp) cc_final: 0.8661 (mmp) REVERT: A 1186 ASP cc_start: 0.9616 (m-30) cc_final: 0.9338 (m-30) REVERT: A 1494 MET cc_start: 0.7916 (mtp) cc_final: 0.7568 (mtp) REVERT: A 1636 MET cc_start: 0.9124 (ppp) cc_final: 0.8765 (ppp) REVERT: A 1731 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9365 (mm) REVERT: A 1984 PHE cc_start: 0.7333 (m-10) cc_final: 0.6945 (p90) REVERT: A 2008 MET cc_start: 0.9279 (ptp) cc_final: 0.8663 (tmm) REVERT: A 2198 MET cc_start: 0.9593 (mpp) cc_final: 0.8970 (mmp) REVERT: A 2203 MET cc_start: 0.9045 (ptp) cc_final: 0.8490 (pmm) REVERT: A 2211 MET cc_start: 0.9126 (mmm) cc_final: 0.8826 (mmp) REVERT: A 2312 MET cc_start: 0.9226 (tmm) cc_final: 0.8883 (tmm) REVERT: A 2530 MET cc_start: 0.9413 (mtm) cc_final: 0.9181 (ptp) REVERT: A 3517 MET cc_start: 0.9447 (mmm) cc_final: 0.8957 (mmm) REVERT: A 3534 MET cc_start: 0.9624 (mmp) cc_final: 0.9417 (mmt) REVERT: A 3638 MET cc_start: 0.6227 (ptt) cc_final: 0.5197 (ppp) REVERT: A 3673 MET cc_start: 0.9488 (mtt) cc_final: 0.9251 (tpp) REVERT: A 3932 ASP cc_start: 0.9353 (m-30) cc_final: 0.8859 (p0) REVERT: A 4047 MET cc_start: 0.9489 (tmm) cc_final: 0.9257 (tmm) REVERT: A 4056 GLU cc_start: 0.9627 (tt0) cc_final: 0.9346 (tp30) REVERT: A 4165 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9153 (mp0) REVERT: A 4184 MET cc_start: 0.9014 (tpt) cc_final: 0.8662 (tpp) REVERT: A 4548 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8520 (mmp-170) REVERT: A 4580 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: A 4680 LYS cc_start: 0.9658 (OUTLIER) cc_final: 0.9428 (mtmm) REVERT: A 4730 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.8797 (p0) REVERT: A 4796 MET cc_start: 0.9418 (tpt) cc_final: 0.9165 (tpt) REVERT: A 4874 MET cc_start: 0.9397 (mmm) cc_final: 0.9147 (mmm) REVERT: A 4880 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8616 (tpp) REVERT: A 4953 ASP cc_start: 0.9220 (t0) cc_final: 0.9010 (t0) REVERT: A 4966 ASP cc_start: 0.9642 (m-30) cc_final: 0.9354 (p0) REVERT: A 4967 TYR cc_start: 0.9281 (t80) cc_final: 0.9063 (t80) REVERT: A 4989 MET cc_start: 0.9414 (tmm) cc_final: 0.8982 (tmm) REVERT: A 5013 MET cc_start: 0.9242 (mtt) cc_final: 0.8852 (mtm) REVERT: A 5035 GLN cc_start: 0.9288 (mp10) cc_final: 0.9051 (mp10) REVERT: B 213 TYR cc_start: 0.7474 (m-80) cc_final: 0.7271 (m-80) REVERT: B 340 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8957 (mtpp) REVERT: B 343 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8370 (mp0) REVERT: B 384 MET cc_start: 0.7536 (tmm) cc_final: 0.7259 (tmm) REVERT: B 403 MET cc_start: 0.9442 (ttm) cc_final: 0.9037 (mtp) REVERT: B 941 MET cc_start: 0.7132 (tpt) cc_final: 0.5669 (mmp) REVERT: B 1108 GLU cc_start: 0.8898 (pm20) cc_final: 0.8686 (pm20) REVERT: B 1152 MET cc_start: 0.9191 (mmp) cc_final: 0.8581 (mmp) REVERT: B 1186 ASP cc_start: 0.9595 (m-30) cc_final: 0.9331 (m-30) REVERT: B 1601 MET cc_start: 0.9031 (mmm) cc_final: 0.8811 (mmm) REVERT: B 1731 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9379 (mm) REVERT: B 1984 PHE cc_start: 0.7325 (m-10) cc_final: 0.6968 (p90) REVERT: B 2008 MET cc_start: 0.9433 (ptp) cc_final: 0.8736 (tmm) REVERT: B 2170 MET cc_start: 0.8329 (tpt) cc_final: 0.8094 (tpt) REVERT: B 2211 MET cc_start: 0.9167 (mmm) cc_final: 0.8866 (mmp) REVERT: B 2312 MET cc_start: 0.9289 (tmm) cc_final: 0.8985 (tmm) REVERT: B 3517 MET cc_start: 0.9456 (mmm) cc_final: 0.9037 (mmm) REVERT: B 3638 MET cc_start: 0.6098 (ptt) cc_final: 0.4934 (ppp) REVERT: B 3673 MET cc_start: 0.9484 (mtt) cc_final: 0.9250 (tpp) REVERT: B 3932 ASP cc_start: 0.9357 (m-30) cc_final: 0.8859 (p0) REVERT: B 4047 MET cc_start: 0.9486 (tmm) cc_final: 0.9256 (tmm) REVERT: B 4056 GLU cc_start: 0.9551 (tt0) cc_final: 0.9300 (tp30) REVERT: B 4059 LEU cc_start: 0.9658 (mt) cc_final: 0.9415 (pp) REVERT: B 4165 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9194 (mp0) REVERT: B 4184 MET cc_start: 0.8954 (tpt) cc_final: 0.8585 (tpp) REVERT: B 4191 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: B 4548 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8521 (mmp-170) REVERT: B 4580 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: B 4730 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.8741 (p0) REVERT: B 4796 MET cc_start: 0.9341 (tpt) cc_final: 0.8781 (tpt) REVERT: B 4874 MET cc_start: 0.9449 (mmm) cc_final: 0.9152 (mmm) REVERT: B 4887 MET cc_start: 0.9190 (tpp) cc_final: 0.8683 (mmt) REVERT: B 4954 MET cc_start: 0.8990 (tpp) cc_final: 0.8553 (tpp) REVERT: B 4966 ASP cc_start: 0.9623 (m-30) cc_final: 0.9315 (p0) REVERT: B 4989 MET cc_start: 0.9388 (tmm) cc_final: 0.8909 (tmm) REVERT: B 5013 MET cc_start: 0.9265 (mtt) cc_final: 0.8871 (mtm) REVERT: B 5020 ASP cc_start: 0.9467 (m-30) cc_final: 0.9257 (m-30) REVERT: B 5035 GLN cc_start: 0.9256 (mp10) cc_final: 0.9020 (mp10) REVERT: C 213 TYR cc_start: 0.7474 (m-80) cc_final: 0.7271 (m-80) REVERT: C 340 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8979 (mtpp) REVERT: C 343 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8371 (mp0) REVERT: C 384 MET cc_start: 0.7536 (tmm) cc_final: 0.7259 (tmm) REVERT: C 403 MET cc_start: 0.9449 (ttm) cc_final: 0.9036 (mtp) REVERT: C 941 MET cc_start: 0.7133 (tpt) cc_final: 0.5674 (mmp) REVERT: C 1108 GLU cc_start: 0.8900 (pm20) cc_final: 0.8687 (pm20) REVERT: C 1152 MET cc_start: 0.9191 (mmp) cc_final: 0.8582 (mmp) REVERT: C 1186 ASP cc_start: 0.9603 (m-30) cc_final: 0.9329 (m-30) REVERT: C 1601 MET cc_start: 0.9033 (mmm) cc_final: 0.8816 (mmm) REVERT: C 1731 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9380 (mm) REVERT: C 1984 PHE cc_start: 0.7326 (m-10) cc_final: 0.6968 (p90) REVERT: C 2008 MET cc_start: 0.9432 (ptp) cc_final: 0.8737 (tmm) REVERT: C 2170 MET cc_start: 0.8331 (tpt) cc_final: 0.8096 (tpt) REVERT: C 2211 MET cc_start: 0.9168 (mmm) cc_final: 0.8866 (mmp) REVERT: C 2297 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9368 (tptp) REVERT: C 2312 MET cc_start: 0.9289 (tmm) cc_final: 0.8985 (tmm) REVERT: C 3517 MET cc_start: 0.9441 (mmm) cc_final: 0.9030 (mmm) REVERT: C 3638 MET cc_start: 0.6086 (ptt) cc_final: 0.4909 (ppp) REVERT: C 3673 MET cc_start: 0.9483 (mtt) cc_final: 0.9251 (tpp) REVERT: C 3932 ASP cc_start: 0.9356 (m-30) cc_final: 0.8835 (p0) REVERT: C 4047 MET cc_start: 0.9487 (tmm) cc_final: 0.9256 (tmm) REVERT: C 4056 GLU cc_start: 0.9551 (tt0) cc_final: 0.9300 (tp30) REVERT: C 4059 LEU cc_start: 0.9657 (mt) cc_final: 0.9415 (pp) REVERT: C 4165 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9193 (mp0) REVERT: C 4184 MET cc_start: 0.8966 (tpt) cc_final: 0.8594 (tpp) REVERT: C 4191 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: C 4548 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8510 (mmp-170) REVERT: C 4580 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: C 4730 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.8751 (p0) REVERT: C 4796 MET cc_start: 0.9340 (tpt) cc_final: 0.8780 (tpt) REVERT: C 4887 MET cc_start: 0.9194 (tpp) cc_final: 0.8685 (mmt) REVERT: C 4954 MET cc_start: 0.8990 (tpp) cc_final: 0.8551 (tpp) REVERT: C 4966 ASP cc_start: 0.9629 (m-30) cc_final: 0.9332 (p0) REVERT: C 4967 TYR cc_start: 0.9325 (t80) cc_final: 0.9096 (t80) REVERT: C 4989 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8911 (tmm) REVERT: C 5013 MET cc_start: 0.9377 (mtt) cc_final: 0.9018 (mtm) REVERT: C 5020 ASP cc_start: 0.9465 (m-30) cc_final: 0.9251 (m-30) REVERT: C 5035 GLN cc_start: 0.9248 (mp10) cc_final: 0.9023 (mp10) REVERT: D 213 TYR cc_start: 0.7477 (m-80) cc_final: 0.7275 (m-80) REVERT: D 340 LYS cc_start: 0.9141 (mtpt) cc_final: 0.8847 (mtpp) REVERT: D 343 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8372 (mp0) REVERT: D 384 MET cc_start: 0.7542 (tmm) cc_final: 0.7262 (tmm) REVERT: D 403 MET cc_start: 0.9450 (ttm) cc_final: 0.9036 (mtp) REVERT: D 941 MET cc_start: 0.7133 (tpt) cc_final: 0.5670 (mmp) REVERT: D 1108 GLU cc_start: 0.8899 (pm20) cc_final: 0.8687 (pm20) REVERT: D 1152 MET cc_start: 0.9189 (mmp) cc_final: 0.8583 (mmp) REVERT: D 1186 ASP cc_start: 0.9597 (m-30) cc_final: 0.9332 (m-30) REVERT: D 1286 MET cc_start: 0.9273 (tpt) cc_final: 0.8891 (tpt) REVERT: D 1601 MET cc_start: 0.9031 (mmm) cc_final: 0.8813 (mmm) REVERT: D 1731 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9380 (mm) REVERT: D 1984 PHE cc_start: 0.7327 (m-10) cc_final: 0.6967 (p90) REVERT: D 2008 MET cc_start: 0.9433 (ptp) cc_final: 0.8736 (tmm) REVERT: D 2170 MET cc_start: 0.8333 (tpt) cc_final: 0.8097 (tpt) REVERT: D 2211 MET cc_start: 0.9168 (mmm) cc_final: 0.8866 (mmp) REVERT: D 2312 MET cc_start: 0.9290 (tmm) cc_final: 0.8986 (tmm) REVERT: D 3517 MET cc_start: 0.9440 (mmm) cc_final: 0.9027 (mmm) REVERT: D 3638 MET cc_start: 0.6098 (ptt) cc_final: 0.4935 (ppp) REVERT: D 3673 MET cc_start: 0.9484 (mtt) cc_final: 0.9251 (tpp) REVERT: D 3932 ASP cc_start: 0.9357 (m-30) cc_final: 0.8836 (p0) REVERT: D 4047 MET cc_start: 0.9487 (tmm) cc_final: 0.9257 (tmm) REVERT: D 4056 GLU cc_start: 0.9551 (tt0) cc_final: 0.9300 (tp30) REVERT: D 4059 LEU cc_start: 0.9658 (mt) cc_final: 0.9415 (pp) REVERT: D 4165 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9195 (mp0) REVERT: D 4184 MET cc_start: 0.8955 (tpt) cc_final: 0.8585 (tpp) REVERT: D 4191 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: D 4548 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8510 (mmp-170) REVERT: D 4580 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: D 4730 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8748 (p0) REVERT: D 4796 MET cc_start: 0.9360 (tpt) cc_final: 0.8759 (tpt) REVERT: D 4887 MET cc_start: 0.9188 (tpp) cc_final: 0.8666 (mmt) REVERT: D 4954 MET cc_start: 0.8991 (tpp) cc_final: 0.8553 (tpp) REVERT: D 4966 ASP cc_start: 0.9630 (m-30) cc_final: 0.9333 (p0) REVERT: D 4967 TYR cc_start: 0.9325 (t80) cc_final: 0.9096 (t80) REVERT: D 4989 MET cc_start: 0.9402 (tmm) cc_final: 0.8918 (tmm) REVERT: D 5013 MET cc_start: 0.9267 (mtt) cc_final: 0.8872 (mtm) REVERT: D 5020 ASP cc_start: 0.9466 (m-30) cc_final: 0.9255 (m-30) REVERT: D 5035 GLN cc_start: 0.9248 (mp10) cc_final: 0.9022 (mp10) REVERT: E 18 LYS cc_start: 0.9180 (mppt) cc_final: 0.8892 (mmtm) REVERT: E 29 MET cc_start: 0.8881 (mtp) cc_final: 0.8333 (ttm) REVERT: F 18 LYS cc_start: 0.9179 (mppt) cc_final: 0.8891 (mmtm) REVERT: F 29 MET cc_start: 0.8876 (mtp) cc_final: 0.8140 (ttm) REVERT: G 18 LYS cc_start: 0.9179 (mppt) cc_final: 0.8891 (mmtm) REVERT: G 29 MET cc_start: 0.8878 (mtp) cc_final: 0.8143 (ttm) REVERT: H 18 LYS cc_start: 0.9178 (mppt) cc_final: 0.8891 (mmtm) REVERT: H 29 MET cc_start: 0.8878 (mtp) cc_final: 0.8139 (ttm) outliers start: 112 outliers final: 63 residues processed: 850 average time/residue: 1.2645 time to fit residues: 1920.7359 Evaluate side-chains 833 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 747 time to evaluate : 11.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 4191 GLU Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4548 ARG Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4981 GLU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 1230 MET Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 4191 GLU Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4214 LYS Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4548 ARG Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 2297 LYS Chi-restraints excluded: chain C residue 4191 GLU Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4214 LYS Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4548 ARG Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4989 MET Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 1230 MET Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 4191 GLU Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4548 ARG 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 4666 VAL Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 20.0000 chunk 1222 optimal weight: 1.9990 chunk 844 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 776 optimal weight: 6.9990 chunk 1092 optimal weight: 20.0000 chunk 1632 optimal weight: 20.0000 chunk 1728 optimal weight: 3.9990 chunk 852 optimal weight: 8.9990 chunk 1547 optimal weight: 10.0000 chunk 465 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS A1041 GLN A2127 GLN ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2584 HIS B ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 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 308 HIS ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 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** B 974 HIS B1041 GLN ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2127 GLN ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2584 HIS B ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 974 HIS C1041 GLN C2127 GLN ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2584 HIS B ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 HIS ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 HIS D1041 GLN D2127 GLN ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2584 HIS B ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 HIS ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 146204 Z= 0.319 Angle : 0.628 15.587 198040 Z= 0.315 Chirality : 0.040 0.170 21784 Planarity : 0.004 0.064 25752 Dihedral : 5.580 72.592 19753 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.89 % Allowed : 9.28 % Favored : 89.83 % 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: 0.80 (0.07), residues: 17832 helix: 1.61 (0.06), residues: 8868 sheet: -0.48 (0.13), residues: 1776 loop : -0.52 (0.08), residues: 7188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A2886 HIS 0.008 0.001 HIS A3771 PHE 0.023 0.002 PHE D2973 TYR 0.048 0.002 TYR B1977 ARG 0.005 0.000 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 726 time to evaluate : 11.930 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: A 213 TYR cc_start: 0.7808 (m-80) cc_final: 0.7423 (t80) REVERT: A 340 LYS cc_start: 0.9318 (mtpt) cc_final: 0.9110 (ttmm) REVERT: A 343 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8539 (mp0) REVERT: A 384 MET cc_start: 0.7627 (tmm) cc_final: 0.7321 (tmm) REVERT: A 403 MET cc_start: 0.9570 (ttm) cc_final: 0.9098 (mtp) REVERT: A 483 MET cc_start: 0.9323 (mmm) cc_final: 0.9044 (mmp) REVERT: A 1152 MET cc_start: 0.9161 (mmp) cc_final: 0.8647 (mmp) REVERT: A 1636 MET cc_start: 0.9026 (ppp) cc_final: 0.8684 (ppp) REVERT: A 1731 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9353 (mm) REVERT: A 1851 MET cc_start: 0.9522 (mtp) cc_final: 0.9299 (mtm) REVERT: A 2211 MET cc_start: 0.9058 (mmm) cc_final: 0.8760 (mmp) REVERT: A 2312 MET cc_start: 0.9221 (tmm) cc_final: 0.8872 (tmm) REVERT: A 2530 MET cc_start: 0.9417 (mtm) cc_final: 0.9195 (ptp) REVERT: A 3106 MET cc_start: 0.9588 (mtt) cc_final: 0.9090 (mmm) REVERT: A 3517 MET cc_start: 0.9460 (mmm) cc_final: 0.9006 (mmm) REVERT: A 3524 MET cc_start: 0.9458 (mmp) cc_final: 0.9194 (mmm) REVERT: A 3638 MET cc_start: 0.6297 (ptt) cc_final: 0.5421 (ppp) REVERT: A 3673 MET cc_start: 0.9565 (mtt) cc_final: 0.9149 (tpp) REVERT: A 3778 MET cc_start: 0.9774 (ttp) cc_final: 0.9316 (tmm) REVERT: A 4047 MET cc_start: 0.9471 (tmm) cc_final: 0.9213 (tmm) REVERT: A 4056 GLU cc_start: 0.9633 (tt0) cc_final: 0.9380 (tp30) REVERT: A 4165 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9248 (pt0) REVERT: A 4184 MET cc_start: 0.9001 (tpt) cc_final: 0.8771 (tpp) REVERT: A 4548 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8492 (mmp-170) REVERT: A 4580 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: A 4676 GLU cc_start: 0.8907 (pt0) cc_final: 0.8606 (pp20) REVERT: A 4680 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.8653 (mtmm) REVERT: A 4730 ASP cc_start: 0.9430 (OUTLIER) cc_final: 0.8864 (p0) REVERT: A 4796 MET cc_start: 0.9423 (tpt) cc_final: 0.9078 (tpt) REVERT: A 4874 MET cc_start: 0.9360 (mmm) cc_final: 0.9114 (mmm) REVERT: A 4887 MET cc_start: 0.9227 (tpp) cc_final: 0.8735 (mmt) REVERT: A 4966 ASP cc_start: 0.9654 (m-30) cc_final: 0.9388 (p0) REVERT: A 4989 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.8981 (tmm) REVERT: B 211 GLU cc_start: 0.9146 (tp30) cc_final: 0.8918 (tm-30) REVERT: B 213 TYR cc_start: 0.7712 (m-80) cc_final: 0.7063 (m-80) REVERT: B 340 LYS cc_start: 0.9244 (mtpt) cc_final: 0.9001 (mtpp) REVERT: B 343 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8473 (mp0) REVERT: B 384 MET cc_start: 0.7646 (tmm) cc_final: 0.7340 (tmm) REVERT: B 403 MET cc_start: 0.9534 (ttm) cc_final: 0.9133 (mtp) REVERT: B 457 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9291 (mp0) REVERT: B 1152 MET cc_start: 0.9170 (mmp) cc_final: 0.8611 (mmp) REVERT: B 1573 MET cc_start: 0.9061 (tpt) cc_final: 0.8807 (tpt) REVERT: B 1601 MET cc_start: 0.9010 (mmm) cc_final: 0.8798 (mmm) REVERT: B 1731 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9347 (mm) REVERT: B 1851 MET cc_start: 0.9537 (mtp) cc_final: 0.9319 (mtm) REVERT: B 2203 MET cc_start: 0.9121 (pmm) cc_final: 0.8861 (pmm) REVERT: B 2211 MET cc_start: 0.8965 (mmm) cc_final: 0.8742 (mmp) REVERT: B 2312 MET cc_start: 0.9267 (tmm) cc_final: 0.8951 (tmm) REVERT: B 3106 MET cc_start: 0.9570 (mtt) cc_final: 0.9058 (mmm) REVERT: B 3517 MET cc_start: 0.9465 (mmm) cc_final: 0.9106 (mmm) REVERT: B 3524 MET cc_start: 0.9428 (mmp) cc_final: 0.9144 (mmm) REVERT: B 3638 MET cc_start: 0.6411 (ptt) cc_final: 0.5458 (ppp) REVERT: B 3673 MET cc_start: 0.9566 (mtt) cc_final: 0.9202 (tpp) REVERT: B 3778 MET cc_start: 0.9770 (ttp) cc_final: 0.9330 (tmm) REVERT: B 3836 MET cc_start: 0.9105 (ttm) cc_final: 0.8666 (ttp) REVERT: B 4047 MET cc_start: 0.9479 (tmm) cc_final: 0.9233 (tmm) REVERT: B 4165 GLU cc_start: 0.9429 (mt-10) cc_final: 0.9203 (pt0) REVERT: B 4184 MET cc_start: 0.8995 (tpt) cc_final: 0.8665 (tpp) REVERT: B 4548 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8544 (mmp-170) REVERT: B 4580 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: B 4730 ASP cc_start: 0.9417 (OUTLIER) cc_final: 0.8775 (p0) REVERT: B 4796 MET cc_start: 0.9365 (tpt) cc_final: 0.8747 (tpt) REVERT: B 4874 MET cc_start: 0.9377 (mmm) cc_final: 0.9109 (mmm) REVERT: B 4966 ASP cc_start: 0.9638 (m-30) cc_final: 0.9363 (p0) REVERT: B 4989 MET cc_start: 0.9314 (tmm) cc_final: 0.8953 (tmm) REVERT: C 211 GLU cc_start: 0.9145 (tp30) cc_final: 0.8918 (tm-30) REVERT: C 213 TYR cc_start: 0.7714 (m-80) cc_final: 0.7061 (m-80) REVERT: C 340 LYS cc_start: 0.9243 (mtpt) cc_final: 0.9000 (mtpp) REVERT: C 343 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8474 (mp0) REVERT: C 384 MET cc_start: 0.7645 (tmm) cc_final: 0.7339 (tmm) REVERT: C 403 MET cc_start: 0.9538 (ttm) cc_final: 0.9126 (mtp) REVERT: C 1152 MET cc_start: 0.9172 (mmp) cc_final: 0.8612 (mmp) REVERT: C 1573 MET cc_start: 0.9063 (tpt) cc_final: 0.8809 (tpt) REVERT: C 1601 MET cc_start: 0.9006 (mmm) cc_final: 0.8794 (mmm) REVERT: C 1731 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9346 (mm) REVERT: C 1851 MET cc_start: 0.9536 (mtp) cc_final: 0.9319 (mtm) REVERT: C 2203 MET cc_start: 0.9121 (pmm) cc_final: 0.8862 (pmm) REVERT: C 2211 MET cc_start: 0.8963 (mmm) cc_final: 0.8738 (mmp) REVERT: C 2312 MET cc_start: 0.9265 (tmm) cc_final: 0.8950 (tmm) REVERT: C 3106 MET cc_start: 0.9565 (mtt) cc_final: 0.9043 (mmm) REVERT: C 3517 MET cc_start: 0.9465 (mmm) cc_final: 0.9105 (mmm) REVERT: C 3524 MET cc_start: 0.9423 (mmp) cc_final: 0.9139 (mmm) REVERT: C 3638 MET cc_start: 0.6400 (ptt) cc_final: 0.5431 (ppp) REVERT: C 3673 MET cc_start: 0.9566 (mtt) cc_final: 0.9203 (tpp) REVERT: C 3778 MET cc_start: 0.9770 (ttp) cc_final: 0.9329 (tmm) REVERT: C 3836 MET cc_start: 0.9103 (ttm) cc_final: 0.8664 (ttp) REVERT: C 4047 MET cc_start: 0.9479 (tmm) cc_final: 0.9233 (tmm) REVERT: C 4165 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9204 (pt0) REVERT: C 4184 MET cc_start: 0.9010 (tpt) cc_final: 0.8677 (tpp) REVERT: C 4548 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8544 (mmp-170) REVERT: C 4580 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: C 4730 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.8773 (p0) REVERT: C 4796 MET cc_start: 0.9365 (tpt) cc_final: 0.8748 (tpt) REVERT: C 4966 ASP cc_start: 0.9647 (m-30) cc_final: 0.9377 (p0) REVERT: C 4989 MET cc_start: 0.9248 (tmm) cc_final: 0.8980 (tmm) REVERT: D 211 GLU cc_start: 0.9147 (tp30) cc_final: 0.8919 (tm-30) REVERT: D 213 TYR cc_start: 0.7714 (m-80) cc_final: 0.7065 (m-80) REVERT: D 340 LYS cc_start: 0.9243 (mtpt) cc_final: 0.9001 (mtpp) REVERT: D 343 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8474 (mp0) REVERT: D 384 MET cc_start: 0.7651 (tmm) cc_final: 0.7342 (tmm) REVERT: D 403 MET cc_start: 0.9537 (ttm) cc_final: 0.9125 (mtp) REVERT: D 457 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9290 (mp0) REVERT: D 1152 MET cc_start: 0.9172 (mmp) cc_final: 0.8612 (mmp) REVERT: D 1286 MET cc_start: 0.9235 (tpt) cc_final: 0.8837 (tpt) REVERT: D 1573 MET cc_start: 0.9061 (tpt) cc_final: 0.8807 (tpt) REVERT: D 1601 MET cc_start: 0.9003 (mmm) cc_final: 0.8791 (mmm) REVERT: D 1731 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9347 (mm) REVERT: D 1851 MET cc_start: 0.9533 (mtp) cc_final: 0.9313 (mtm) REVERT: D 2203 MET cc_start: 0.9119 (pmm) cc_final: 0.8861 (pmm) REVERT: D 2211 MET cc_start: 0.8964 (mmm) cc_final: 0.8739 (mmp) REVERT: D 2312 MET cc_start: 0.9266 (tmm) cc_final: 0.8952 (tmm) REVERT: D 3106 MET cc_start: 0.9565 (mtt) cc_final: 0.9041 (mmm) REVERT: D 3517 MET cc_start: 0.9465 (mmm) cc_final: 0.9103 (mmm) REVERT: D 3524 MET cc_start: 0.9424 (mmp) cc_final: 0.9139 (mmm) REVERT: D 3638 MET cc_start: 0.6409 (ptt) cc_final: 0.5458 (ppp) REVERT: D 3673 MET cc_start: 0.9566 (mtt) cc_final: 0.9204 (tpp) REVERT: D 3778 MET cc_start: 0.9770 (ttp) cc_final: 0.9329 (tmm) REVERT: D 3836 MET cc_start: 0.9103 (ttm) cc_final: 0.8664 (ttp) REVERT: D 4047 MET cc_start: 0.9479 (tmm) cc_final: 0.9234 (tmm) REVERT: D 4165 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9206 (pt0) REVERT: D 4184 MET cc_start: 0.8995 (tpt) cc_final: 0.8665 (tpp) REVERT: D 4548 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8544 (mmp-170) REVERT: D 4580 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: D 4730 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.8771 (p0) REVERT: D 4796 MET cc_start: 0.9365 (tpt) cc_final: 0.8745 (tpt) REVERT: D 4966 ASP cc_start: 0.9647 (m-30) cc_final: 0.9377 (p0) REVERT: D 4989 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8954 (tmm) REVERT: E 29 MET cc_start: 0.8853 (mtp) cc_final: 0.8125 (ttm) REVERT: F 29 MET cc_start: 0.8825 (mtp) cc_final: 0.8214 (ttm) REVERT: G 29 MET cc_start: 0.8826 (mtp) cc_final: 0.8214 (ttm) REVERT: H 29 MET cc_start: 0.8826 (mtp) cc_final: 0.8212 (ttm) outliers start: 123 outliers final: 81 residues processed: 816 average time/residue: 1.1955 time to fit residues: 1737.9788 Evaluate side-chains 807 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 707 time to evaluate : 11.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1511 HIS Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4548 ARG Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4695 ASP Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4548 ARG Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4695 ASP Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5027 CYS Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2259 GLU Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4548 ARG Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4695 ASP Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5016 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4548 ARG Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4695 ASP Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 8.9990 chunk 981 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 1286 optimal weight: 0.6980 chunk 713 optimal weight: 30.0000 chunk 1474 optimal weight: 6.9990 chunk 1194 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 882 optimal weight: 9.9990 chunk 1551 optimal weight: 2.9990 chunk 436 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2173 GLN ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 146204 Z= 0.191 Angle : 0.554 10.011 198040 Z= 0.279 Chirality : 0.039 0.168 21784 Planarity : 0.004 0.063 25752 Dihedral : 5.393 72.006 19725 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.83 % Allowed : 10.07 % Favored : 89.09 % 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: 0.99 (0.07), residues: 17832 helix: 1.77 (0.06), residues: 8856 sheet: -0.41 (0.13), residues: 1832 loop : -0.41 (0.08), residues: 7144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.001 TRP D2886 HIS 0.009 0.001 HIS D3771 PHE 0.025 0.001 PHE A2973 TYR 0.028 0.001 TYR A4080 ARG 0.004 0.000 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 718 time to evaluate : 12.016 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: A 213 TYR cc_start: 0.7946 (m-80) cc_final: 0.7271 (m-80) REVERT: A 384 MET cc_start: 0.7562 (tmm) cc_final: 0.7353 (tmm) REVERT: A 403 MET cc_start: 0.9534 (ttm) cc_final: 0.9244 (mtp) REVERT: A 483 MET cc_start: 0.9309 (mmm) cc_final: 0.9067 (mmt) REVERT: A 941 MET cc_start: 0.6982 (tpt) cc_final: 0.5854 (mtm) REVERT: A 1152 MET cc_start: 0.9114 (mmp) cc_final: 0.8632 (mmp) REVERT: A 1494 MET cc_start: 0.7854 (mtp) cc_final: 0.7575 (mtp) REVERT: A 1636 MET cc_start: 0.8984 (ppp) cc_final: 0.8644 (ppp) REVERT: A 1731 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9337 (mm) REVERT: A 1851 MET cc_start: 0.9525 (mtp) cc_final: 0.9295 (mtm) REVERT: A 2008 MET cc_start: 0.9320 (ptp) cc_final: 0.8581 (tmm) REVERT: A 2312 MET cc_start: 0.9213 (tmm) cc_final: 0.8868 (tmm) REVERT: A 3106 MET cc_start: 0.9574 (mtt) cc_final: 0.9081 (mmt) REVERT: A 3517 MET cc_start: 0.9453 (mmm) cc_final: 0.9004 (mmm) REVERT: A 3524 MET cc_start: 0.9410 (mmp) cc_final: 0.9143 (mmm) REVERT: A 3638 MET cc_start: 0.6238 (ptt) cc_final: 0.5355 (ppp) REVERT: A 3778 MET cc_start: 0.9759 (ttp) cc_final: 0.9302 (tmm) REVERT: A 3955 MET cc_start: 0.9516 (mmp) cc_final: 0.9141 (mtm) REVERT: A 4047 MET cc_start: 0.9467 (tmm) cc_final: 0.9140 (tmm) REVERT: A 4056 GLU cc_start: 0.9625 (tt0) cc_final: 0.9369 (tp30) REVERT: A 4165 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9229 (pt0) REVERT: A 4184 MET cc_start: 0.9026 (tpt) cc_final: 0.8792 (tpp) REVERT: A 4580 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: A 4676 GLU cc_start: 0.8866 (pt0) cc_final: 0.8590 (pp20) REVERT: A 4680 LYS cc_start: 0.9667 (OUTLIER) cc_final: 0.8673 (mtmm) REVERT: A 4730 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.8886 (p0) REVERT: A 4796 MET cc_start: 0.9394 (tpt) cc_final: 0.9083 (tpt) REVERT: A 4874 MET cc_start: 0.9277 (mmm) cc_final: 0.9050 (mmm) REVERT: A 4879 MET cc_start: 0.9060 (tpt) cc_final: 0.8851 (tpp) REVERT: A 4966 ASP cc_start: 0.9640 (m-30) cc_final: 0.9364 (p0) REVERT: A 4989 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8978 (tmm) REVERT: A 5013 MET cc_start: 0.9400 (mtt) cc_final: 0.9110 (mtm) REVERT: B 211 GLU cc_start: 0.9199 (tp30) cc_final: 0.8680 (tm-30) REVERT: B 213 TYR cc_start: 0.7550 (m-80) cc_final: 0.7266 (m-80) REVERT: B 340 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8952 (mtpp) REVERT: B 343 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8433 (mp0) REVERT: B 384 MET cc_start: 0.7580 (tmm) cc_final: 0.7369 (tmm) REVERT: B 403 MET cc_start: 0.9504 (ttm) cc_final: 0.9094 (mtp) REVERT: B 941 MET cc_start: 0.6972 (tpt) cc_final: 0.6135 (mmm) REVERT: B 1100 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: B 1152 MET cc_start: 0.9134 (mmp) cc_final: 0.8619 (mmp) REVERT: B 1170 MET cc_start: 0.9107 (tpp) cc_final: 0.8658 (tpp) REVERT: B 1601 MET cc_start: 0.8994 (mmm) cc_final: 0.8763 (mmm) REVERT: B 1636 MET cc_start: 0.8551 (tmm) cc_final: 0.8194 (tmm) REVERT: B 1731 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9323 (mm) REVERT: B 1851 MET cc_start: 0.9532 (mtp) cc_final: 0.9323 (mtm) REVERT: B 2008 MET cc_start: 0.9442 (ptp) cc_final: 0.8784 (tmm) REVERT: B 2203 MET cc_start: 0.9074 (pmm) cc_final: 0.8799 (pmm) REVERT: B 2312 MET cc_start: 0.9265 (tmm) cc_final: 0.8927 (tmm) REVERT: B 3517 MET cc_start: 0.9438 (mmm) cc_final: 0.9059 (mmm) REVERT: B 3524 MET cc_start: 0.9328 (mmp) cc_final: 0.9047 (mmm) REVERT: B 3638 MET cc_start: 0.6350 (ptt) cc_final: 0.5389 (ppp) REVERT: B 3673 MET cc_start: 0.9534 (mtt) cc_final: 0.9137 (tpp) REVERT: B 3778 MET cc_start: 0.9743 (ttp) cc_final: 0.9285 (tmm) REVERT: B 3955 MET cc_start: 0.9518 (mmp) cc_final: 0.9138 (mtm) REVERT: B 4047 MET cc_start: 0.9464 (tmm) cc_final: 0.9204 (tmm) REVERT: B 4059 LEU cc_start: 0.9567 (mt) cc_final: 0.9352 (pp) REVERT: B 4165 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9225 (pt0) REVERT: B 4184 MET cc_start: 0.9001 (tpt) cc_final: 0.8691 (tpp) REVERT: B 4580 TYR cc_start: 0.9311 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: B 4730 ASP cc_start: 0.9410 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 4796 MET cc_start: 0.9413 (tpt) cc_final: 0.8926 (tpt) REVERT: B 4874 MET cc_start: 0.9348 (mmm) cc_final: 0.9085 (mmm) REVERT: B 4887 MET cc_start: 0.8923 (mmm) cc_final: 0.8610 (tpp) REVERT: B 4966 ASP cc_start: 0.9625 (m-30) cc_final: 0.9356 (p0) REVERT: B 4989 MET cc_start: 0.9335 (tmm) cc_final: 0.8967 (tmm) REVERT: B 5013 MET cc_start: 0.9433 (mtt) cc_final: 0.9151 (mtm) REVERT: C 211 GLU cc_start: 0.9200 (tp30) cc_final: 0.8682 (tm-30) REVERT: C 213 TYR cc_start: 0.7554 (m-80) cc_final: 0.7268 (m-80) REVERT: C 340 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8952 (mtpp) REVERT: C 343 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8434 (mp0) REVERT: C 384 MET cc_start: 0.7581 (tmm) cc_final: 0.7369 (tmm) REVERT: C 403 MET cc_start: 0.9507 (ttm) cc_final: 0.9091 (mtp) REVERT: C 941 MET cc_start: 0.6976 (tpt) cc_final: 0.6141 (mmm) REVERT: C 1100 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8460 (mtt) REVERT: C 1152 MET cc_start: 0.9136 (mmp) cc_final: 0.8622 (mmp) REVERT: C 1170 MET cc_start: 0.9114 (tpp) cc_final: 0.8667 (tpp) REVERT: C 1601 MET cc_start: 0.8988 (mmm) cc_final: 0.8760 (mmm) REVERT: C 1636 MET cc_start: 0.8555 (tmm) cc_final: 0.8196 (tmm) REVERT: C 1731 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9324 (mm) REVERT: C 1851 MET cc_start: 0.9532 (mtp) cc_final: 0.9322 (mtm) REVERT: C 2008 MET cc_start: 0.9441 (ptp) cc_final: 0.8784 (tmm) REVERT: C 2203 MET cc_start: 0.9074 (pmm) cc_final: 0.8800 (pmm) REVERT: C 2312 MET cc_start: 0.9265 (tmm) cc_final: 0.8927 (tmm) REVERT: C 3517 MET cc_start: 0.9439 (mmm) cc_final: 0.9060 (mmm) REVERT: C 3524 MET cc_start: 0.9342 (mmp) cc_final: 0.9042 (mmm) REVERT: C 3638 MET cc_start: 0.6452 (ptt) cc_final: 0.5378 (ppp) REVERT: C 3673 MET cc_start: 0.9533 (mtt) cc_final: 0.9138 (tpp) REVERT: C 3778 MET cc_start: 0.9743 (ttp) cc_final: 0.9286 (tmm) REVERT: C 3955 MET cc_start: 0.9518 (mmp) cc_final: 0.9138 (mtm) REVERT: C 4047 MET cc_start: 0.9465 (tmm) cc_final: 0.9128 (tmm) REVERT: C 4059 LEU cc_start: 0.9567 (mt) cc_final: 0.9353 (pp) REVERT: C 4165 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9225 (pt0) REVERT: C 4184 MET cc_start: 0.9025 (tpt) cc_final: 0.8703 (tpp) REVERT: C 4580 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: C 4730 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.8844 (p0) REVERT: C 4796 MET cc_start: 0.9414 (tpt) cc_final: 0.8930 (tpt) REVERT: C 4887 MET cc_start: 0.8918 (mmm) cc_final: 0.8608 (tpp) REVERT: C 4966 ASP cc_start: 0.9635 (m-30) cc_final: 0.9369 (p0) REVERT: C 4989 MET cc_start: 0.9271 (tmm) cc_final: 0.8976 (tmm) REVERT: C 5013 MET cc_start: 0.9414 (mtt) cc_final: 0.9070 (mtm) REVERT: D 211 GLU cc_start: 0.9200 (tp30) cc_final: 0.8680 (tm-30) REVERT: D 213 TYR cc_start: 0.7554 (m-80) cc_final: 0.7269 (m-80) REVERT: D 340 LYS cc_start: 0.9207 (mtpt) cc_final: 0.8953 (mtpp) REVERT: D 343 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8434 (mp0) REVERT: D 384 MET cc_start: 0.7589 (tmm) cc_final: 0.7373 (tmm) REVERT: D 403 MET cc_start: 0.9508 (ttm) cc_final: 0.9091 (mtp) REVERT: D 941 MET cc_start: 0.6975 (tpt) cc_final: 0.6139 (mmm) REVERT: D 1100 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8458 (mtt) REVERT: D 1152 MET cc_start: 0.9135 (mmp) cc_final: 0.8621 (mmp) REVERT: D 1170 MET cc_start: 0.9113 (tpp) cc_final: 0.8665 (tpp) REVERT: D 1601 MET cc_start: 0.8986 (mmm) cc_final: 0.8758 (mmm) REVERT: D 1636 MET cc_start: 0.8547 (tmm) cc_final: 0.8189 (tmm) REVERT: D 1731 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9324 (mm) REVERT: D 1851 MET cc_start: 0.9531 (mtp) cc_final: 0.9324 (mtm) REVERT: D 2008 MET cc_start: 0.9442 (ptp) cc_final: 0.8783 (tmm) REVERT: D 2203 MET cc_start: 0.9073 (pmm) cc_final: 0.8799 (pmm) REVERT: D 2312 MET cc_start: 0.9265 (tmm) cc_final: 0.8927 (tmm) REVERT: D 3517 MET cc_start: 0.9439 (mmm) cc_final: 0.9058 (mmm) REVERT: D 3524 MET cc_start: 0.9363 (mmp) cc_final: 0.9029 (mmm) REVERT: D 3638 MET cc_start: 0.6347 (ptt) cc_final: 0.5386 (ppp) REVERT: D 3673 MET cc_start: 0.9534 (mtt) cc_final: 0.9138 (tpp) REVERT: D 3778 MET cc_start: 0.9743 (ttp) cc_final: 0.9285 (tmm) REVERT: D 3955 MET cc_start: 0.9518 (mmp) cc_final: 0.9139 (mtm) REVERT: D 4047 MET cc_start: 0.9464 (tmm) cc_final: 0.9205 (tmm) REVERT: D 4059 LEU cc_start: 0.9567 (mt) cc_final: 0.9353 (pp) REVERT: D 4165 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9245 (pt0) REVERT: D 4184 MET cc_start: 0.8994 (tpt) cc_final: 0.8689 (tpp) REVERT: D 4580 TYR cc_start: 0.9361 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: D 4730 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.8850 (p0) REVERT: D 4796 MET cc_start: 0.9413 (tpt) cc_final: 0.8926 (tpt) REVERT: D 4887 MET cc_start: 0.8918 (mmm) cc_final: 0.8607 (tpp) REVERT: D 4966 ASP cc_start: 0.9635 (m-30) cc_final: 0.9369 (p0) REVERT: D 4989 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8942 (tmm) REVERT: D 5013 MET cc_start: 0.9435 (mtt) cc_final: 0.9142 (mtm) REVERT: E 29 MET cc_start: 0.8832 (mtp) cc_final: 0.8183 (ttm) REVERT: F 29 MET cc_start: 0.8828 (mtp) cc_final: 0.8177 (ttm) REVERT: G 29 MET cc_start: 0.8828 (mtp) cc_final: 0.8176 (ttm) REVERT: H 29 MET cc_start: 0.8828 (mtp) cc_final: 0.8175 (ttm) outliers start: 110 outliers final: 70 residues processed: 800 average time/residue: 1.2859 time to fit residues: 1859.4783 Evaluate side-chains 794 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 706 time to evaluate : 11.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 9.9990 chunk 1556 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 chunk 1014 optimal weight: 5.9990 chunk 426 optimal weight: 2.9990 chunk 1729 optimal weight: 6.9990 chunk 1436 optimal weight: 6.9990 chunk 800 optimal weight: 3.9990 chunk 143 optimal weight: 0.0060 chunk 572 optimal weight: 20.0000 chunk 908 optimal weight: 0.5980 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3325 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4094 GLN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3325 ASN C4094 GLN ** C4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3325 ASN D4094 GLN ** D4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 146204 Z= 0.173 Angle : 0.543 9.997 198040 Z= 0.272 Chirality : 0.039 0.177 21784 Planarity : 0.004 0.063 25752 Dihedral : 5.235 71.938 19708 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.98 % Allowed : 10.16 % Favored : 88.86 % 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: 1.08 (0.07), residues: 17832 helix: 1.86 (0.06), residues: 8876 sheet: -0.47 (0.12), residues: 1832 loop : -0.36 (0.08), residues: 7124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP B2886 HIS 0.009 0.001 HIS D3771 PHE 0.025 0.001 PHE D2973 TYR 0.029 0.001 TYR A4080 ARG 0.004 0.000 ARG D4563 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 720 time to evaluate : 12.065 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: A 403 MET cc_start: 0.9535 (ttm) cc_final: 0.9082 (mtp) REVERT: A 483 MET cc_start: 0.9293 (mmm) cc_final: 0.9068 (mmt) REVERT: A 1152 MET cc_start: 0.9072 (mmt) cc_final: 0.8622 (mmt) REVERT: A 1494 MET cc_start: 0.7870 (mtp) cc_final: 0.7663 (mtp) REVERT: A 1636 MET cc_start: 0.9007 (ppp) cc_final: 0.8654 (ppp) REVERT: A 1731 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9329 (mm) REVERT: A 1851 MET cc_start: 0.9510 (mtp) cc_final: 0.9300 (mtm) REVERT: A 2008 MET cc_start: 0.9264 (ptp) cc_final: 0.8554 (tmm) REVERT: A 2203 MET cc_start: 0.9066 (pmm) cc_final: 0.8841 (pmm) REVERT: A 2312 MET cc_start: 0.9206 (tmm) cc_final: 0.8853 (tmm) REVERT: A 2932 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5206 (pmm) REVERT: A 3467 MET cc_start: 0.8902 (mmm) cc_final: 0.8238 (ppp) REVERT: A 3517 MET cc_start: 0.9440 (mmm) cc_final: 0.9016 (mmm) REVERT: A 3524 MET cc_start: 0.9359 (mmp) cc_final: 0.9136 (mmp) REVERT: A 3638 MET cc_start: 0.6415 (ptt) cc_final: 0.5173 (ppp) REVERT: A 3673 MET cc_start: 0.9651 (mmm) cc_final: 0.9082 (tpp) REVERT: A 3778 MET cc_start: 0.9759 (ttp) cc_final: 0.9297 (tmm) REVERT: A 3793 MET cc_start: 0.8857 (tpp) cc_final: 0.8605 (tpp) REVERT: A 3955 MET cc_start: 0.9528 (mmp) cc_final: 0.9136 (mtm) REVERT: A 4047 MET cc_start: 0.9481 (tmm) cc_final: 0.9151 (tmm) REVERT: A 4056 GLU cc_start: 0.9632 (tt0) cc_final: 0.9386 (tp30) REVERT: A 4165 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9235 (pt0) REVERT: A 4184 MET cc_start: 0.9045 (tpt) cc_final: 0.8758 (tpp) REVERT: A 4580 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: A 4627 MET cc_start: 0.7320 (tmm) cc_final: 0.6938 (tmm) REVERT: A 4680 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9406 (mtmm) REVERT: A 4730 ASP cc_start: 0.9414 (OUTLIER) cc_final: 0.8798 (p0) REVERT: A 4796 MET cc_start: 0.9395 (tpt) cc_final: 0.9083 (tpt) REVERT: A 4874 MET cc_start: 0.9279 (mmm) cc_final: 0.9045 (mmm) REVERT: A 4879 MET cc_start: 0.9085 (tpt) cc_final: 0.8867 (tpp) REVERT: A 4887 MET cc_start: 0.8959 (mmm) cc_final: 0.8716 (tpp) REVERT: A 4989 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8964 (tmm) REVERT: B 211 GLU cc_start: 0.9014 (tp30) cc_final: 0.8742 (tm-30) REVERT: B 340 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8879 (mtpp) REVERT: B 343 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8443 (mp0) REVERT: B 403 MET cc_start: 0.9520 (ttm) cc_final: 0.9153 (mtp) REVERT: B 1100 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8558 (mtt) REVERT: B 1152 MET cc_start: 0.9078 (mmt) cc_final: 0.8597 (mmt) REVERT: B 1170 MET cc_start: 0.9178 (tpp) cc_final: 0.8784 (tpp) REVERT: B 1601 MET cc_start: 0.8978 (mmm) cc_final: 0.8747 (mmm) REVERT: B 1731 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9300 (mm) REVERT: B 2008 MET cc_start: 0.9430 (ptp) cc_final: 0.8773 (tmm) REVERT: B 2170 MET cc_start: 0.8678 (tpt) cc_final: 0.8193 (tpt) REVERT: B 2203 MET cc_start: 0.9088 (pmm) cc_final: 0.8800 (pmm) REVERT: B 2312 MET cc_start: 0.9234 (tmm) cc_final: 0.8877 (tmm) REVERT: B 2932 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5485 (pmm) REVERT: B 3106 MET cc_start: 0.9594 (mmt) cc_final: 0.9054 (mmt) REVERT: B 3517 MET cc_start: 0.9442 (mmm) cc_final: 0.9053 (mmm) REVERT: B 3524 MET cc_start: 0.9349 (mmp) cc_final: 0.9132 (mmp) REVERT: B 3638 MET cc_start: 0.6362 (ptt) cc_final: 0.5125 (ppp) REVERT: B 3673 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.9158 (tpp) REVERT: B 3778 MET cc_start: 0.9742 (ttp) cc_final: 0.9473 (tmm) REVERT: B 3955 MET cc_start: 0.9530 (mmp) cc_final: 0.9134 (mtm) REVERT: B 4047 MET cc_start: 0.9466 (tmm) cc_final: 0.9132 (tmm) REVERT: B 4184 MET cc_start: 0.9020 (tpt) cc_final: 0.8713 (tpp) REVERT: B 4207 MET cc_start: 0.9227 (mmp) cc_final: 0.9020 (mmp) REVERT: B 4580 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: B 4730 ASP cc_start: 0.9412 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 4796 MET cc_start: 0.9396 (tpt) cc_final: 0.8947 (tpt) REVERT: B 4874 MET cc_start: 0.9359 (mmm) cc_final: 0.9113 (mmm) REVERT: B 4887 MET cc_start: 0.8870 (mmm) cc_final: 0.8507 (tpp) REVERT: B 4989 MET cc_start: 0.9337 (tmm) cc_final: 0.8946 (tmm) REVERT: C 211 GLU cc_start: 0.9015 (tp30) cc_final: 0.8743 (tm-30) REVERT: C 340 LYS cc_start: 0.9168 (mtpt) cc_final: 0.8880 (mtpp) REVERT: C 343 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8443 (mp0) REVERT: C 403 MET cc_start: 0.9521 (ttm) cc_final: 0.9149 (mtp) REVERT: C 1100 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8559 (mtt) REVERT: C 1152 MET cc_start: 0.9082 (mmt) cc_final: 0.8598 (mmt) REVERT: C 1170 MET cc_start: 0.9185 (tpp) cc_final: 0.8791 (tpp) REVERT: C 1601 MET cc_start: 0.8980 (mmm) cc_final: 0.8749 (mmm) REVERT: C 1731 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9301 (mm) REVERT: C 2008 MET cc_start: 0.9430 (ptp) cc_final: 0.8773 (tmm) REVERT: C 2170 MET cc_start: 0.8679 (tpt) cc_final: 0.8192 (tpt) REVERT: C 2203 MET cc_start: 0.9090 (pmm) cc_final: 0.8801 (pmm) REVERT: C 2312 MET cc_start: 0.9233 (tmm) cc_final: 0.8876 (tmm) REVERT: C 2932 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5485 (pmm) REVERT: C 3106 MET cc_start: 0.9595 (mmt) cc_final: 0.9054 (mmt) REVERT: C 3517 MET cc_start: 0.9441 (mmm) cc_final: 0.9053 (mmm) REVERT: C 3524 MET cc_start: 0.9346 (mmp) cc_final: 0.9128 (mmp) REVERT: C 3638 MET cc_start: 0.6575 (ptt) cc_final: 0.5993 (ppp) REVERT: C 3673 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.9158 (tpp) REVERT: C 3778 MET cc_start: 0.9741 (ttp) cc_final: 0.9474 (tmm) REVERT: C 3793 MET cc_start: 0.8844 (tpp) cc_final: 0.8568 (tpp) REVERT: C 3955 MET cc_start: 0.9530 (mmp) cc_final: 0.9133 (mtm) REVERT: C 4047 MET cc_start: 0.9467 (tmm) cc_final: 0.9133 (tmm) REVERT: C 4184 MET cc_start: 0.9036 (tpt) cc_final: 0.8718 (tpp) REVERT: C 4207 MET cc_start: 0.9226 (mmp) cc_final: 0.9020 (mmp) REVERT: C 4580 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: C 4730 ASP cc_start: 0.9416 (OUTLIER) cc_final: 0.8848 (p0) REVERT: C 4796 MET cc_start: 0.9397 (tpt) cc_final: 0.8949 (tpt) REVERT: C 4887 MET cc_start: 0.8866 (mmm) cc_final: 0.8502 (tpp) REVERT: C 4989 MET cc_start: 0.9266 (tmm) cc_final: 0.8942 (tmm) REVERT: D 211 GLU cc_start: 0.9016 (tp30) cc_final: 0.8744 (tm-30) REVERT: D 340 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8881 (mtpp) REVERT: D 343 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8443 (mp0) REVERT: D 403 MET cc_start: 0.9521 (ttm) cc_final: 0.9151 (mtp) REVERT: D 1100 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: D 1152 MET cc_start: 0.9081 (mmt) cc_final: 0.8599 (mmt) REVERT: D 1170 MET cc_start: 0.9182 (tpp) cc_final: 0.8788 (tpp) REVERT: D 1601 MET cc_start: 0.8978 (mmm) cc_final: 0.8747 (mmm) REVERT: D 1731 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9300 (mm) REVERT: D 2008 MET cc_start: 0.9431 (ptp) cc_final: 0.8772 (tmm) REVERT: D 2170 MET cc_start: 0.8677 (tpt) cc_final: 0.8191 (tpt) REVERT: D 2203 MET cc_start: 0.9089 (pmm) cc_final: 0.8801 (pmm) REVERT: D 2312 MET cc_start: 0.9234 (tmm) cc_final: 0.8877 (tmm) REVERT: D 2932 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5482 (pmm) REVERT: D 3106 MET cc_start: 0.9595 (mmt) cc_final: 0.9054 (mmt) REVERT: D 3517 MET cc_start: 0.9442 (mmm) cc_final: 0.9050 (mmm) REVERT: D 3524 MET cc_start: 0.9362 (mmp) cc_final: 0.9155 (mmp) REVERT: D 3638 MET cc_start: 0.6360 (ptt) cc_final: 0.5123 (ppp) REVERT: D 3673 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.9159 (tpp) REVERT: D 3778 MET cc_start: 0.9742 (ttp) cc_final: 0.9473 (tmm) REVERT: D 3955 MET cc_start: 0.9529 (mmp) cc_final: 0.9133 (mtm) REVERT: D 4047 MET cc_start: 0.9466 (tmm) cc_final: 0.9133 (tmm) REVERT: D 4165 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9253 (pt0) REVERT: D 4184 MET cc_start: 0.9016 (tpt) cc_final: 0.8711 (tpp) REVERT: D 4207 MET cc_start: 0.9227 (mmp) cc_final: 0.9020 (mmp) REVERT: D 4580 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: D 4730 ASP cc_start: 0.9415 (OUTLIER) cc_final: 0.8846 (p0) REVERT: D 4796 MET cc_start: 0.9396 (tpt) cc_final: 0.8946 (tpt) REVERT: D 4887 MET cc_start: 0.8867 (mmm) cc_final: 0.8504 (tpp) REVERT: D 4989 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8918 (tmm) REVERT: E 29 MET cc_start: 0.8776 (mtp) cc_final: 0.8110 (ttm) REVERT: F 29 MET cc_start: 0.8772 (mtp) cc_final: 0.8103 (ttm) REVERT: G 29 MET cc_start: 0.8771 (mtp) cc_final: 0.8103 (ttm) REVERT: H 29 MET cc_start: 0.8771 (mtp) cc_final: 0.8104 (ttm) outliers start: 132 outliers final: 85 residues processed: 812 average time/residue: 1.2099 time to fit residues: 1759.3836 Evaluate side-chains 812 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 702 time to evaluate : 11.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2886 TRP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4680 LYS Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2886 TRP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3673 MET Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2886 TRP Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3673 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR 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 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 2886 TRP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 985 optimal weight: 8.9990 chunk 1263 optimal weight: 5.9990 chunk 978 optimal weight: 10.0000 chunk 1456 optimal weight: 10.0000 chunk 966 optimal weight: 0.0570 chunk 1723 optimal weight: 7.9990 chunk 1078 optimal weight: 9.9990 chunk 1050 optimal weight: 10.0000 chunk 795 optimal weight: 10.0000 overall best weight: 5.8106 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4857 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2173 GLN ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4162 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 GLN ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2173 GLN ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4162 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 GLN ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 146204 Z= 0.318 Angle : 0.629 11.763 198040 Z= 0.314 Chirality : 0.040 0.183 21784 Planarity : 0.004 0.063 25752 Dihedral : 5.294 72.603 19706 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.07 % Allowed : 10.59 % Favored : 88.34 % 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: 0.99 (0.07), residues: 17832 helix: 1.78 (0.06), residues: 8884 sheet: -0.60 (0.12), residues: 1864 loop : -0.38 (0.08), residues: 7084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP A2886 HIS 0.012 0.001 HIS A 273 PHE 0.021 0.001 PHE A2973 TYR 0.027 0.001 TYR A4080 ARG 0.005 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 711 time to evaluate : 11.983 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: A 213 TYR cc_start: 0.8312 (m-80) cc_final: 0.7459 (t80) REVERT: A 343 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8495 (mp0) REVERT: A 403 MET cc_start: 0.9584 (ttm) cc_final: 0.9332 (mtp) REVERT: A 483 MET cc_start: 0.9289 (mmm) cc_final: 0.9041 (mmp) REVERT: A 941 MET cc_start: 0.6652 (tpt) cc_final: 0.5721 (mmp) REVERT: A 1152 MET cc_start: 0.9054 (mmt) cc_final: 0.8616 (mmt) REVERT: A 1186 ASP cc_start: 0.9493 (m-30) cc_final: 0.8888 (p0) REVERT: A 1636 MET cc_start: 0.8973 (ppp) cc_final: 0.8653 (ppp) REVERT: A 1731 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9311 (mm) REVERT: A 1851 MET cc_start: 0.9541 (mtp) cc_final: 0.9334 (mtm) REVERT: A 2008 MET cc_start: 0.9330 (ptp) cc_final: 0.8759 (tmm) REVERT: A 2170 MET cc_start: 0.8698 (tpt) cc_final: 0.8368 (tpt) REVERT: A 2178 MET cc_start: 0.9192 (ttp) cc_final: 0.8903 (tmm) REVERT: A 2203 MET cc_start: 0.9013 (pmm) cc_final: 0.8787 (pmm) REVERT: A 2312 MET cc_start: 0.9198 (tmm) cc_final: 0.8856 (tmm) REVERT: A 2932 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5322 (pmm) REVERT: A 3106 MET cc_start: 0.9316 (mmt) cc_final: 0.8974 (mmm) REVERT: A 3467 MET cc_start: 0.8897 (mmm) cc_final: 0.8371 (ppp) REVERT: A 3517 MET cc_start: 0.9455 (mmm) cc_final: 0.9041 (mmm) REVERT: A 3638 MET cc_start: 0.6521 (ptt) cc_final: 0.5691 (ppp) REVERT: A 3673 MET cc_start: 0.9640 (mmm) cc_final: 0.9109 (tpp) REVERT: A 3778 MET cc_start: 0.9768 (ttp) cc_final: 0.9347 (tmm) REVERT: A 3955 MET cc_start: 0.9548 (mmp) cc_final: 0.9147 (mtm) REVERT: A 4047 MET cc_start: 0.9452 (tmm) cc_final: 0.9136 (tmm) REVERT: A 4056 GLU cc_start: 0.9611 (tt0) cc_final: 0.9345 (tp30) REVERT: A 4165 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9203 (mt-10) REVERT: A 4168 GLU cc_start: 0.9511 (pm20) cc_final: 0.9184 (pm20) REVERT: A 4184 MET cc_start: 0.9008 (tpt) cc_final: 0.8735 (tpp) REVERT: A 4246 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8991 (mp10) REVERT: A 4580 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: A 4627 MET cc_start: 0.7357 (tmm) cc_final: 0.6979 (tmm) REVERT: A 4730 ASP cc_start: 0.9450 (OUTLIER) cc_final: 0.8902 (p0) REVERT: A 4796 MET cc_start: 0.9432 (tpt) cc_final: 0.8989 (tpt) REVERT: A 4874 MET cc_start: 0.9212 (mmm) cc_final: 0.8969 (mmm) REVERT: A 4879 MET cc_start: 0.9158 (tpt) cc_final: 0.8871 (tpp) REVERT: A 4887 MET cc_start: 0.8930 (mmm) cc_final: 0.8632 (tpp) REVERT: A 4954 MET cc_start: 0.9073 (tpp) cc_final: 0.8641 (mmm) REVERT: A 4989 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9007 (tmm) REVERT: A 5013 MET cc_start: 0.9473 (mtt) cc_final: 0.9207 (mtm) REVERT: B 211 GLU cc_start: 0.8999 (tp30) cc_final: 0.8735 (tm-30) REVERT: B 340 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8875 (mtpp) REVERT: B 343 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8491 (mp0) REVERT: B 403 MET cc_start: 0.9571 (ttm) cc_final: 0.9213 (mtp) REVERT: B 941 MET cc_start: 0.7012 (tpt) cc_final: 0.6128 (mmp) REVERT: B 1100 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8583 (mtt) REVERT: B 1152 MET cc_start: 0.9073 (mmt) cc_final: 0.8599 (mmt) REVERT: B 1170 MET cc_start: 0.9218 (tpp) cc_final: 0.8936 (tpp) REVERT: B 1186 ASP cc_start: 0.9501 (m-30) cc_final: 0.8873 (p0) REVERT: B 1494 MET cc_start: 0.7709 (mtp) cc_final: 0.7493 (ttm) REVERT: B 1601 MET cc_start: 0.8983 (mmm) cc_final: 0.8761 (mmm) REVERT: B 1731 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9308 (mm) REVERT: B 2008 MET cc_start: 0.9449 (ptp) cc_final: 0.8792 (tmm) REVERT: B 2170 MET cc_start: 0.8474 (tpt) cc_final: 0.8208 (tpt) REVERT: B 2198 MET cc_start: 0.9509 (mmp) cc_final: 0.9214 (mpp) REVERT: B 2203 MET cc_start: 0.9066 (pmm) cc_final: 0.8820 (pmm) REVERT: B 2312 MET cc_start: 0.9225 (tmm) cc_final: 0.8898 (tmm) REVERT: B 2932 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5641 (pmm) REVERT: B 3106 MET cc_start: 0.9572 (mmt) cc_final: 0.9042 (mmt) REVERT: B 3517 MET cc_start: 0.9437 (mmm) cc_final: 0.9053 (mmm) REVERT: B 3638 MET cc_start: 0.6497 (ptt) cc_final: 0.5657 (ppp) REVERT: B 3673 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9213 (tpp) REVERT: B 3778 MET cc_start: 0.9750 (ttp) cc_final: 0.9329 (tmm) REVERT: B 3955 MET cc_start: 0.9550 (mmp) cc_final: 0.9145 (mtm) REVERT: B 4047 MET cc_start: 0.9451 (tmm) cc_final: 0.9163 (tmm) REVERT: B 4184 MET cc_start: 0.9012 (tpt) cc_final: 0.8735 (tpp) REVERT: B 4207 MET cc_start: 0.9250 (mmp) cc_final: 0.9049 (mmp) REVERT: B 4246 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9014 (mp10) REVERT: B 4580 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: B 4730 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.8882 (p0) REVERT: B 4796 MET cc_start: 0.9465 (tpt) cc_final: 0.8948 (tpt) REVERT: B 4874 MET cc_start: 0.9326 (mmm) cc_final: 0.9071 (mmm) REVERT: B 4880 MET cc_start: 0.9050 (mmm) cc_final: 0.8367 (mmm) REVERT: B 4954 MET cc_start: 0.9111 (tpp) cc_final: 0.8584 (mmm) REVERT: B 4989 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8994 (tmm) REVERT: C 211 GLU cc_start: 0.8999 (tp30) cc_final: 0.8735 (tm-30) REVERT: C 340 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8876 (mtpp) REVERT: C 343 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8492 (mp0) REVERT: C 403 MET cc_start: 0.9572 (ttm) cc_final: 0.9212 (mtp) REVERT: C 1100 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: C 1152 MET cc_start: 0.9076 (mmt) cc_final: 0.8603 (mmt) REVERT: C 1170 MET cc_start: 0.9223 (tpp) cc_final: 0.8942 (tpp) REVERT: C 1186 ASP cc_start: 0.9501 (m-30) cc_final: 0.8873 (p0) REVERT: C 1494 MET cc_start: 0.7704 (mtp) cc_final: 0.7491 (ttm) REVERT: C 1731 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9310 (mm) REVERT: C 2008 MET cc_start: 0.9448 (ptp) cc_final: 0.8793 (tmm) REVERT: C 2170 MET cc_start: 0.8463 (tpt) cc_final: 0.8188 (tpt) REVERT: C 2198 MET cc_start: 0.9509 (mmp) cc_final: 0.9216 (mpp) REVERT: C 2203 MET cc_start: 0.9068 (pmm) cc_final: 0.8821 (pmm) REVERT: C 2312 MET cc_start: 0.9224 (tmm) cc_final: 0.8898 (tmm) REVERT: C 2932 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5644 (pmm) REVERT: C 3106 MET cc_start: 0.9572 (mmt) cc_final: 0.9039 (mmt) REVERT: C 3517 MET cc_start: 0.9438 (mmm) cc_final: 0.9055 (mmm) REVERT: C 3638 MET cc_start: 0.6492 (ptt) cc_final: 0.5652 (ppp) REVERT: C 3673 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9212 (tpp) REVERT: C 3778 MET cc_start: 0.9750 (ttp) cc_final: 0.9329 (tmm) REVERT: C 3955 MET cc_start: 0.9550 (mmp) cc_final: 0.9144 (mtm) REVERT: C 4047 MET cc_start: 0.9451 (tmm) cc_final: 0.9162 (tmm) REVERT: C 4184 MET cc_start: 0.9019 (tpt) cc_final: 0.8737 (tpp) REVERT: C 4207 MET cc_start: 0.9250 (mmp) cc_final: 0.9049 (mmp) REVERT: C 4246 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9015 (mp10) REVERT: C 4580 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: C 4730 ASP cc_start: 0.9462 (OUTLIER) cc_final: 0.8889 (p0) REVERT: C 4796 MET cc_start: 0.9465 (tpt) cc_final: 0.8951 (tpt) REVERT: C 4880 MET cc_start: 0.9046 (mmm) cc_final: 0.8368 (mmm) REVERT: C 4954 MET cc_start: 0.9106 (tpp) cc_final: 0.8601 (mmm) REVERT: C 4989 MET cc_start: 0.9305 (tmm) cc_final: 0.8999 (tmm) REVERT: D 211 GLU cc_start: 0.9000 (tp30) cc_final: 0.8736 (tm-30) REVERT: D 340 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8876 (mtpp) REVERT: D 343 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8492 (mp0) REVERT: D 403 MET cc_start: 0.9573 (ttm) cc_final: 0.9214 (mtp) REVERT: D 1100 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8578 (mtt) REVERT: D 1152 MET cc_start: 0.9074 (mmt) cc_final: 0.8601 (mmt) REVERT: D 1170 MET cc_start: 0.9223 (tpp) cc_final: 0.8942 (tpp) REVERT: D 1186 ASP cc_start: 0.9501 (m-30) cc_final: 0.8873 (p0) REVERT: D 1494 MET cc_start: 0.7703 (mtp) cc_final: 0.7493 (ttm) REVERT: D 1731 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9309 (mm) REVERT: D 2008 MET cc_start: 0.9449 (ptp) cc_final: 0.8792 (tmm) REVERT: D 2170 MET cc_start: 0.8473 (tpt) cc_final: 0.8207 (tpt) REVERT: D 2198 MET cc_start: 0.9510 (mmp) cc_final: 0.9215 (mpp) REVERT: D 2203 MET cc_start: 0.9067 (pmm) cc_final: 0.8821 (pmm) REVERT: D 2312 MET cc_start: 0.9224 (tmm) cc_final: 0.8899 (tmm) REVERT: D 2932 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5638 (pmm) REVERT: D 3106 MET cc_start: 0.9571 (mmt) cc_final: 0.9039 (mmt) REVERT: D 3517 MET cc_start: 0.9438 (mmm) cc_final: 0.9052 (mmm) REVERT: D 3638 MET cc_start: 0.6491 (ptt) cc_final: 0.5651 (ppp) REVERT: D 3673 MET cc_start: 0.9602 (OUTLIER) cc_final: 0.9214 (tpp) REVERT: D 3778 MET cc_start: 0.9750 (ttp) cc_final: 0.9329 (tmm) REVERT: D 3955 MET cc_start: 0.9549 (mmp) cc_final: 0.9144 (mtm) REVERT: D 4047 MET cc_start: 0.9453 (tmm) cc_final: 0.9165 (tmm) REVERT: D 4165 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9186 (pt0) REVERT: D 4168 GLU cc_start: 0.9519 (pm20) cc_final: 0.9199 (pm20) REVERT: D 4184 MET cc_start: 0.9007 (tpt) cc_final: 0.8732 (tpp) REVERT: D 4207 MET cc_start: 0.9251 (mmp) cc_final: 0.9050 (mmp) REVERT: D 4246 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9014 (mp10) REVERT: D 4580 TYR cc_start: 0.9369 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: D 4730 ASP cc_start: 0.9462 (OUTLIER) cc_final: 0.8889 (p0) REVERT: D 4796 MET cc_start: 0.9465 (tpt) cc_final: 0.8947 (tpt) REVERT: D 4880 MET cc_start: 0.9047 (mmm) cc_final: 0.8370 (mmm) REVERT: D 4954 MET cc_start: 0.9109 (tpp) cc_final: 0.8600 (mmm) REVERT: D 4989 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8975 (tmm) REVERT: E 29 MET cc_start: 0.8784 (mtp) cc_final: 0.8118 (ttm) REVERT: F 29 MET cc_start: 0.8782 (mtp) cc_final: 0.8086 (ttm) REVERT: G 29 MET cc_start: 0.8783 (mtp) cc_final: 0.8088 (ttm) REVERT: H 29 MET cc_start: 0.8784 (mtp) cc_final: 0.8089 (ttm) outliers start: 146 outliers final: 103 residues processed: 814 average time/residue: 1.1838 time to fit residues: 1726.1394 Evaluate side-chains 841 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 709 time to evaluate : 11.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2886 TRP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR 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 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4866 SER Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3673 MET Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4214 LYS Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain B residue 5020 ASP Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2259 GLU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3673 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR 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 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4866 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain C residue 5020 ASP Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4866 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain D residue 5001 THR Chi-restraints excluded: chain D residue 5020 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 10.0000 chunk 688 optimal weight: 50.0000 chunk 1029 optimal weight: 4.9990 chunk 519 optimal weight: 20.0000 chunk 338 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 1095 optimal weight: 7.9990 chunk 1174 optimal weight: 3.9990 chunk 852 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 1354 optimal weight: 0.0050 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4094 GLN A4120 ASN ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1614 GLN ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4833 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 146204 Z= 0.177 Angle : 0.565 10.554 198040 Z= 0.282 Chirality : 0.039 0.176 21784 Planarity : 0.004 0.063 25752 Dihedral : 5.180 71.704 19706 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.94 % Allowed : 10.83 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.07), residues: 17832 helix: 1.92 (0.06), residues: 8812 sheet: -0.50 (0.13), residues: 1828 loop : -0.34 (0.08), residues: 7192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP A2886 HIS 0.008 0.001 HIS D3771 PHE 0.024 0.001 PHE B2973 TYR 0.028 0.001 TYR A4080 ARG 0.004 0.000 ARG D4563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 712 time to evaluate : 12.018 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: A 213 TYR cc_start: 0.8265 (m-80) cc_final: 0.7412 (t80) REVERT: A 403 MET cc_start: 0.9529 (ttm) cc_final: 0.9272 (mtp) REVERT: A 483 MET cc_start: 0.9284 (mmm) cc_final: 0.9044 (mmt) REVERT: A 667 MET cc_start: 0.9035 (tpp) cc_final: 0.8534 (tpp) REVERT: A 941 MET cc_start: 0.6805 (tpt) cc_final: 0.6109 (mmp) REVERT: A 1152 MET cc_start: 0.9027 (mmt) cc_final: 0.8587 (mmt) REVERT: A 1186 ASP cc_start: 0.9420 (m-30) cc_final: 0.8814 (p0) REVERT: A 1636 MET cc_start: 0.8943 (ppp) cc_final: 0.8724 (ppp) REVERT: A 1731 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9311 (mm) REVERT: A 1851 MET cc_start: 0.9500 (mtp) cc_final: 0.9292 (mtm) REVERT: A 2008 MET cc_start: 0.9301 (ptp) cc_final: 0.8724 (tmm) REVERT: A 2178 MET cc_start: 0.8962 (ttp) cc_final: 0.8265 (tmm) REVERT: A 2198 MET cc_start: 0.9455 (mmp) cc_final: 0.9248 (mpp) REVERT: A 2203 MET cc_start: 0.9061 (pmm) cc_final: 0.8825 (pmm) REVERT: A 2312 MET cc_start: 0.9191 (tmm) cc_final: 0.8839 (tmm) REVERT: A 2618 MET cc_start: 0.8639 (mpp) cc_final: 0.8419 (mpp) REVERT: A 2932 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5249 (pmm) REVERT: A 3106 MET cc_start: 0.9304 (mmt) cc_final: 0.8938 (mmt) REVERT: A 3467 MET cc_start: 0.8861 (mmm) cc_final: 0.8286 (ppp) REVERT: A 3517 MET cc_start: 0.9430 (mmm) cc_final: 0.9045 (mmm) REVERT: A 3638 MET cc_start: 0.6805 (ptt) cc_final: 0.5807 (ppp) REVERT: A 3673 MET cc_start: 0.9653 (mmm) cc_final: 0.9063 (tpp) REVERT: A 3778 MET cc_start: 0.9751 (ttp) cc_final: 0.9261 (tmm) REVERT: A 3955 MET cc_start: 0.9539 (mmp) cc_final: 0.9122 (mtm) REVERT: A 4047 MET cc_start: 0.9466 (tmm) cc_final: 0.9137 (tmm) REVERT: A 4056 GLU cc_start: 0.9594 (tt0) cc_final: 0.9324 (tp30) REVERT: A 4165 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9167 (pt0) REVERT: A 4168 GLU cc_start: 0.9501 (pm20) cc_final: 0.9152 (pm20) REVERT: A 4184 MET cc_start: 0.9015 (tpt) cc_final: 0.8740 (tpp) REVERT: A 4246 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8941 (mp10) REVERT: A 4580 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: A 4627 MET cc_start: 0.7462 (tmm) cc_final: 0.6918 (tmm) REVERT: A 4730 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 4796 MET cc_start: 0.9405 (tpt) cc_final: 0.9108 (tpt) REVERT: A 4874 MET cc_start: 0.9221 (mmm) cc_final: 0.9001 (mmm) REVERT: A 4879 MET cc_start: 0.9129 (tpt) cc_final: 0.8876 (tpp) REVERT: A 4887 MET cc_start: 0.8835 (mmm) cc_final: 0.8421 (tpp) REVERT: A 4954 MET cc_start: 0.9051 (tpp) cc_final: 0.8617 (mmm) REVERT: A 4989 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8969 (tmm) REVERT: A 5013 MET cc_start: 0.9454 (mtt) cc_final: 0.9186 (mtm) REVERT: B 211 GLU cc_start: 0.9000 (tp30) cc_final: 0.8739 (tm-30) REVERT: B 340 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8891 (mtpp) REVERT: B 343 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8409 (mp0) REVERT: B 403 MET cc_start: 0.9522 (ttm) cc_final: 0.9168 (mtp) REVERT: B 453 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8697 (mm-30) REVERT: B 667 MET cc_start: 0.8968 (tpp) cc_final: 0.8556 (tpp) REVERT: B 941 MET cc_start: 0.7005 (tpt) cc_final: 0.6228 (mmp) REVERT: B 1100 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8641 (mtt) REVERT: B 1152 MET cc_start: 0.9046 (mmt) cc_final: 0.8589 (mmt) REVERT: B 1170 MET cc_start: 0.9242 (tpp) cc_final: 0.8995 (tpp) REVERT: B 1186 ASP cc_start: 0.9411 (m-30) cc_final: 0.8788 (p0) REVERT: B 1494 MET cc_start: 0.7459 (mtp) cc_final: 0.7143 (ttm) REVERT: B 1601 MET cc_start: 0.8963 (mmm) cc_final: 0.8613 (mmm) REVERT: B 1731 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9273 (mm) REVERT: B 1851 MET cc_start: 0.9525 (mtp) cc_final: 0.9307 (mtm) REVERT: B 2008 MET cc_start: 0.9433 (ptp) cc_final: 0.8763 (tmm) REVERT: B 2170 MET cc_start: 0.8464 (tpt) cc_final: 0.8063 (tpt) REVERT: B 2203 MET cc_start: 0.9108 (pmm) cc_final: 0.8829 (pmm) REVERT: B 2312 MET cc_start: 0.9134 (tmm) cc_final: 0.8808 (tmm) REVERT: B 2932 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5595 (pmm) REVERT: B 3106 MET cc_start: 0.9575 (mmt) cc_final: 0.9001 (mmt) REVERT: B 3517 MET cc_start: 0.9432 (mmm) cc_final: 0.9056 (mmm) REVERT: B 3638 MET cc_start: 0.6765 (ptt) cc_final: 0.6352 (ppp) REVERT: B 3778 MET cc_start: 0.9735 (ttp) cc_final: 0.9243 (tmm) REVERT: B 3955 MET cc_start: 0.9541 (mmp) cc_final: 0.9120 (mtm) REVERT: B 4047 MET cc_start: 0.9462 (tmm) cc_final: 0.9130 (tmm) REVERT: B 4184 MET cc_start: 0.9013 (tpt) cc_final: 0.8732 (tpp) REVERT: B 4207 MET cc_start: 0.9233 (mmp) cc_final: 0.8984 (mmp) REVERT: B 4246 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8997 (mp10) REVERT: B 4580 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: B 4730 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.8896 (p0) REVERT: B 4796 MET cc_start: 0.9427 (tpt) cc_final: 0.8968 (tpt) REVERT: B 4839 MET cc_start: 0.8897 (mmt) cc_final: 0.8677 (mmm) REVERT: B 4874 MET cc_start: 0.9302 (mmm) cc_final: 0.9055 (mmm) REVERT: B 4989 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9008 (tmm) REVERT: B 5013 MET cc_start: 0.9413 (mtt) cc_final: 0.8980 (mtm) REVERT: C 211 GLU cc_start: 0.9001 (tp30) cc_final: 0.8739 (tm-30) REVERT: C 340 LYS cc_start: 0.9200 (mtpt) cc_final: 0.8933 (mtpp) REVERT: C 343 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8410 (mp0) REVERT: C 403 MET cc_start: 0.9526 (ttm) cc_final: 0.9167 (mtp) REVERT: C 453 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8695 (mm-30) REVERT: C 667 MET cc_start: 0.8974 (tpp) cc_final: 0.8542 (tpp) REVERT: C 941 MET cc_start: 0.7013 (tpt) cc_final: 0.6243 (mmp) REVERT: C 1100 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8639 (mtt) REVERT: C 1152 MET cc_start: 0.9050 (mmt) cc_final: 0.8591 (mmt) REVERT: C 1170 MET cc_start: 0.9248 (tpp) cc_final: 0.9000 (tpp) REVERT: C 1186 ASP cc_start: 0.9411 (m-30) cc_final: 0.8788 (p0) REVERT: C 1494 MET cc_start: 0.7461 (mtp) cc_final: 0.7147 (ttm) REVERT: C 1601 MET cc_start: 0.8980 (mmm) cc_final: 0.8674 (mmm) REVERT: C 1731 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9274 (mm) REVERT: C 1851 MET cc_start: 0.9525 (mtp) cc_final: 0.9305 (mtm) REVERT: C 2008 MET cc_start: 0.9432 (ptp) cc_final: 0.8764 (tmm) REVERT: C 2170 MET cc_start: 0.8463 (tpt) cc_final: 0.8067 (tpt) REVERT: C 2203 MET cc_start: 0.9109 (pmm) cc_final: 0.8829 (pmm) REVERT: C 2312 MET cc_start: 0.9134 (tmm) cc_final: 0.8808 (tmm) REVERT: C 2932 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5596 (pmm) REVERT: C 3106 MET cc_start: 0.9576 (mmt) cc_final: 0.8998 (mmt) REVERT: C 3517 MET cc_start: 0.9433 (mmm) cc_final: 0.9056 (mmm) REVERT: C 3638 MET cc_start: 0.6752 (ptt) cc_final: 0.6348 (ppp) REVERT: C 3778 MET cc_start: 0.9735 (ttp) cc_final: 0.9242 (tmm) REVERT: C 3955 MET cc_start: 0.9540 (mmp) cc_final: 0.9119 (mtm) REVERT: C 4047 MET cc_start: 0.9462 (tmm) cc_final: 0.9129 (tmm) REVERT: C 4184 MET cc_start: 0.9009 (tpt) cc_final: 0.8730 (tpp) REVERT: C 4207 MET cc_start: 0.9233 (mmp) cc_final: 0.8983 (mmp) REVERT: C 4246 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8998 (mp10) REVERT: C 4580 TYR cc_start: 0.9345 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: C 4730 ASP cc_start: 0.9453 (OUTLIER) cc_final: 0.8929 (p0) REVERT: C 4796 MET cc_start: 0.9430 (tpt) cc_final: 0.8972 (tpt) REVERT: C 4989 MET cc_start: 0.9300 (tmm) cc_final: 0.9005 (tmm) REVERT: C 5013 MET cc_start: 0.9387 (mtt) cc_final: 0.9097 (mtm) REVERT: D 211 GLU cc_start: 0.9000 (tp30) cc_final: 0.8739 (tm-30) REVERT: D 340 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8886 (mtpp) REVERT: D 343 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8410 (mp0) REVERT: D 403 MET cc_start: 0.9526 (ttm) cc_final: 0.9168 (mtp) REVERT: D 453 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8695 (mm-30) REVERT: D 667 MET cc_start: 0.8971 (tpp) cc_final: 0.8540 (tpp) REVERT: D 941 MET cc_start: 0.7017 (tpt) cc_final: 0.6245 (mmp) REVERT: D 1100 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8636 (mtt) REVERT: D 1152 MET cc_start: 0.9050 (mmt) cc_final: 0.8591 (mmt) REVERT: D 1170 MET cc_start: 0.9247 (tpp) cc_final: 0.8999 (tpp) REVERT: D 1186 ASP cc_start: 0.9410 (m-30) cc_final: 0.8788 (p0) REVERT: D 1494 MET cc_start: 0.7456 (mtp) cc_final: 0.7141 (ttm) REVERT: D 1601 MET cc_start: 0.8979 (mmm) cc_final: 0.8673 (mmm) REVERT: D 1731 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9272 (mm) REVERT: D 1851 MET cc_start: 0.9523 (mtp) cc_final: 0.9303 (mtm) REVERT: D 2008 MET cc_start: 0.9434 (ptp) cc_final: 0.8762 (tmm) REVERT: D 2170 MET cc_start: 0.8463 (tpt) cc_final: 0.8063 (tpt) REVERT: D 2203 MET cc_start: 0.9107 (pmm) cc_final: 0.8829 (pmm) REVERT: D 2312 MET cc_start: 0.9134 (tmm) cc_final: 0.8808 (tmm) REVERT: D 2932 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5589 (pmm) REVERT: D 3106 MET cc_start: 0.9575 (mmt) cc_final: 0.8998 (mmt) REVERT: D 3517 MET cc_start: 0.9433 (mmm) cc_final: 0.9054 (mmm) REVERT: D 3638 MET cc_start: 0.6763 (ptt) cc_final: 0.6349 (ppp) REVERT: D 3778 MET cc_start: 0.9735 (ttp) cc_final: 0.9243 (tmm) REVERT: D 3955 MET cc_start: 0.9540 (mmp) cc_final: 0.9119 (mtm) REVERT: D 4047 MET cc_start: 0.9460 (tmm) cc_final: 0.9204 (tmm) REVERT: D 4165 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9189 (pt0) REVERT: D 4168 GLU cc_start: 0.9504 (pm20) cc_final: 0.9191 (pm20) REVERT: D 4184 MET cc_start: 0.9007 (tpt) cc_final: 0.8727 (tpp) REVERT: D 4207 MET cc_start: 0.9233 (mmp) cc_final: 0.8983 (mmp) REVERT: D 4246 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8997 (mp10) REVERT: D 4580 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: D 4730 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.8900 (p0) REVERT: D 4796 MET cc_start: 0.9428 (tpt) cc_final: 0.8969 (tpt) REVERT: D 4989 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8971 (tmm) REVERT: D 5013 MET cc_start: 0.9415 (mtt) cc_final: 0.8982 (mtm) REVERT: E 29 MET cc_start: 0.8764 (mtp) cc_final: 0.8138 (ttm) REVERT: F 29 MET cc_start: 0.8764 (mtp) cc_final: 0.8134 (ttm) REVERT: G 29 MET cc_start: 0.8764 (mtp) cc_final: 0.8134 (ttm) REVERT: H 29 MET cc_start: 0.8763 (mtp) cc_final: 0.8134 (ttm) outliers start: 126 outliers final: 81 residues processed: 803 average time/residue: 1.2916 time to fit residues: 1874.6788 Evaluate side-chains 812 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 705 time to evaluate : 11.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4997 ASN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2886 TRP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4997 ASN Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2886 TRP Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4214 LYS Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER 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 4730 ASP Chi-restraints excluded: chain C residue 4866 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4997 ASN Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2886 TRP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4866 SER Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4997 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 9.9990 chunk 1651 optimal weight: 3.9990 chunk 1506 optimal weight: 9.9990 chunk 1605 optimal weight: 7.9990 chunk 1650 optimal weight: 5.9990 chunk 966 optimal weight: 0.5980 chunk 699 optimal weight: 6.9990 chunk 1261 optimal weight: 0.9980 chunk 492 optimal weight: 0.7980 chunk 1451 optimal weight: 6.9990 chunk 1518 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2176 ASN ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4120 ASN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4120 ASN ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4120 ASN ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 146204 Z= 0.180 Angle : 0.561 10.959 198040 Z= 0.279 Chirality : 0.039 0.213 21784 Planarity : 0.004 0.062 25752 Dihedral : 5.101 71.867 19696 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.79 % Allowed : 10.96 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.07), residues: 17832 helix: 1.98 (0.06), residues: 8776 sheet: -0.49 (0.13), residues: 1828 loop : -0.31 (0.08), residues: 7228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A2886 HIS 0.008 0.001 HIS D3771 PHE 0.024 0.001 PHE A2973 TYR 0.029 0.001 TYR A4080 ARG 0.003 0.000 ARG D4563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 708 time to evaluate : 12.647 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: A 213 TYR cc_start: 0.8271 (m-80) cc_final: 0.7397 (t80) REVERT: A 343 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8481 (mp0) REVERT: A 403 MET cc_start: 0.9540 (ttm) cc_final: 0.9296 (mtp) REVERT: A 483 MET cc_start: 0.9265 (mmm) cc_final: 0.9020 (mmt) REVERT: A 667 MET cc_start: 0.9110 (tpp) cc_final: 0.8652 (tpp) REVERT: A 941 MET cc_start: 0.6905 (tpt) cc_final: 0.6348 (mmp) REVERT: A 1152 MET cc_start: 0.9035 (mmt) cc_final: 0.8622 (mmt) REVERT: A 1186 ASP cc_start: 0.9424 (m-30) cc_final: 0.8805 (p0) REVERT: A 1636 MET cc_start: 0.8959 (ppp) cc_final: 0.8726 (ppp) REVERT: A 1731 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9297 (mm) REVERT: A 1851 MET cc_start: 0.9498 (mtp) cc_final: 0.9291 (mtm) REVERT: A 2008 MET cc_start: 0.9301 (ptp) cc_final: 0.8722 (tmm) REVERT: A 2170 MET cc_start: 0.8818 (tpt) cc_final: 0.8546 (tpt) REVERT: A 2198 MET cc_start: 0.9479 (mmp) cc_final: 0.9265 (mpp) REVERT: A 2203 MET cc_start: 0.9034 (pmm) cc_final: 0.8796 (pmm) REVERT: A 2312 MET cc_start: 0.9185 (tmm) cc_final: 0.8832 (tmm) REVERT: A 2618 MET cc_start: 0.8637 (mpp) cc_final: 0.8422 (mpp) REVERT: A 2932 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5259 (pmm) REVERT: A 3106 MET cc_start: 0.9312 (mmt) cc_final: 0.8936 (mmt) REVERT: A 3467 MET cc_start: 0.8860 (mmm) cc_final: 0.8286 (ppp) REVERT: A 3517 MET cc_start: 0.9427 (mmm) cc_final: 0.9047 (mmm) REVERT: A 3638 MET cc_start: 0.6850 (ptt) cc_final: 0.6319 (ppp) REVERT: A 3673 MET cc_start: 0.9659 (mmm) cc_final: 0.9105 (tpp) REVERT: A 3778 MET cc_start: 0.9757 (ttp) cc_final: 0.9491 (tmm) REVERT: A 3955 MET cc_start: 0.9539 (mmp) cc_final: 0.9123 (mtm) REVERT: A 4047 MET cc_start: 0.9464 (tmm) cc_final: 0.9138 (tmm) REVERT: A 4056 GLU cc_start: 0.9587 (tt0) cc_final: 0.9320 (tp30) REVERT: A 4165 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9192 (pt0) REVERT: A 4184 MET cc_start: 0.8999 (tpt) cc_final: 0.8746 (tpp) REVERT: A 4246 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8958 (mp10) REVERT: A 4580 TYR cc_start: 0.9259 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: A 4627 MET cc_start: 0.7553 (tmm) cc_final: 0.7107 (tmm) REVERT: A 4730 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 4796 MET cc_start: 0.9403 (tpt) cc_final: 0.9107 (tpt) REVERT: A 4874 MET cc_start: 0.9192 (mmm) cc_final: 0.8975 (mmm) REVERT: A 4879 MET cc_start: 0.9130 (tpt) cc_final: 0.8877 (tpp) REVERT: A 4887 MET cc_start: 0.8836 (mmm) cc_final: 0.8412 (tpp) REVERT: A 4954 MET cc_start: 0.9032 (tpp) cc_final: 0.8533 (mmm) REVERT: A 4989 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8957 (tmm) REVERT: A 5013 MET cc_start: 0.9453 (mtt) cc_final: 0.9186 (mtm) REVERT: B 211 GLU cc_start: 0.9010 (tp30) cc_final: 0.8743 (tm-30) REVERT: B 340 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8905 (mtpp) REVERT: B 343 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8424 (mp0) REVERT: B 403 MET cc_start: 0.9489 (ttm) cc_final: 0.9012 (mtp) REVERT: B 667 MET cc_start: 0.9039 (tpp) cc_final: 0.8622 (tpp) REVERT: B 941 MET cc_start: 0.7115 (tpt) cc_final: 0.6524 (mmp) REVERT: B 1100 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8593 (mtt) REVERT: B 1152 MET cc_start: 0.9073 (mmt) cc_final: 0.8634 (mmt) REVERT: B 1170 MET cc_start: 0.9222 (tpp) cc_final: 0.8974 (tpp) REVERT: B 1186 ASP cc_start: 0.9430 (m-30) cc_final: 0.8809 (p0) REVERT: B 1494 MET cc_start: 0.7584 (mtp) cc_final: 0.7380 (ttm) REVERT: B 1601 MET cc_start: 0.8959 (mmm) cc_final: 0.8670 (mmm) REVERT: B 1731 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9293 (mm) REVERT: B 1851 MET cc_start: 0.9527 (mtp) cc_final: 0.9314 (mtm) REVERT: B 2008 MET cc_start: 0.9428 (ptp) cc_final: 0.8761 (tmm) REVERT: B 2198 MET cc_start: 0.9458 (mmp) cc_final: 0.9196 (mpp) REVERT: B 2203 MET cc_start: 0.9052 (pmm) cc_final: 0.8791 (pmm) REVERT: B 2312 MET cc_start: 0.9134 (tmm) cc_final: 0.8805 (tmm) REVERT: B 2514 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8913 (p0) REVERT: B 2932 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5604 (pmm) REVERT: B 3106 MET cc_start: 0.9566 (mmt) cc_final: 0.8971 (mmt) REVERT: B 3517 MET cc_start: 0.9433 (mmm) cc_final: 0.9089 (mmm) REVERT: B 3638 MET cc_start: 0.6715 (ptt) cc_final: 0.6252 (ppp) REVERT: B 3673 MET cc_start: 0.9646 (mmm) cc_final: 0.9115 (tpp) REVERT: B 3778 MET cc_start: 0.9735 (ttp) cc_final: 0.9466 (tmm) REVERT: B 3955 MET cc_start: 0.9543 (mmp) cc_final: 0.9122 (mtm) REVERT: B 4047 MET cc_start: 0.9485 (tmm) cc_final: 0.9142 (tmm) REVERT: B 4168 GLU cc_start: 0.9523 (pm20) cc_final: 0.9167 (pm20) REVERT: B 4184 MET cc_start: 0.8972 (tpt) cc_final: 0.8691 (tpp) REVERT: B 4207 MET cc_start: 0.9247 (mmp) cc_final: 0.8989 (mmp) REVERT: B 4246 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8937 (mp10) REVERT: B 4580 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: B 4730 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.8901 (p0) REVERT: B 4796 MET cc_start: 0.9426 (tpt) cc_final: 0.8969 (tpt) REVERT: B 4839 MET cc_start: 0.8903 (mmt) cc_final: 0.8679 (mmm) REVERT: B 4874 MET cc_start: 0.9293 (mmm) cc_final: 0.9046 (mmm) REVERT: B 4989 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8995 (tmm) REVERT: B 5013 MET cc_start: 0.9400 (mtt) cc_final: 0.8974 (mtm) REVERT: C 211 GLU cc_start: 0.9010 (tp30) cc_final: 0.8742 (tm-30) REVERT: C 340 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8905 (mtpp) REVERT: C 343 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8424 (mp0) REVERT: C 403 MET cc_start: 0.9491 (ttm) cc_final: 0.9014 (mtp) REVERT: C 667 MET cc_start: 0.9042 (tpp) cc_final: 0.8607 (tpp) REVERT: C 941 MET cc_start: 0.7084 (tpt) cc_final: 0.6453 (mmp) REVERT: C 1100 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8593 (mtt) REVERT: C 1152 MET cc_start: 0.9074 (mmt) cc_final: 0.8636 (mmt) REVERT: C 1170 MET cc_start: 0.9228 (tpp) cc_final: 0.8979 (tpp) REVERT: C 1186 ASP cc_start: 0.9431 (m-30) cc_final: 0.8810 (p0) REVERT: C 1494 MET cc_start: 0.7582 (mtp) cc_final: 0.7381 (ttm) REVERT: C 1599 MET cc_start: 0.8726 (ptm) cc_final: 0.8309 (ptp) REVERT: C 1731 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9294 (mm) REVERT: C 1851 MET cc_start: 0.9526 (mtp) cc_final: 0.9314 (mtm) REVERT: C 2008 MET cc_start: 0.9427 (ptp) cc_final: 0.8762 (tmm) REVERT: C 2198 MET cc_start: 0.9457 (mmp) cc_final: 0.9196 (mpp) REVERT: C 2203 MET cc_start: 0.9053 (pmm) cc_final: 0.8791 (pmm) REVERT: C 2312 MET cc_start: 0.9135 (tmm) cc_final: 0.8806 (tmm) REVERT: C 2514 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8914 (p0) REVERT: C 2932 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5605 (pmm) REVERT: C 3106 MET cc_start: 0.9567 (mmt) cc_final: 0.8970 (mmt) REVERT: C 3517 MET cc_start: 0.9434 (mmm) cc_final: 0.9091 (mmm) REVERT: C 3638 MET cc_start: 0.6713 (ptt) cc_final: 0.6238 (ppp) REVERT: C 3673 MET cc_start: 0.9646 (mmm) cc_final: 0.9114 (tpp) REVERT: C 3778 MET cc_start: 0.9734 (ttp) cc_final: 0.9466 (tmm) REVERT: C 3955 MET cc_start: 0.9542 (mmp) cc_final: 0.9121 (mtm) REVERT: C 4047 MET cc_start: 0.9486 (tmm) cc_final: 0.9207 (tmm) REVERT: C 4168 GLU cc_start: 0.9522 (pm20) cc_final: 0.9167 (pm20) REVERT: C 4184 MET cc_start: 0.8971 (tpt) cc_final: 0.8689 (tpp) REVERT: C 4207 MET cc_start: 0.9246 (mmp) cc_final: 0.8989 (mmp) REVERT: C 4246 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8936 (mp10) REVERT: C 4580 TYR cc_start: 0.9350 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: C 4730 ASP cc_start: 0.9431 (OUTLIER) cc_final: 0.8905 (p0) REVERT: C 4796 MET cc_start: 0.9427 (tpt) cc_final: 0.8972 (tpt) REVERT: C 4989 MET cc_start: 0.9308 (tmm) cc_final: 0.8990 (tmm) REVERT: C 5013 MET cc_start: 0.9369 (mtt) cc_final: 0.9087 (mtm) REVERT: D 211 GLU cc_start: 0.9010 (tp30) cc_final: 0.8743 (tm-30) REVERT: D 340 LYS cc_start: 0.9186 (mtpt) cc_final: 0.8905 (mtpp) REVERT: D 343 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8425 (mp0) REVERT: D 403 MET cc_start: 0.9492 (ttm) cc_final: 0.9014 (mtp) REVERT: D 667 MET cc_start: 0.9043 (tpp) cc_final: 0.8607 (tpp) REVERT: D 941 MET cc_start: 0.7127 (tpt) cc_final: 0.6542 (mmp) REVERT: D 1100 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8590 (mtt) REVERT: D 1152 MET cc_start: 0.9074 (mmt) cc_final: 0.8637 (mmt) REVERT: D 1170 MET cc_start: 0.9226 (tpp) cc_final: 0.8978 (tpp) REVERT: D 1186 ASP cc_start: 0.9429 (m-30) cc_final: 0.8808 (p0) REVERT: D 1494 MET cc_start: 0.7577 (mtp) cc_final: 0.7376 (ttm) REVERT: D 1599 MET cc_start: 0.8725 (ptm) cc_final: 0.8309 (ptp) REVERT: D 1731 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9293 (mm) REVERT: D 1851 MET cc_start: 0.9526 (mtp) cc_final: 0.9313 (mtm) REVERT: D 2008 MET cc_start: 0.9428 (ptp) cc_final: 0.8761 (tmm) REVERT: D 2198 MET cc_start: 0.9458 (mmp) cc_final: 0.9196 (mpp) REVERT: D 2203 MET cc_start: 0.9053 (pmm) cc_final: 0.8791 (pmm) REVERT: D 2312 MET cc_start: 0.9134 (tmm) cc_final: 0.8805 (tmm) REVERT: D 2514 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8914 (p0) REVERT: D 2932 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5600 (pmm) REVERT: D 3106 MET cc_start: 0.9567 (mmt) cc_final: 0.8968 (mmt) REVERT: D 3517 MET cc_start: 0.9434 (mmm) cc_final: 0.9089 (mmm) REVERT: D 3638 MET cc_start: 0.6713 (ptt) cc_final: 0.6249 (ppp) REVERT: D 3673 MET cc_start: 0.9646 (mmm) cc_final: 0.9114 (tpp) REVERT: D 3778 MET cc_start: 0.9734 (ttp) cc_final: 0.9467 (tmm) REVERT: D 3955 MET cc_start: 0.9542 (mmp) cc_final: 0.9120 (mtm) REVERT: D 4047 MET cc_start: 0.9482 (tmm) cc_final: 0.9138 (tmm) REVERT: D 4184 MET cc_start: 0.8994 (tpt) cc_final: 0.8734 (tpp) REVERT: D 4207 MET cc_start: 0.9247 (mmp) cc_final: 0.8990 (mmp) REVERT: D 4246 GLN cc_start: 0.9277 (OUTLIER) cc_final: 0.8936 (mp10) REVERT: D 4580 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: D 4730 ASP cc_start: 0.9432 (OUTLIER) cc_final: 0.8906 (p0) REVERT: D 4796 MET cc_start: 0.9426 (tpt) cc_final: 0.8969 (tpt) REVERT: D 4989 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.8966 (tmm) REVERT: D 5013 MET cc_start: 0.9402 (mtt) cc_final: 0.8977 (mtm) REVERT: E 29 MET cc_start: 0.8758 (mtp) cc_final: 0.8105 (ttm) REVERT: F 29 MET cc_start: 0.8759 (mtp) cc_final: 0.8078 (ttm) REVERT: G 29 MET cc_start: 0.8758 (mtp) cc_final: 0.8079 (ttm) REVERT: H 29 MET cc_start: 0.8759 (mtp) cc_final: 0.8079 (ttm) outliers start: 103 outliers final: 74 residues processed: 787 average time/residue: 1.2246 time to fit residues: 1728.8240 Evaluate side-chains 801 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 698 time to evaluate : 11.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4214 LYS Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4214 LYS Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR 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 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4866 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4866 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 30.0000 chunk 1054 optimal weight: 30.0000 chunk 1698 optimal weight: 7.9990 chunk 1036 optimal weight: 10.0000 chunk 805 optimal weight: 10.0000 chunk 1180 optimal weight: 3.9990 chunk 1781 optimal weight: 5.9990 chunk 1639 optimal weight: 10.0000 chunk 1418 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 1095 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1484 HIS ** A2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1484 HIS ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4857 ASN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1484 HIS ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4120 ASN ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4857 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4857 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 146204 Z= 0.404 Angle : 0.694 11.155 198040 Z= 0.347 Chirality : 0.041 0.286 21784 Planarity : 0.004 0.064 25752 Dihedral : 5.274 72.618 19688 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.82 % Allowed : 11.01 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.23 % 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: 0.90 (0.07), residues: 17832 helix: 1.72 (0.06), residues: 8840 sheet: -0.64 (0.12), residues: 1860 loop : -0.44 (0.08), residues: 7132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP D2886 HIS 0.007 0.001 HIS C4983 PHE 0.020 0.002 PHE D4163 TYR 0.026 0.002 TYR A4080 ARG 0.006 0.001 ARG D 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 706 time to evaluate : 12.130 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 343 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8570 (mp0) REVERT: A 403 MET cc_start: 0.9595 (ttm) cc_final: 0.9357 (mtp) REVERT: A 667 MET cc_start: 0.9057 (tpp) cc_final: 0.8633 (tpp) REVERT: A 941 MET cc_start: 0.6794 (tpt) cc_final: 0.6267 (mmp) REVERT: A 1152 MET cc_start: 0.9031 (mmt) cc_final: 0.8579 (mmt) REVERT: A 1170 MET cc_start: 0.8988 (tpp) cc_final: 0.8721 (tpp) REVERT: A 1186 ASP cc_start: 0.9464 (m-30) cc_final: 0.8866 (p0) REVERT: A 1636 MET cc_start: 0.8923 (ppp) cc_final: 0.8618 (ppp) REVERT: A 1731 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9275 (mm) REVERT: A 2008 MET cc_start: 0.9360 (ptp) cc_final: 0.8761 (tmm) REVERT: A 2170 MET cc_start: 0.8667 (tpt) cc_final: 0.8381 (tpt) REVERT: A 2198 MET cc_start: 0.9501 (mmp) cc_final: 0.9284 (mpp) REVERT: A 2203 MET cc_start: 0.9004 (pmm) cc_final: 0.8791 (pmm) REVERT: A 2312 MET cc_start: 0.9176 (tmm) cc_final: 0.8821 (tmm) REVERT: A 2932 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5222 (pmm) REVERT: A 3467 MET cc_start: 0.8932 (mmm) cc_final: 0.8391 (ppp) REVERT: A 3517 MET cc_start: 0.9462 (mmm) cc_final: 0.9088 (mmm) REVERT: A 3638 MET cc_start: 0.6633 (ptt) cc_final: 0.6035 (ppp) REVERT: A 3673 MET cc_start: 0.9627 (mmm) cc_final: 0.9094 (tpp) REVERT: A 3778 MET cc_start: 0.9748 (ttp) cc_final: 0.9337 (tmm) REVERT: A 3955 MET cc_start: 0.9546 (mmp) cc_final: 0.9124 (mtm) REVERT: A 4047 MET cc_start: 0.9432 (tmm) cc_final: 0.9158 (tmm) REVERT: A 4056 GLU cc_start: 0.9597 (tt0) cc_final: 0.9352 (tp30) REVERT: A 4165 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9179 (mp0) REVERT: A 4184 MET cc_start: 0.8996 (tpt) cc_final: 0.8785 (tpp) REVERT: A 4580 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.8585 (m-10) REVERT: A 4627 MET cc_start: 0.7742 (tmm) cc_final: 0.7309 (tmm) REVERT: A 4730 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.8893 (p0) REVERT: A 4796 MET cc_start: 0.9429 (tpt) cc_final: 0.8993 (tpt) REVERT: A 4874 MET cc_start: 0.9130 (mmm) cc_final: 0.8909 (mmm) REVERT: A 4879 MET cc_start: 0.9158 (tpt) cc_final: 0.8868 (tpp) REVERT: A 4954 MET cc_start: 0.9058 (tpp) cc_final: 0.8549 (mmm) REVERT: A 4955 GLU cc_start: 0.8031 (mp0) cc_final: 0.7829 (mp0) REVERT: A 4989 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.9014 (tmm) REVERT: A 5013 MET cc_start: 0.9463 (mtt) cc_final: 0.9202 (mtm) REVERT: B 211 GLU cc_start: 0.8990 (tp30) cc_final: 0.8788 (tm-30) REVERT: B 340 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8890 (mtpp) REVERT: B 343 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8526 (mp0) REVERT: B 403 MET cc_start: 0.9587 (ttm) cc_final: 0.9093 (mtp) REVERT: B 667 MET cc_start: 0.9090 (tpp) cc_final: 0.8665 (tpp) REVERT: B 941 MET cc_start: 0.7185 (tpt) cc_final: 0.6781 (mmm) REVERT: B 1100 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8626 (mtt) REVERT: B 1152 MET cc_start: 0.9042 (mmt) cc_final: 0.8550 (mmt) REVERT: B 1170 MET cc_start: 0.9249 (tpp) cc_final: 0.9009 (tpp) REVERT: B 1186 ASP cc_start: 0.9468 (m-30) cc_final: 0.8862 (p0) REVERT: B 1494 MET cc_start: 0.7860 (mtp) cc_final: 0.7513 (ttm) REVERT: B 1599 MET cc_start: 0.8799 (ptm) cc_final: 0.8500 (ptp) REVERT: B 1731 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9277 (mm) REVERT: B 1851 MET cc_start: 0.9550 (mtp) cc_final: 0.9344 (mtm) REVERT: B 2008 MET cc_start: 0.9465 (ptp) cc_final: 0.8745 (tmm) REVERT: B 2198 MET cc_start: 0.9484 (mmp) cc_final: 0.9275 (mpp) REVERT: B 2203 MET cc_start: 0.9043 (pmm) cc_final: 0.8774 (pmm) REVERT: B 2312 MET cc_start: 0.9174 (tmm) cc_final: 0.8845 (tmm) REVERT: B 2932 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5284 (pmm) REVERT: B 3517 MET cc_start: 0.9461 (mmm) cc_final: 0.9118 (mmm) REVERT: B 3673 MET cc_start: 0.9620 (mmm) cc_final: 0.9101 (tpp) REVERT: B 3955 MET cc_start: 0.9549 (mmp) cc_final: 0.9122 (mtm) REVERT: B 4047 MET cc_start: 0.9429 (tmm) cc_final: 0.9151 (tmm) REVERT: B 4168 GLU cc_start: 0.9551 (pm20) cc_final: 0.9340 (pm20) REVERT: B 4184 MET cc_start: 0.9003 (tpt) cc_final: 0.8798 (tpp) REVERT: B 4207 MET cc_start: 0.9245 (mmp) cc_final: 0.9021 (mmp) REVERT: B 4580 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.8559 (m-10) REVERT: B 4730 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.8859 (p0) REVERT: B 4796 MET cc_start: 0.9453 (tpt) cc_final: 0.9003 (tpt) REVERT: B 4839 MET cc_start: 0.9043 (mmt) cc_final: 0.8837 (mmm) REVERT: B 4874 MET cc_start: 0.9245 (mmm) cc_final: 0.9016 (mmm) REVERT: B 4989 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9027 (tmm) REVERT: B 5013 MET cc_start: 0.9414 (mtt) cc_final: 0.9030 (mtm) REVERT: C 211 GLU cc_start: 0.8991 (tp30) cc_final: 0.8789 (tm-30) REVERT: C 340 LYS cc_start: 0.9233 (mtpt) cc_final: 0.8890 (mtpp) REVERT: C 343 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8526 (mp0) REVERT: C 403 MET cc_start: 0.9589 (ttm) cc_final: 0.9093 (mtp) REVERT: C 667 MET cc_start: 0.9092 (tpp) cc_final: 0.8650 (tpp) REVERT: C 1100 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: C 1152 MET cc_start: 0.9040 (mmt) cc_final: 0.8552 (mmt) REVERT: C 1170 MET cc_start: 0.9253 (tpp) cc_final: 0.9013 (tpp) REVERT: C 1186 ASP cc_start: 0.9468 (m-30) cc_final: 0.8862 (p0) REVERT: C 1494 MET cc_start: 0.7858 (mtp) cc_final: 0.7513 (ttm) REVERT: C 1599 MET cc_start: 0.8774 (ptm) cc_final: 0.8478 (ptp) REVERT: C 1731 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9273 (mm) REVERT: C 1851 MET cc_start: 0.9549 (mtp) cc_final: 0.9345 (mtm) REVERT: C 2008 MET cc_start: 0.9464 (ptp) cc_final: 0.8745 (tmm) REVERT: C 2198 MET cc_start: 0.9471 (mmp) cc_final: 0.9262 (mpp) REVERT: C 2203 MET cc_start: 0.9044 (pmm) cc_final: 0.8775 (pmm) REVERT: C 2312 MET cc_start: 0.9175 (tmm) cc_final: 0.8846 (tmm) REVERT: C 2932 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5286 (pmm) REVERT: C 3517 MET cc_start: 0.9463 (mmm) cc_final: 0.9121 (mmm) REVERT: C 3673 MET cc_start: 0.9619 (mmm) cc_final: 0.9100 (tpp) REVERT: C 3955 MET cc_start: 0.9549 (mmp) cc_final: 0.9121 (mtm) REVERT: C 4047 MET cc_start: 0.9430 (tmm) cc_final: 0.9154 (tmm) REVERT: C 4168 GLU cc_start: 0.9551 (pm20) cc_final: 0.9340 (pm20) REVERT: C 4184 MET cc_start: 0.8996 (tpt) cc_final: 0.8794 (tpp) REVERT: C 4207 MET cc_start: 0.9244 (mmp) cc_final: 0.9020 (mmp) REVERT: C 4580 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: C 4730 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.8862 (p0) REVERT: C 4796 MET cc_start: 0.9454 (tpt) cc_final: 0.9005 (tpt) REVERT: C 4989 MET cc_start: 0.9343 (tmm) cc_final: 0.9043 (tmm) REVERT: C 5013 MET cc_start: 0.9406 (mtt) cc_final: 0.9157 (mtm) REVERT: D 211 GLU cc_start: 0.8991 (tp30) cc_final: 0.8789 (tm-30) REVERT: D 340 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8890 (mtpp) REVERT: D 343 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8526 (mp0) REVERT: D 403 MET cc_start: 0.9589 (ttm) cc_final: 0.9091 (mtp) REVERT: D 667 MET cc_start: 0.9093 (tpp) cc_final: 0.8650 (tpp) REVERT: D 1100 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8622 (mtt) REVERT: D 1152 MET cc_start: 0.9041 (mmt) cc_final: 0.8553 (mmt) REVERT: D 1170 MET cc_start: 0.9253 (tpp) cc_final: 0.9012 (tpp) REVERT: D 1186 ASP cc_start: 0.9467 (m-30) cc_final: 0.8861 (p0) REVERT: D 1494 MET cc_start: 0.7856 (mtp) cc_final: 0.7511 (ttm) REVERT: D 1599 MET cc_start: 0.8773 (ptm) cc_final: 0.8476 (ptp) REVERT: D 1731 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9277 (mm) REVERT: D 1851 MET cc_start: 0.9550 (mtp) cc_final: 0.9344 (mtm) REVERT: D 2008 MET cc_start: 0.9465 (ptp) cc_final: 0.8746 (tmm) REVERT: D 2198 MET cc_start: 0.9485 (mmp) cc_final: 0.9274 (mpp) REVERT: D 2203 MET cc_start: 0.9044 (pmm) cc_final: 0.8774 (pmm) REVERT: D 2312 MET cc_start: 0.9174 (tmm) cc_final: 0.8845 (tmm) REVERT: D 2932 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5282 (pmm) REVERT: D 3517 MET cc_start: 0.9462 (mmm) cc_final: 0.9118 (mmm) REVERT: D 3673 MET cc_start: 0.9620 (mmm) cc_final: 0.9101 (tpp) REVERT: D 3955 MET cc_start: 0.9549 (mmp) cc_final: 0.9122 (mtm) REVERT: D 4047 MET cc_start: 0.9427 (tmm) cc_final: 0.9152 (tmm) REVERT: D 4184 MET cc_start: 0.8999 (tpt) cc_final: 0.8791 (tpp) REVERT: D 4207 MET cc_start: 0.9245 (mmp) cc_final: 0.9022 (mmp) REVERT: D 4580 TYR cc_start: 0.9383 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: D 4730 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.8865 (p0) REVERT: D 4796 MET cc_start: 0.9453 (tpt) cc_final: 0.9001 (tpt) REVERT: D 4989 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9035 (tmm) REVERT: D 5013 MET cc_start: 0.9414 (mtt) cc_final: 0.9031 (mtm) REVERT: E 29 MET cc_start: 0.8754 (mtp) cc_final: 0.7987 (ttm) REVERT: F 29 MET cc_start: 0.8756 (mtp) cc_final: 0.7974 (ttm) REVERT: G 29 MET cc_start: 0.8757 (mtp) cc_final: 0.7975 (ttm) REVERT: H 29 MET cc_start: 0.8756 (mtp) cc_final: 0.7971 (ttm) outliers start: 108 outliers final: 83 residues processed: 788 average time/residue: 1.2038 time to fit residues: 1702.1516 Evaluate side-chains 799 residues out of total 15544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 694 time to evaluate : 10.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1731 LEU Chi-restraints excluded: chain A residue 1929 MET Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2514 ASN Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 4044 MET Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4214 LYS Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4636 THR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4730 ASP Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 4989 MET Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 208 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 1100 MET Chi-restraints excluded: chain B residue 1512 THR Chi-restraints excluded: chain B residue 1731 LEU Chi-restraints excluded: chain B residue 1929 MET Chi-restraints excluded: chain B residue 2514 ASN Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4214 LYS Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR 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 4730 ASP Chi-restraints excluded: chain B residue 4866 SER Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 4989 MET Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 208 CYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 1100 MET Chi-restraints excluded: chain C residue 1512 THR Chi-restraints excluded: chain C residue 1731 LEU Chi-restraints excluded: chain C residue 1929 MET Chi-restraints excluded: chain C residue 2514 ASN Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4214 LYS Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR 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 4720 VAL Chi-restraints excluded: chain C residue 4730 ASP Chi-restraints excluded: chain C residue 4866 SER Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 208 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1512 THR Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1929 MET Chi-restraints excluded: chain D residue 2514 ASN Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4214 LYS Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4730 ASP Chi-restraints excluded: chain D residue 4866 SER Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 4989 MET Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 3.9990 chunk 1126 optimal weight: 30.0000 chunk 1510 optimal weight: 7.9990 chunk 434 optimal weight: 1.9990 chunk 1307 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 394 optimal weight: 0.0170 chunk 1420 optimal weight: 6.9990 chunk 594 optimal weight: 0.9990 chunk 1458 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN A2414 ASN ** A2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4833 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1614 GLN ** B2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2414 ASN ** B2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4833 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2414 ASN ** C2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4833 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1614 GLN ** D2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2414 ASN ** D2971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.048158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.033202 restraints weight = 2727403.741| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 8.20 r_work: 0.2763 rms_B_bonded: 7.99 restraints_weight: 2.0000 r_work: 0.2866 rms_B_bonded: 5.56 restraints_weight: 4.0000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 146204 Z= 0.181 Angle : 0.583 12.455 198040 Z= 0.291 Chirality : 0.039 0.189 21784 Planarity : 0.004 0.064 25752 Dihedral : 5.168 71.680 19688 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.81 % Allowed : 11.20 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.07), residues: 17832 helix: 1.90 (0.06), residues: 8820 sheet: -0.56 (0.12), residues: 1856 loop : -0.32 (0.08), residues: 7156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP C2886 HIS 0.008 0.001 HIS C3771 PHE 0.023 0.001 PHE B2973 TYR 0.027 0.001 TYR A4080 ARG 0.004 0.000 ARG D4563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38357.20 seconds wall clock time: 669 minutes 54.22 seconds (40194.22 seconds total)