Starting phenix.real_space_refine (version: dev) on Sat May 14 03:31:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0s_22615/05_2022/7k0s_22615_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 1181": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A GLU 3755": "OE1" <-> "OE2" Residue "A GLU 3928": "OE1" <-> "OE2" Residue "A GLU 4212": "OE1" <-> "OE2" Residue "A GLU 4239": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 2115": "OE1" <-> "OE2" Residue "B GLU 2209": "OE1" <-> "OE2" Residue "B GLU 3754": "OE1" <-> "OE2" Residue "B GLU 4212": "OE1" <-> "OE2" Residue "B GLU 4948": "OE1" <-> "OE2" Residue "B GLU 4952": "OE1" <-> "OE2" Residue "B GLU 5007": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1181": "OE1" <-> "OE2" Residue "C GLU 2115": "OE1" <-> "OE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C GLU 3754": "OE1" <-> "OE2" Residue "C PHE 4093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4212": "OE1" <-> "OE2" Residue "C GLU 4867": "OE1" <-> "OE2" Residue "C GLU 4869": "OE1" <-> "OE2" Residue "C GLU 4871": "OE1" <-> "OE2" Residue "C GLU 4981": "OE1" <-> "OE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1181": "OE1" <-> "OE2" Residue "D GLU 2209": "OE1" <-> "OE2" Residue "D PHE 4093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4172": "OE1" <-> "OE2" Residue "D GLU 4182": "OE1" <-> "OE2" Residue "D GLU 4212": "OE1" <-> "OE2" Residue "D GLU 4244": "OE1" <-> "OE2" Residue "D ARG 4892": "NH1" <-> "NH2" Residue "D GLU 5002": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 116057 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 28942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28942 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1228} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3000 Unresolved non-hydrogen angles: 4185 Unresolved non-hydrogen dihedrals: 1869 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 886, 'ASP:plan': 44, 'TYR:plan': 2, 'ASN:plan1': 17, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 5, 'GLU:plan': 87, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1765 Chain: "B" Number of atoms: 28941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4110, 28941 Classifications: {'peptide': 4110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1228} Link IDs: {'PTRANS': 147, 'TRANS': 3962} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 3002 Unresolved non-hydrogen angles: 4190 Unresolved non-hydrogen dihedrals: 1873 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 19, 'UNK:plan-1': 886, 'ASP:plan': 44, 'TYR:plan': 2, 'ASN:plan1': 16, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 88, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1768 Chain: "C" Number of atoms: 29087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4127, 29087 Classifications: {'peptide': 4127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1223} Link IDs: {'PTRANS': 151, 'TRANS': 3975} Chain breaks: 25 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 2978 Unresolved non-hydrogen angles: 4160 Unresolved non-hydrogen dihedrals: 1851 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 887, 'ASP:plan': 44, 'TYR:plan': 3, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 84, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1747 Chain: "D" Number of atoms: 28954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4109, 28954 Classifications: {'peptide': 4109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1227} Link IDs: {'PTRANS': 147, 'TRANS': 3961} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 2987 Unresolved non-hydrogen angles: 4167 Unresolved non-hydrogen dihedrals: 1856 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 18, 'UNK:plan-1': 886, 'ASP:plan': 44, 'TYR:plan': 1, 'ASN:plan1': 17, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 87, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1752 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 1, 'ACP': 1, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 1, 'ACP': 1, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' ZN': 1, 'ACP': 1, ' MG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 1, 'ACP': 1, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28277 SG CYS A4958 180.882 178.034 121.709 1.00 20.03 S ATOM 28302 SG CYS A4961 180.776 176.002 118.403 1.00 20.49 S ATOM 57215 SG CYS B4958 205.130 179.256 121.759 1.00 26.15 S ATOM 57240 SG CYS B4961 205.762 181.597 118.738 1.00 26.27 S ATOM 86301 SG CYS C4958 178.051 204.221 121.706 1.00 24.98 S ATOM 86326 SG CYS C4961 175.842 202.810 118.184 1.00 32.62 S ATOM A0BRR SG CYS D4958 204.318 205.083 121.685 1.00 28.50 S ATOM A0BSG SG CYS D4961 201.669 205.874 118.968 1.00 28.72 S Time building chain proxies: 48.12, per 1000 atoms: 0.41 Number of scatterers: 116057 At special positions: 0 Unit cell: (383.52, 384.88, 212.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 625 16.00 P 12 15.00 Mg 5 11.99 O 21345 8.00 N 20570 7.00 C 73496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " 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: 37.06 Conformation dependent library (CDL) restraints added in 10.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4983 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 6 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31198 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 471 helices and 53 sheets defined 55.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.85 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 5.046A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 removed outlier: 4.054A pdb=" N GLN A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 5.440A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.736A 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 364 through 371 removed outlier: 3.995A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.950A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.995A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.521A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.139A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.864A pdb=" N GLU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 506' Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.783A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.314A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 541' Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.787A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.749A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.731A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.844A pdb=" N LYS A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.961A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.970A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 4.171A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 removed outlier: 4.287A pdb=" N TYR A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 950 removed outlier: 6.093A pdb=" N ASP A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1002 removed outlier: 4.537A pdb=" N THR A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 985 " --> pdb=" O GLN A 981 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1050 removed outlier: 4.446A pdb=" N GLN A1041 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A1044 " --> pdb=" O CYS A1040 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A1048 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1580 removed outlier: 4.347A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1657 removed outlier: 3.915A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1652 through 1657' Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.758A pdb=" N ALA A1675 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.506A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 removed outlier: 4.940A pdb=" N LEU A1695 " --> pdb=" O GLN A1691 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1724 removed outlier: 3.953A pdb=" N TYR A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A1713 " --> pdb=" O ALA A1709 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER A1722 " --> pdb=" O ILE A1718 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA A1723 " --> pdb=" O HIS A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1731 removed outlier: 3.640A pdb=" N MET A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.828A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.633A pdb=" N ARG A1820 " --> pdb=" O GLY A1816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 4.122A pdb=" N VAL A1839 " --> pdb=" O GLU A1835 " (cutoff:3.500A) Proline residue: A1840 - end of helix removed outlier: 5.111A pdb=" N LYS A1843 " --> pdb=" O VAL A1839 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1867 removed outlier: 3.907A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A1866 " --> pdb=" O ILE A1862 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1981 removed outlier: 4.629A pdb=" N LEU A1937 " --> pdb=" O GLU A1933 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1971 " --> pdb=" O ASP A1967 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A1972 " --> pdb=" O LYS A1968 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1979 " --> pdb=" O SER A1975 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1980 " --> pdb=" O ARG A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1999 removed outlier: 3.539A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 4.151A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 5.996A pdb=" N ARG A2028 " --> pdb=" O PRO A2024 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN A2029 " --> pdb=" O GLU A2025 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.589A pdb=" N LEU A2097 " --> pdb=" O SER A2093 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.600A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A2128 " --> pdb=" O LEU A2124 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 4.151A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2188 removed outlier: 4.020A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A2185 " --> pdb=" O SER A2181 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2195 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.677A pdb=" N VAL A2207 " --> pdb=" O MET A2203 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N MET A2208 " --> pdb=" O HIS A2204 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU A2209 " --> pdb=" O GLU A2205 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A2210 " --> pdb=" O THR A2206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A2211 " --> pdb=" O VAL A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2243 removed outlier: 3.504A pdb=" N PHE A2235 " --> pdb=" O SER A2231 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2252 removed outlier: 4.031A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A2250 " --> pdb=" O ASN A2246 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A2251 " --> pdb=" O GLN A2247 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2245 through 2252' Processing helix chain 'A' and resid 2253 through 2262 removed outlier: 4.157A pdb=" N GLU A2259 " --> pdb=" O SER A2255 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2282 removed outlier: 4.017A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 4.130A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2286 through 2291' Processing helix chain 'A' and resid 2294 through 2308 removed outlier: 3.846A pdb=" N VAL A2298 " --> pdb=" O ASP A2294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 4.372A pdb=" N ALA A2315 " --> pdb=" O PRO A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 4.070A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A2336 " --> pdb=" O LEU A2332 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A2339 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.627A pdb=" N ALA A2350 " --> pdb=" O VAL A2346 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A2353 " --> pdb=" O ASN A2349 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2365 through 2370 removed outlier: 3.750A pdb=" N GLY A2370 " --> pdb=" O PRO A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 4.158A pdb=" N ALA A2421 " --> pdb=" O HIS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2441 through 2447 removed outlier: 4.005A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2448 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2472 removed outlier: 4.226A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A2472 " --> pdb=" O GLY A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2741 through 2746 removed outlier: 4.918A pdb=" N ILE A2746 " --> pdb=" O THR A2742 " (cutoff:3.500A) Processing helix chain 'A' and resid 2750 through 2774 removed outlier: 4.653A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2798 removed outlier: 4.091A pdb=" N PHE A2797 " --> pdb=" O PRO A2793 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A2798 " --> pdb=" O TYR A2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2793 through 2798' Processing helix chain 'A' and resid 2799 through 2806 removed outlier: 5.166A pdb=" N GLU A2803 " --> pdb=" O GLU A2799 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) Processing helix chain 'A' and resid 2809 through 2820 removed outlier: 4.623A pdb=" N ALA A2815 " --> pdb=" O GLU A2811 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET A2816 " --> pdb=" O SER A2812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A2818 " --> pdb=" O LYS A2814 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2898 removed outlier: 3.618A pdb=" N MET A2874 " --> pdb=" O GLU A2870 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A2896 " --> pdb=" O GLN A2892 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A2897 " --> pdb=" O GLU A2893 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A2898 " --> pdb=" O LEU A2894 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 3.838A pdb=" N LYS A2916 " --> pdb=" O THR A2912 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG A2920 " --> pdb=" O LYS A2916 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A2921 " --> pdb=" O ALA A2917 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN A2933 " --> pdb=" O PHE A2929 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY A2934 " --> pdb=" O LEU A2930 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3658 removed outlier: 4.716A pdb=" N LYS A3658 " --> pdb=" O LEU A3654 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3683 removed outlier: 4.494A pdb=" N ILE A3674 " --> pdb=" O GLU A3670 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A3675 " --> pdb=" O ASP A3671 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A3677 " --> pdb=" O MET A3673 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A3678 " --> pdb=" O ILE A3674 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 removed outlier: 3.595A pdb=" N THR A3711 " --> pdb=" O ARG A3707 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3739 removed outlier: 3.639A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3771 removed outlier: 4.038A pdb=" N LYS A3756 " --> pdb=" O SER A3752 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A3757 " --> pdb=" O PHE A3753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS A3771 " --> pdb=" O GLN A3767 " (cutoff:3.500A) Processing helix chain 'A' and resid 3775 through 3786 removed outlier: 4.786A pdb=" N VAL A3779 " --> pdb=" O ALA A3775 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A3785 " --> pdb=" O GLN A3781 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 4.180A pdb=" N LYS A3799 " --> pdb=" O SER A3795 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A3800 " --> pdb=" O SER A3796 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A3801 " --> pdb=" O THR A3797 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 4.078A pdb=" N GLN A3813 " --> pdb=" O ASN A3809 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A3814 " --> pdb=" O ALA A3810 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A3815 " --> pdb=" O GLU A3811 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 7.174A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3858 removed outlier: 3.831A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N MET A3858 " --> pdb=" O GLU A3854 " (cutoff:3.500A) Processing helix chain 'A' and resid 3879 through 3893 removed outlier: 4.629A pdb=" N ASP A3883 " --> pdb=" O GLU A3879 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A3884 " --> pdb=" O PHE A3880 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE A3885 " --> pdb=" O THR A3881 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 6.604A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.821A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 4.351A pdb=" N GLU A3967 " --> pdb=" O ASN A3963 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A3968 " --> pdb=" O SER A3964 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 3.830A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A3983 " --> pdb=" O SER A3979 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4003 removed outlier: 3.542A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N MET A3999 " --> pdb=" O VAL A3995 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET A4000 " --> pdb=" O PHE A3996 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.729A pdb=" N LEU A4013 " --> pdb=" O GLN A4009 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4052 Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 5.278A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A4058 " --> pdb=" O ASN A4054 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 4.041A pdb=" N GLN A4078 " --> pdb=" O SER A4074 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 4.014A pdb=" N PHE A4093 " --> pdb=" O SER A4089 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.016A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4154 removed outlier: 3.670A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A4131 " --> pdb=" O GLU A4127 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix removed outlier: 4.307A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.767A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 3.840A 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 removed outlier: 5.004A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A4206 " --> pdb=" O ARG A4202 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 removed outlier: 3.704A pdb=" N ASN A4223 " --> pdb=" O PHE A4219 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A4224 " --> pdb=" O ASP A4220 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 4.529A pdb=" N LEU A4233 " --> pdb=" O GLU A4229 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A4234 " --> pdb=" O LYS A4230 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A4235 " --> pdb=" O MET A4231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A4236 " --> pdb=" O GLU A4232 " (cutoff:3.500A) Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 3.877A pdb=" N GLU A4545 " --> pdb=" O TRP A4541 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.992A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4684 removed outlier: 4.413A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix removed outlier: 4.005A pdb=" N ILE A4670 " --> pdb=" O VAL A4666 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4701 removed outlier: 3.743A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 removed outlier: 4.238A pdb=" N LYS A4723 " --> pdb=" O PHE A4719 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A4724 " --> pdb=" O VAL A4720 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4749 through 4755 removed outlier: 3.535A pdb=" N ASN A4754 " --> pdb=" O ILE A4750 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A4755 " --> pdb=" O THR A4751 " (cutoff:3.500A) Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.621A pdb=" N SER A4770 " --> pdb=" O THR A4766 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 3.544A pdb=" N VAL A4782 " --> pdb=" O TRP A4778 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 5.023A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 3.842A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A4819 " --> pdb=" O ALA A4815 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4822 through 4859 removed outlier: 4.283A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A4834 " --> pdb=" O VAL A4830 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS A4835 " --> pdb=" O THR A4831 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLN A4836 " --> pdb=" O HIS A4832 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A4838 " --> pdb=" O GLY A4834 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET A4839 " --> pdb=" O LYS A4835 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4894 removed outlier: 5.078A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A4894 " --> pdb=" O GLY A4890 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 5.276A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4957 removed outlier: 4.175A pdb=" N ARG A4913 " --> pdb=" O TYR A4909 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A4916 " --> pdb=" O TYR A4912 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A4927 " --> pdb=" O PHE A4923 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU A4928 " --> pdb=" O VAL A4924 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU A4929 " --> pdb=" O ILE A4925 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.671A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP A4969 " --> pdb=" O SER A4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4964 through 4969' Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 6.595A pdb=" N TYR A4988 " --> pdb=" O ALA A4984 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A4996 " --> pdb=" O LEU A4992 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5032 removed outlier: 6.454A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A5032 " --> pdb=" O PHE A5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5027 through 5032' Processing helix chain 'A' and resid 3861 through 3867 removed outlier: 5.145A pdb=" N THR A3864 " --> pdb=" O GLU A3861 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A3865 " --> pdb=" O ASP A3862 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE A3866 " --> pdb=" O GLY A3863 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN A3867 " --> pdb=" O THR A3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3861 through 3867' Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'B' and resid 61 through 66 removed outlier: 5.107A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 4.878A 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 removed outlier: 4.139A pdb=" N GLN B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 5.847A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.916A 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: 6.835A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.039A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.938A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 5.045A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.547A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.634A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.797A pdb=" N GLU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 506' Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.734A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.411A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 541' Processing helix chain 'B' and resid 542 through 551 removed outlier: 4.525A pdb=" N TRP B 546 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.632A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.862A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.462A pdb=" N LYS B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 585 " --> pdb=" O ASN B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.878A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 3.960A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 4.168A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 4.300A pdb=" N TYR B 920 " --> pdb=" O PRO B 916 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 950 removed outlier: 6.106A pdb=" N ASP B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1002 removed outlier: 4.522A pdb=" N THR B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 984 " --> pdb=" O ALA B 980 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 985 " --> pdb=" O GLN B 981 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1050 removed outlier: 4.443A pdb=" N GLN B1041 " --> pdb=" O ASP B1037 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA B1042 " --> pdb=" O SER B1038 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B1044 " --> pdb=" O CYS B1040 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B1048 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B1049 " --> pdb=" O THR B1045 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY B1050 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 4.337A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1657 removed outlier: 3.774A pdb=" N ARG B1656 " --> pdb=" O GLU B1652 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1652 through 1657' Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.878A pdb=" N ALA B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1690 Processing helix chain 'B' and resid 1691 through 1701 removed outlier: 4.909A pdb=" N LEU B1695 " --> pdb=" O GLN B1691 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1724 removed outlier: 3.958A pdb=" N TYR B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B1713 " --> pdb=" O ALA B1709 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU B1721 " --> pdb=" O SER B1717 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N SER B1722 " --> pdb=" O ILE B1718 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA B1723 " --> pdb=" O HIS B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1725 through 1732 removed outlier: 4.460A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.845A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.689A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 removed outlier: 4.122A pdb=" N VAL B1839 " --> pdb=" O GLU B1835 " (cutoff:3.500A) Proline residue: B1840 - end of helix removed outlier: 5.102A pdb=" N LYS B1843 " --> pdb=" O VAL B1839 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1867 removed outlier: 3.926A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B1866 " --> pdb=" O ILE B1862 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1984 removed outlier: 3.771A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B1971 " --> pdb=" O ASP B1967 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B1972 " --> pdb=" O LYS B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 1999 removed outlier: 3.566A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 4.204A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2024 through 2043 removed outlier: 5.974A pdb=" N ARG B2028 " --> pdb=" O PRO B2024 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLN B2029 " --> pdb=" O GLU B2025 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.502A pdb=" N LEU B2097 " --> pdb=" O SER B2093 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.668A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B2128 " --> pdb=" O LEU B2124 " (cutoff:3.500A) removed outlier: 4.272A 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: 5.287A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 4.227A pdb=" N THR B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2188 removed outlier: 3.799A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET B2186 " --> pdb=" O ILE B2182 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2195 through 2202 Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 4.436A pdb=" N MET B2208 " --> pdb=" O HIS B2204 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLU B2209 " --> pdb=" O GLU B2205 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B2211 " --> pdb=" O VAL B2207 " (cutoff:3.500A) Processing helix chain 'B' and resid 2227 through 2243 removed outlier: 4.351A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B2235 " --> pdb=" O SER B2231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2252 removed outlier: 4.064A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET B2250 " --> pdb=" O ASN B2246 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B2251 " --> pdb=" O GLN B2247 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2245 through 2252' Processing helix chain 'B' and resid 2253 through 2261 removed outlier: 4.154A pdb=" N GLU B2259 " --> pdb=" O SER B2255 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2282 removed outlier: 3.699A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 4.024A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2286 through 2291' Processing helix chain 'B' and resid 2294 through 2308 removed outlier: 4.083A pdb=" N VAL B2298 " --> pdb=" O ASP B2294 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B2306 " --> pdb=" O LEU B2302 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B2307 " --> pdb=" O ALA B2303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 4.405A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 4.115A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B2336 " --> pdb=" O LEU B2332 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B2339 " --> pdb=" O LEU B2335 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B2340 " --> pdb=" O ARG B2336 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.603A pdb=" N ALA B2350 " --> pdb=" O VAL B2346 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B2353 " --> pdb=" O ASN B2349 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2365 through 2370 Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 removed outlier: 4.164A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2447 through 2462 removed outlier: 3.917A pdb=" N LEU B2451 " --> pdb=" O LYS B2447 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2472 removed outlier: 4.066A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B2472 " --> pdb=" O GLY B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2741 through 2746 removed outlier: 4.920A pdb=" N ILE B2746 " --> pdb=" O THR B2742 " (cutoff:3.500A) Processing helix chain 'B' and resid 2750 through 2774 removed outlier: 4.676A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) Processing helix chain 'B' and resid 2793 through 2798 removed outlier: 4.074A pdb=" N PHE B2797 " --> pdb=" O PRO B2793 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER B2798 " --> pdb=" O TYR B2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2793 through 2798' Processing helix chain 'B' and resid 2799 through 2806 removed outlier: 5.163A pdb=" N GLU B2803 " --> pdb=" O GLU B2799 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Processing helix chain 'B' and resid 2809 through 2820 removed outlier: 4.829A pdb=" N ALA B2815 " --> pdb=" O GLU B2811 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET B2816 " --> pdb=" O SER B2812 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B2817 " --> pdb=" O LEU B2813 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B2818 " --> pdb=" O LYS B2814 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2898 removed outlier: 3.600A pdb=" N MET B2874 " --> pdb=" O GLU B2870 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B2896 " --> pdb=" O GLN B2892 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B2897 " --> pdb=" O GLU B2893 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B2898 " --> pdb=" O LEU B2894 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2934 removed outlier: 3.841A pdb=" N LYS B2916 " --> pdb=" O THR B2912 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B2917 " --> pdb=" O ALA B2913 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B2921 " --> pdb=" O ALA B2917 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN B2933 " --> pdb=" O PHE B2929 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY B2934 " --> pdb=" O LEU B2930 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3662 removed outlier: 4.640A pdb=" N LYS B3658 " --> pdb=" O LEU B3654 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B3659 " --> pdb=" O GLU B3655 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA B3660 " --> pdb=" O SER B3656 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3683 removed outlier: 4.783A pdb=" N ILE B3674 " --> pdb=" O GLU B3670 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B3677 " --> pdb=" O MET B3673 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B3678 " --> pdb=" O ILE B3674 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.631A pdb=" N THR B3711 " --> pdb=" O ARG B3707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3739 removed outlier: 3.649A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3771 removed outlier: 3.951A pdb=" N LYS B3756 " --> pdb=" O SER B3752 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU B3757 " --> pdb=" O PHE B3753 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B3771 " --> pdb=" O GLN B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3775 through 3786 removed outlier: 4.944A pdb=" N VAL B3779 " --> pdb=" O ALA B3775 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B3785 " --> pdb=" O GLN B3781 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N CYS B3786 " --> pdb=" O MET B3782 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 4.233A pdb=" N LYS B3799 " --> pdb=" O SER B3795 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B3800 " --> pdb=" O SER B3796 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B3801 " --> pdb=" O THR B3797 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 4.169A pdb=" N GLN B3813 " --> pdb=" O ASN B3809 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B3814 " --> pdb=" O ALA B3810 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B3815 " --> pdb=" O GLU B3811 " (cutoff:3.500A) Processing helix chain 'B' and resid 3827 through 3839 removed outlier: 4.248A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3858 removed outlier: 3.880A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B3856 " --> pdb=" O LYS B3852 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N MET B3858 " --> pdb=" O GLU B3854 " (cutoff:3.500A) Processing helix chain 'B' and resid 3878 through 3893 removed outlier: 3.606A pdb=" N GLN B3882 " --> pdb=" O ASP B3878 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B3884 " --> pdb=" O PHE B3880 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 6.531A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3938 removed outlier: 3.700A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.721A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 3.906A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B3983 " --> pdb=" O SER B3979 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 3998 removed outlier: 3.591A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.888A pdb=" N LEU B4013 " --> pdb=" O GLN B4009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4052 Processing helix chain 'B' and resid 4053 through 4071 removed outlier: 6.021A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE B4058 " --> pdb=" O ASN B4054 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4081 removed outlier: 4.070A pdb=" N GLN B4078 " --> pdb=" O SER B4074 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.865A pdb=" N PHE B4093 " --> pdb=" O SER B4089 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.071A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4154 removed outlier: 3.695A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B4131 " --> pdb=" O GLU B4127 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix removed outlier: 4.196A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.790A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 3.878A 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 removed outlier: 4.909A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B4206 " --> pdb=" O ARG B4202 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 removed outlier: 3.631A pdb=" N VAL B4222 " --> pdb=" O ILE B4218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B4223 " --> pdb=" O PHE B4219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B4224 " --> pdb=" O ASP B4220 " (cutoff:3.500A) Processing helix chain 'B' and resid 4229 through 4253 removed outlier: 4.825A pdb=" N LEU B4233 " --> pdb=" O GLU B4229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B4234 " --> pdb=" O LYS B4230 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B4235 " --> pdb=" O MET B4231 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B4236 " --> pdb=" O GLU B4232 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU B4253 " --> pdb=" O ALA B4249 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4559 removed outlier: 4.844A pdb=" N VAL B4546 " --> pdb=" O GLY B4542 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN B4547 " --> pdb=" O GLU B4543 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B4555 " --> pdb=" O PHE B4551 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 5.150A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4641 through 4664 removed outlier: 4.498A pdb=" N CYS B4645 " --> pdb=" O PRO B4641 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B4648 " --> pdb=" O TRP B4644 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS B4663 " --> pdb=" O ILE B4659 " (cutoff:3.500A) Processing helix chain 'B' and resid 4666 through 4684 removed outlier: 5.073A pdb=" N ILE B4670 " --> pdb=" O VAL B4666 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4701 removed outlier: 3.769A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4729 removed outlier: 4.290A pdb=" N LYS B4723 " --> pdb=" O PHE B4719 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B4724 " --> pdb=" O VAL B4720 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4749 through 4756 removed outlier: 3.754A pdb=" N GLU B4755 " --> pdb=" O THR B4751 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG B4756 " --> pdb=" O ALA B4752 " (cutoff:3.500A) Processing helix chain 'B' and resid 4766 through 4771 removed outlier: 3.573A pdb=" N SER B4770 " --> pdb=" O THR B4766 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.512A pdb=" N VAL B4782 " --> pdb=" O TRP B4778 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B4783 " --> pdb=" O LYS B4779 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.555A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 4.514A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B4819 " --> pdb=" O ALA B4815 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 4.443A pdb=" N THR B4825 " --> pdb=" O LYS B4821 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 removed outlier: 3.794A pdb=" N VAL B4838 " --> pdb=" O GLY B4834 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N MET B4839 " --> pdb=" O LYS B4835 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.494A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4902 removed outlier: 3.857A pdb=" N ILE B4901 " --> pdb=" O ILE B4897 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4897 through 4902' Processing helix chain 'B' and resid 4909 through 4957 removed outlier: 4.467A pdb=" N ARG B4913 " --> pdb=" O TYR B4909 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B4926 " --> pdb=" O PHE B4922 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B4927 " --> pdb=" O PHE B4923 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B4928 " --> pdb=" O VAL B4924 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU B4929 " --> pdb=" O ILE B4925 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 4.620A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B4969 " --> pdb=" O SER B4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4964 through 4969' Processing helix chain 'B' and resid 4973 through 4981 removed outlier: 3.692A pdb=" N THR B4979 " --> pdb=" O PHE B4975 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B4981 " --> pdb=" O THR B4977 " (cutoff:3.500A) Processing helix chain 'B' and resid 4984 through 4999 removed outlier: 6.615A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B4996 " --> pdb=" O LEU B4992 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP B4999 " --> pdb=" O LEU B4995 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5027 through 5032 removed outlier: 6.401A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR B5032 " --> pdb=" O PHE B5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5027 through 5032' Processing helix chain 'B' and resid 3861 through 3867 removed outlier: 5.141A pdb=" N THR B3864 " --> pdb=" O GLU B3861 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL B3865 " --> pdb=" O ASP B3862 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B3866 " --> pdb=" O GLY B3863 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN B3867 " --> pdb=" O THR B3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3861 through 3867' Processing helix chain 'B' and resid 54 through 59 Proline residue: B 59 - end of helix No H-bonds generated for 'chain 'B' and resid 54 through 59' Processing helix chain 'B' and resid 3999 through 4004 removed outlier: 3.988A pdb=" N ALA B4004 " --> pdb=" O MET B3999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3999 through 4004' Processing helix chain 'C' and resid 61 through 66 removed outlier: 5.125A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.845A 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 removed outlier: 4.646A pdb=" N GLN C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 4.132A pdb=" N CYS C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 256' Processing helix chain 'C' and resid 308 through 313 removed outlier: 6.889A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.115A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.932A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.833A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.556A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.605A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 removed outlier: 4.855A pdb=" N GLU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 506' Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.537A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP C 515 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 529 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 4.416A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 541' Processing helix chain 'C' and resid 542 through 551 removed outlier: 4.528A pdb=" N TRP C 546 " --> pdb=" O THR C 542 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 572 removed outlier: 3.680A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER C 571 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Proline residue: C 572 - end of helix Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.804A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 5.036A pdb=" N LYS C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 585 " --> pdb=" O ASN C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.921A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 3.975A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 4.169A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 4.307A pdb=" N TYR C 920 " --> pdb=" O PRO C 916 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY C 936 " --> pdb=" O LEU C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 950 removed outlier: 6.109A pdb=" N ASP C 948 " --> pdb=" O GLU C 944 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1002 removed outlier: 4.474A pdb=" N THR C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU C 984 " --> pdb=" O ALA C 980 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 986 " --> pdb=" O THR C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1050 removed outlier: 4.445A pdb=" N GLN C1041 " --> pdb=" O ASP C1037 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL C1043 " --> pdb=" O LEU C1039 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG C1044 " --> pdb=" O CYS C1040 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR C1045 " --> pdb=" O GLN C1041 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C1048 " --> pdb=" O ARG C1044 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C1049 " --> pdb=" O THR C1045 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY C1050 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1580 removed outlier: 4.370A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1574 through 1580' Processing helix chain 'C' and resid 1652 through 1657 removed outlier: 3.950A pdb=" N ARG C1656 " --> pdb=" O GLU C1652 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1652 through 1657' Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.827A pdb=" N ALA C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 Processing helix chain 'C' and resid 1691 through 1701 removed outlier: 4.923A pdb=" N LEU C1695 " --> pdb=" O GLN C1691 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1707 through 1724 removed outlier: 3.960A pdb=" N TYR C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP C1713 " --> pdb=" O ALA C1709 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU C1721 " --> pdb=" O SER C1717 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER C1722 " --> pdb=" O ILE C1718 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA C1723 " --> pdb=" O HIS C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1725 through 1732 removed outlier: 4.615A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.880A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.700A pdb=" N ARG C1820 " --> pdb=" O GLY C1816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 removed outlier: 4.139A pdb=" N VAL C1839 " --> pdb=" O GLU C1835 " (cutoff:3.500A) Proline residue: C1840 - end of helix removed outlier: 5.145A pdb=" N LYS C1843 " --> pdb=" O VAL C1839 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1867 removed outlier: 3.949A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE C1866 " --> pdb=" O ILE C1862 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1984 removed outlier: 4.614A pdb=" N LEU C1937 " --> pdb=" O GLU C1933 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C1971 " --> pdb=" O ASP C1967 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN C1972 " --> pdb=" O LYS C1968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 1999 removed outlier: 3.641A pdb=" N ARG C1996 " --> pdb=" O ALA C1992 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 4.225A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2024 through 2043 removed outlier: 5.966A pdb=" N ARG C2028 " --> pdb=" O PRO C2024 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLN C2029 " --> pdb=" O GLU C2025 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP C2030 " --> pdb=" O ASP C2026 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.574A pdb=" N LEU C2097 " --> pdb=" O SER C2093 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.641A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C2128 " --> pdb=" O LEU C2124 " (cutoff:3.500A) removed outlier: 4.328A 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: 5.298A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 4.183A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2188 removed outlier: 4.055A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C2185 " --> pdb=" O SER C2181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET C2186 " --> pdb=" O ILE C2182 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 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 2216 removed outlier: 4.573A pdb=" N MET C2208 " --> pdb=" O HIS C2204 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU C2209 " --> pdb=" O GLU C2205 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL C2210 " --> pdb=" O THR C2206 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET C2211 " --> pdb=" O VAL C2207 " (cutoff:3.500A) Processing helix chain 'C' and resid 2227 through 2243 removed outlier: 4.410A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C2235 " --> pdb=" O SER C2231 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 3.913A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET C2250 " --> pdb=" O ASN C2246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C2251 " --> pdb=" O GLN C2247 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2265 removed outlier: 4.461A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 removed outlier: 3.992A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2308 removed outlier: 7.203A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C2296 " --> pdb=" O GLU C2292 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS C2297 " --> pdb=" O GLN C2293 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C2298 " --> pdb=" O ASP C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 4.391A pdb=" N ALA C2315 " --> pdb=" O PRO C2311 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 4.109A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C2336 " --> pdb=" O LEU C2332 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL C2339 " --> pdb=" O LEU C2335 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C2340 " --> pdb=" O ARG C2336 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.655A pdb=" N ALA C2350 " --> pdb=" O VAL C2346 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL C2353 " --> pdb=" O ASN C2349 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2365 through 2370 Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 removed outlier: 4.215A pdb=" N ALA C2421 " --> pdb=" O HIS C2417 " (cutoff:3.500A) Processing helix chain 'C' and resid 2447 through 2462 removed outlier: 4.034A pdb=" N LEU C2451 " --> pdb=" O LYS C2447 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2472 removed outlier: 3.840A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C2472 " --> pdb=" O GLY C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2741 through 2746 removed outlier: 4.899A pdb=" N ILE C2746 " --> pdb=" O THR C2742 " (cutoff:3.500A) Processing helix chain 'C' and resid 2750 through 2774 removed outlier: 4.638A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2793 through 2798 removed outlier: 4.048A pdb=" N PHE C2797 " --> pdb=" O PRO C2793 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER C2798 " --> pdb=" O TYR C2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2793 through 2798' Processing helix chain 'C' and resid 2799 through 2806 removed outlier: 5.180A pdb=" N GLU C2803 " --> pdb=" O GLU C2799 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) Processing helix chain 'C' and resid 2811 through 2820 removed outlier: 4.860A pdb=" N ALA C2815 " --> pdb=" O GLU C2811 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET C2816 " --> pdb=" O SER C2812 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C2817 " --> pdb=" O LEU C2813 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C2818 " --> pdb=" O LYS C2814 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2898 removed outlier: 3.610A pdb=" N MET C2874 " --> pdb=" O GLU C2870 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS C2897 " --> pdb=" O GLU C2893 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C2898 " --> pdb=" O LEU C2894 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 3.849A pdb=" N LYS C2916 " --> pdb=" O THR C2912 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C2917 " --> pdb=" O ALA C2913 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG C2920 " --> pdb=" O LYS C2916 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU C2921 " --> pdb=" O ALA C2917 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN C2933 " --> pdb=" O PHE C2929 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY C2934 " --> pdb=" O LEU C2930 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3658 removed outlier: 4.586A pdb=" N LYS C3658 " --> pdb=" O LEU C3654 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3683 removed outlier: 4.248A pdb=" N ILE C3674 " --> pdb=" O GLU C3670 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C3677 " --> pdb=" O MET C3673 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C3678 " --> pdb=" O ILE C3674 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 removed outlier: 3.643A pdb=" N THR C3711 " --> pdb=" O ARG C3707 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3739 removed outlier: 3.673A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C3736 " --> pdb=" O SER C3732 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3771 removed outlier: 3.601A pdb=" N LYS C3756 " --> pdb=" O SER C3752 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C3757 " --> pdb=" O PHE C3753 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS C3771 " --> pdb=" O GLN C3767 " (cutoff:3.500A) Processing helix chain 'C' and resid 3775 through 3786 removed outlier: 5.010A pdb=" N VAL C3779 " --> pdb=" O ALA C3775 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C3785 " --> pdb=" O GLN C3781 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C3786 " --> pdb=" O MET C3782 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.973A pdb=" N LYS C3799 " --> pdb=" O SER C3795 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C3800 " --> pdb=" O SER C3796 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C3801 " --> pdb=" O THR C3797 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 removed outlier: 3.898A pdb=" N GLN C3813 " --> pdb=" O ASN C3809 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN C3814 " --> pdb=" O ALA C3810 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C3815 " --> pdb=" O GLU C3811 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C3820 " --> pdb=" O MET C3816 " (cutoff:3.500A) Processing helix chain 'C' and resid 3827 through 3839 removed outlier: 4.237A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3858 removed outlier: 3.843A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU C3856 " --> pdb=" O LYS C3852 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N MET C3858 " --> pdb=" O GLU C3854 " (cutoff:3.500A) Processing helix chain 'C' and resid 3878 through 3893 removed outlier: 3.598A pdb=" N GLN C3882 " --> pdb=" O ASP C3878 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP C3883 " --> pdb=" O GLU C3879 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C3884 " --> pdb=" O PHE C3880 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C3885 " --> pdb=" O THR C3881 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 6.571A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3938 removed outlier: 3.757A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C3936 " --> pdb=" O ASP C3932 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.767A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C3967 " --> pdb=" O ASN C3963 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3983 removed outlier: 3.865A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C3983 " --> pdb=" O SER C3979 " (cutoff:3.500A) Processing helix chain 'C' and resid 3984 through 4003 removed outlier: 3.619A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET C3999 " --> pdb=" O VAL C3995 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N MET C4000 " --> pdb=" O PHE C3996 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.867A pdb=" N LEU C4013 " --> pdb=" O GLN C4009 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4052 Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 5.304A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C4058 " --> pdb=" O ASN C4054 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4081 removed outlier: 4.006A pdb=" N GLN C4078 " --> pdb=" O SER C4074 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.999A pdb=" N PHE C4093 " --> pdb=" O SER C4089 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.127A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4154 removed outlier: 3.683A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C4131 " --> pdb=" O GLU C4127 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix removed outlier: 4.296A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.745A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 3.835A 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 removed outlier: 4.918A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU C4206 " --> pdb=" O ARG C4202 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4225 removed outlier: 3.733A pdb=" N VAL C4222 " --> pdb=" O ILE C4218 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C4223 " --> pdb=" O PHE C4219 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C4224 " --> pdb=" O ASP C4220 " (cutoff:3.500A) Processing helix chain 'C' and resid 4229 through 4252 removed outlier: 4.273A pdb=" N LEU C4233 " --> pdb=" O GLU C4229 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C4234 " --> pdb=" O LYS C4230 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C4235 " --> pdb=" O MET C4231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C4236 " --> pdb=" O GLU C4232 " (cutoff:3.500A) Processing helix chain 'C' and resid 4542 through 4559 removed outlier: 4.741A pdb=" N VAL C4546 " --> pdb=" O GLY C4542 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C4547 " --> pdb=" O GLU C4543 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.970A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4641 through 4684 removed outlier: 3.601A pdb=" N ILE C4659 " --> pdb=" O PHE C4655 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix removed outlier: 4.237A pdb=" N ILE C4670 " --> pdb=" O VAL C4666 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C4671 " --> pdb=" O PRO C4667 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4701 removed outlier: 3.558A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4729 removed outlier: 4.191A pdb=" N LYS C4723 " --> pdb=" O PHE C4719 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C4724 " --> pdb=" O VAL C4720 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4749 through 4756 removed outlier: 4.136A pdb=" N GLU C4755 " --> pdb=" O THR C4751 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG C4756 " --> pdb=" O ALA C4752 " (cutoff:3.500A) Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.632A pdb=" N SER C4770 " --> pdb=" O THR C4766 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.561A pdb=" N VAL C4782 " --> pdb=" O TRP C4778 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C4783 " --> pdb=" O LYS C4779 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4803 Processing helix chain 'C' and resid 4808 through 4821 removed outlier: 4.372A pdb=" N ALA C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C4821 " --> pdb=" O ALA C4817 " (cutoff:3.500A) Processing helix chain 'C' and resid 4822 through 4832 removed outlier: 3.923A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 removed outlier: 3.826A pdb=" N VAL C4838 " --> pdb=" O GLY C4834 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET C4839 " --> pdb=" O LYS C4835 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4897 through 4902 removed outlier: 3.942A pdb=" N ILE C4901 " --> pdb=" O ILE C4897 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4897 through 4902' Processing helix chain 'C' and resid 4909 through 4957 removed outlier: 3.836A pdb=" N ARG C4913 " --> pdb=" O TYR C4909 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE C4925 " --> pdb=" O PHE C4921 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL C4926 " --> pdb=" O PHE C4922 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C4927 " --> pdb=" O PHE C4923 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C4928 " --> pdb=" O VAL C4924 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU C4929 " --> pdb=" O ILE C4925 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C4950 " --> pdb=" O GLN C4946 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C4951 " --> pdb=" O GLN C4947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C4956 " --> pdb=" O GLU C4952 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.739A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP C4969 " --> pdb=" O SER C4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4964 through 4969' Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4999 removed outlier: 6.748A pdb=" N TYR C4988 " --> pdb=" O ALA C4984 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C4996 " --> pdb=" O LEU C4992 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C4997 " --> pdb=" O MET C4993 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP C4999 " --> pdb=" O LEU C4995 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5027 through 5032 removed outlier: 6.434A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR C5032 " --> pdb=" O PHE C5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5027 through 5032' Processing helix chain 'C' and resid 2861 through 2866 removed outlier: 4.322A pdb=" N GLY C2864 " --> pdb=" O ASP C2861 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C2865 " --> pdb=" O LEU C2862 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THR C2866 " --> pdb=" O SER C2863 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2861 through 2866' Processing helix chain 'C' and resid 3861 through 3867 removed outlier: 5.151A pdb=" N THR C3864 " --> pdb=" O GLU C3861 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C3865 " --> pdb=" O ASP C3862 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE C3866 " --> pdb=" O GLY C3863 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN C3867 " --> pdb=" O THR C3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3861 through 3867' Processing helix chain 'C' and resid 54 through 59 Proline residue: C 59 - end of helix No H-bonds generated for 'chain 'C' and resid 54 through 59' Processing helix chain 'D' and resid 61 through 66 removed outlier: 5.261A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 4.379A 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 removed outlier: 4.301A pdb=" N GLN D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 256 removed outlier: 5.594A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.898A 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 364 through 371 removed outlier: 4.020A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 3.864A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.833A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.560A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.536A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 506 removed outlier: 4.758A pdb=" N GLU D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 501 through 506' Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.631A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP D 515 " --> pdb=" O ALA D 511 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN D 520 " --> pdb=" O LYS D 516 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 529 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 4.405A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 541' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.777A pdb=" N VAL D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.774A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 3.713A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 removed outlier: 4.340A pdb=" N LYS D 584 " --> pdb=" O GLU D 580 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 585 " --> pdb=" O ASN D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.932A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 3.982A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 4.170A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 removed outlier: 4.306A pdb=" N TYR D 920 " --> pdb=" O PRO D 916 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY D 936 " --> pdb=" O LEU D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 950 removed outlier: 6.066A pdb=" N ASP D 948 " --> pdb=" O GLU D 944 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1002 removed outlier: 4.489A pdb=" N THR D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU D 984 " --> pdb=" O ALA D 980 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D 985 " --> pdb=" O GLN D 981 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 986 " --> pdb=" O THR D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1050 removed outlier: 4.434A pdb=" N GLN D1041 " --> pdb=" O ASP D1037 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA D1042 " --> pdb=" O SER D1038 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL D1043 " --> pdb=" O LEU D1039 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG D1044 " --> pdb=" O CYS D1040 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D1048 " --> pdb=" O ARG D1044 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D1049 " --> pdb=" O THR D1045 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY D1050 " --> pdb=" O LEU D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1580 removed outlier: 4.441A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1652 through 1657 removed outlier: 4.011A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1652 through 1657' Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.807A pdb=" N ALA D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1690 Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 4.844A pdb=" N LEU D1695 " --> pdb=" O GLN D1691 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1707 through 1724 removed outlier: 3.923A pdb=" N TYR D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP D1713 " --> pdb=" O ALA D1709 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU D1721 " --> pdb=" O SER D1717 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER D1722 " --> pdb=" O ILE D1718 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA D1723 " --> pdb=" O HIS D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1725 through 1731 removed outlier: 3.781A pdb=" N MET D1730 " --> pdb=" O SER D1726 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.786A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.517A pdb=" N ARG D1820 " --> pdb=" O GLY D1816 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 removed outlier: 4.212A pdb=" N VAL D1839 " --> pdb=" O GLU D1835 " (cutoff:3.500A) Proline residue: D1840 - end of helix removed outlier: 5.141A pdb=" N LYS D1843 " --> pdb=" O VAL D1839 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D1852 " --> pdb=" O LEU D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1867 removed outlier: 4.102A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE D1866 " --> pdb=" O ILE D1862 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1981 removed outlier: 4.502A pdb=" N LEU D1937 " --> pdb=" O GLU D1933 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA D1971 " --> pdb=" O ASP D1967 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D1972 " --> pdb=" O LYS D1968 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D1979 " --> pdb=" O SER D1975 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D1980 " --> pdb=" O ARG D1976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1999 removed outlier: 3.581A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 4.193A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 5.967A pdb=" N ARG D2028 " --> pdb=" O PRO D2024 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D2029 " --> pdb=" O GLU D2025 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 5.035A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.625A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR D2128 " --> pdb=" O LEU D2124 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.151A pdb=" N THR D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.930A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D2185 " --> pdb=" O SER D2181 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET D2186 " --> pdb=" O ILE D2182 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2195 through 2202 Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 3.596A pdb=" N VAL D2207 " --> pdb=" O MET D2203 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET D2208 " --> pdb=" O HIS D2204 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU D2209 " --> pdb=" O GLU D2205 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL D2210 " --> pdb=" O THR D2206 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET D2211 " --> pdb=" O VAL D2207 " (cutoff:3.500A) Processing helix chain 'D' and resid 2227 through 2243 removed outlier: 4.444A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D2235 " --> pdb=" O SER D2231 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2252 removed outlier: 3.971A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET D2250 " --> pdb=" O ASN D2246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE D2251 " --> pdb=" O GLN D2247 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2245 through 2252' Processing helix chain 'D' and resid 2253 through 2261 removed outlier: 4.222A pdb=" N GLU D2259 " --> pdb=" O SER D2255 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 3.693A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2308 removed outlier: 7.293A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU D2296 " --> pdb=" O GLU D2292 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS D2297 " --> pdb=" O GLN D2293 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL D2298 " --> pdb=" O ASP D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 4.398A pdb=" N ALA D2315 " --> pdb=" O PRO D2311 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 4.101A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D2336 " --> pdb=" O LEU D2332 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL D2339 " --> pdb=" O LEU D2335 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D2340 " --> pdb=" O ARG D2336 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.727A pdb=" N ALA D2350 " --> pdb=" O VAL D2346 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL D2353 " --> pdb=" O ASN D2349 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2365 through 2370 removed outlier: 3.750A pdb=" N GLY D2370 " --> pdb=" O PRO D2366 " (cutoff:3.500A) Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 4.172A pdb=" N ALA D2421 " --> pdb=" O HIS D2417 " (cutoff:3.500A) Processing helix chain 'D' and resid 2447 through 2462 removed outlier: 3.906A pdb=" N LEU D2451 " --> pdb=" O LYS D2447 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2472 removed outlier: 4.056A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2741 through 2746 removed outlier: 4.939A pdb=" N ILE D2746 " --> pdb=" O THR D2742 " (cutoff:3.500A) Processing helix chain 'D' and resid 2750 through 2774 removed outlier: 4.693A pdb=" N PHE D2754 " --> pdb=" O LYS D2750 " (cutoff:3.500A) Processing helix chain 'D' and resid 2793 through 2798 removed outlier: 4.024A pdb=" N PHE D2797 " --> pdb=" O PRO D2793 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER D2798 " --> pdb=" O TYR D2794 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2793 through 2798' Processing helix chain 'D' and resid 2799 through 2806 removed outlier: 5.222A pdb=" N GLU D2803 " --> pdb=" O GLU D2799 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) Processing helix chain 'D' and resid 2809 through 2820 removed outlier: 4.597A pdb=" N ALA D2815 " --> pdb=" O GLU D2811 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET D2816 " --> pdb=" O SER D2812 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2898 removed outlier: 3.594A pdb=" N MET D2874 " --> pdb=" O GLU D2870 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D2896 " --> pdb=" O GLN D2892 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D2897 " --> pdb=" O GLU D2893 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D2898 " --> pdb=" O LEU D2894 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2934 removed outlier: 3.834A pdb=" N LYS D2916 " --> pdb=" O THR D2912 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D2917 " --> pdb=" O ALA D2913 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG D2920 " --> pdb=" O LYS D2916 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU D2921 " --> pdb=" O ALA D2917 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN D2933 " --> pdb=" O PHE D2929 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY D2934 " --> pdb=" O LEU D2930 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3658 removed outlier: 4.453A pdb=" N LYS D3658 " --> pdb=" O LEU D3654 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3688 removed outlier: 4.934A pdb=" N ILE D3674 " --> pdb=" O GLU D3670 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D3678 " --> pdb=" O ILE D3674 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU D3684 " --> pdb=" O ALA D3680 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU D3685 " --> pdb=" O GLY D3681 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU D3686 " --> pdb=" O GLU D3682 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU D3687 " --> pdb=" O GLN D3683 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU D3688 " --> pdb=" O GLU D3684 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 removed outlier: 3.659A pdb=" N THR D3711 " --> pdb=" O ARG D3707 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3739 removed outlier: 3.798A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU D3736 " --> pdb=" O SER D3732 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3771 removed outlier: 4.057A pdb=" N GLN D3767 " --> pdb=" O LEU D3763 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D3768 " --> pdb=" O LEU D3764 " (cutoff:3.500A) Processing helix chain 'D' and resid 3775 through 3786 removed outlier: 5.292A pdb=" N VAL D3779 " --> pdb=" O ALA D3775 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA D3785 " --> pdb=" O GLN D3781 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N CYS D3786 " --> pdb=" O MET D3782 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.815A pdb=" N LYS D3799 " --> pdb=" O SER D3795 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D3800 " --> pdb=" O SER D3796 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D3801 " --> pdb=" O THR D3797 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 3.879A pdb=" N GLN D3813 " --> pdb=" O ASN D3809 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN D3814 " --> pdb=" O ALA D3810 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D3815 " --> pdb=" O GLU D3811 " (cutoff:3.500A) Processing helix chain 'D' and resid 3827 through 3839 removed outlier: 4.165A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3858 removed outlier: 3.836A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N MET D3858 " --> pdb=" O GLU D3854 " (cutoff:3.500A) Processing helix chain 'D' and resid 3879 through 3893 removed outlier: 4.809A pdb=" N ASP D3883 " --> pdb=" O GLU D3879 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D3884 " --> pdb=" O PHE D3880 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D3885 " --> pdb=" O THR D3881 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 6.544A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.790A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.695A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D3967 " --> pdb=" O ASN D3963 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 3.902A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER D3983 " --> pdb=" O SER D3979 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4003 removed outlier: 3.566A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET D3999 " --> pdb=" O VAL D3995 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET D4000 " --> pdb=" O PHE D3996 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.862A pdb=" N LEU D4013 " --> pdb=" O GLN D4009 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4056 removed outlier: 5.416A pdb=" N SER D4053 " --> pdb=" O VAL D4049 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASN D4054 " --> pdb=" O GLU D4050 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D4055 " --> pdb=" O SER D4051 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D4056 " --> pdb=" O SER D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4057 through 4072 removed outlier: 3.636A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4081 removed outlier: 4.097A pdb=" N GLN D4078 " --> pdb=" O SER D4074 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR D4080 " --> pdb=" O ALA D4076 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.991A pdb=" N PHE D4093 " --> pdb=" O SER D4089 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.112A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4154 removed outlier: 3.685A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D4131 " --> pdb=" O GLU D4127 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix removed outlier: 4.124A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.693A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 3.892A 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 removed outlier: 4.975A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D4206 " --> pdb=" O ARG D4202 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 removed outlier: 3.584A pdb=" N VAL D4222 " --> pdb=" O ILE D4218 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN D4223 " --> pdb=" O PHE D4219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU D4224 " --> pdb=" O ASP D4220 " (cutoff:3.500A) Processing helix chain 'D' and resid 4229 through 4253 removed outlier: 4.807A pdb=" N LEU D4233 " --> pdb=" O GLU D4229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D4234 " --> pdb=" O LYS D4230 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU D4253 " --> pdb=" O ALA D4249 " (cutoff:3.500A) Processing helix chain 'D' and resid 4542 through 4559 removed outlier: 4.815A pdb=" N VAL D4546 " --> pdb=" O GLY D4542 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN D4547 " --> pdb=" O GLU D4543 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.930A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4641 through 4684 removed outlier: 4.406A pdb=" N CYS D4645 " --> pdb=" O PRO D4641 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D4659 " --> pdb=" O PHE D4655 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 4.251A pdb=" N ILE D4670 " --> pdb=" O VAL D4666 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D4671 " --> pdb=" O PRO D4667 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4701 removed outlier: 3.550A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4729 removed outlier: 4.188A pdb=" N LYS D4723 " --> pdb=" O PHE D4719 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D4724 " --> pdb=" O VAL D4720 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4749 through 4756 removed outlier: 4.020A pdb=" N GLU D4755 " --> pdb=" O THR D4751 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG D4756 " --> pdb=" O ALA D4752 " (cutoff:3.500A) Processing helix chain 'D' and resid 4766 through 4771 removed outlier: 3.616A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.588A pdb=" N VAL D4782 " --> pdb=" O TRP D4778 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D4783 " --> pdb=" O LYS D4779 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.504A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 3.845A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY D4819 " --> pdb=" O ALA D4815 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL D4820 " --> pdb=" O ILE D4816 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 4.711A pdb=" N THR D4825 " --> pdb=" O LYS D4821 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.784A pdb=" N VAL D4838 " --> pdb=" O GLY D4834 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET D4839 " --> pdb=" O LYS D4835 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4889 Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 4.275A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4897 through 4902' Processing helix chain 'D' and resid 4909 through 4957 removed outlier: 4.465A pdb=" N ARG D4913 " --> pdb=" O TYR D4909 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D4925 " --> pdb=" O PHE D4921 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL D4926 " --> pdb=" O PHE D4922 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE D4927 " --> pdb=" O PHE D4923 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D4928 " --> pdb=" O VAL D4924 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU D4929 " --> pdb=" O ILE D4925 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D4951 " --> pdb=" O GLN D4947 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 4.638A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP D4969 " --> pdb=" O SER D4965 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4964 through 4969' Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 6.422A pdb=" N TYR D4988 " --> pdb=" O ALA D4984 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D4996 " --> pdb=" O LEU D4992 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5032 removed outlier: 6.456A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR D5032 " --> pdb=" O PHE D5028 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5027 through 5032' Processing helix chain 'D' and resid 3861 through 3867 removed outlier: 5.158A pdb=" N THR D3864 " --> pdb=" O GLU D3861 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL D3865 " --> pdb=" O ASP D3862 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D3866 " --> pdb=" O GLY D3863 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN D3867 " --> pdb=" O THR D3864 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3861 through 3867' Processing helix chain 'D' and resid 54 through 59 Proline residue: D 59 - end of helix No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.531A pdb=" N CYS A 36 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 52 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 14.372A 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: 6.924A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 105 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 119 through 122 removed outlier: 4.040A pdb=" N ASP A 134 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 229 through 233 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'A' and resid 288 through 291 removed outlier: 4.755A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL A 285 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N LEU A 259 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 313 through 318 removed outlier: 7.888A pdb=" N SER A 313 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 348 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 714 through 717 removed outlier: 3.564A pdb=" N TRP A 686 " --> pdb=" O TYR A 714 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 684 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 754 through 759 removed outlier: 5.826A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY A 660 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU A 665 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 829 through 832 removed outlier: 5.451A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A1088 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A1153 " --> pdb=" O TRP A1088 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A1090 " --> pdb=" O CYS A1151 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 891 through 894 removed outlier: 3.710A pdb=" N GLY A 894 " --> pdb=" O HIS A 904 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 1134 through 1138 removed outlier: 3.591A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A1237 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 2775 through 2778 removed outlier: 4.831A pdb=" N GLY A2778 " --> pdb=" O HIS A2788 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 4178 through 4184 removed outlier: 4.028A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 4580 through 4584 Processing sheet with id= 15, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.636A pdb=" N PHE B 48 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 38 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 36 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 52 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.403A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 205 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.505A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 105 " --> pdb=" O MET B 150 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 119 through 122 removed outlier: 4.026A pdb=" N ASP B 134 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 288 through 291 removed outlier: 4.759A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 285 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N LEU B 259 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 314 through 318 removed outlier: 6.461A pdb=" N VAL B 348 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 714 through 717 removed outlier: 3.524A pdb=" N TRP B 686 " --> pdb=" O TYR B 714 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 684 " --> pdb=" O PHE B 716 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 754 through 759 removed outlier: 4.033A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 748 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 750 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY B 660 " --> pdb=" O ALA B 750 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 829 through 832 removed outlier: 5.264A pdb=" N TYR B 829 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP B1088 " --> pdb=" O ILE B1153 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B1153 " --> pdb=" O TRP B1088 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B1151 " --> pdb=" O PHE B1090 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 891 through 894 removed outlier: 3.567A pdb=" N GLY B 894 " --> pdb=" O HIS B 904 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL B 896 " --> pdb=" O PRO B 905 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 1072 through 1076 removed outlier: 6.386A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY B1129 " --> pdb=" O PRO B1138 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG B1131 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER B1136 " --> pdb=" O ARG B1131 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1133 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 2775 through 2778 removed outlier: 4.821A pdb=" N GLY B2778 " --> pdb=" O HIS B2788 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 4178 through 4184 removed outlier: 3.658A pdb=" N PHE B4195 " --> pdb=" O GLY B4179 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 4580 through 4584 Processing sheet with id= 28, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.585A pdb=" N PHE C 48 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 38 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 52 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 14.382A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.638A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS C 105 " --> pdb=" O MET C 150 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 288 through 291 removed outlier: 4.758A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL C 285 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU C 259 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 314 through 318 removed outlier: 6.436A pdb=" N VAL C 348 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 681 through 686 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'C' and resid 754 through 759 removed outlier: 4.089A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS C 746 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP C 662 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU C 665 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 838 through 841 removed outlier: 5.777A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP C1088 " --> pdb=" O ILE C1153 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C1153 " --> pdb=" O TRP C1088 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C1090 " --> pdb=" O CYS C1151 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C1094 " --> pdb=" O ASP C1147 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 891 through 894 removed outlier: 3.628A pdb=" N GLY C 894 " --> pdb=" O HIS C 904 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 1134 through 1138 removed outlier: 3.615A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C1237 " --> pdb=" O ARG C1076 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 1254 through 1261 removed outlier: 7.244A pdb=" N HIS C1254 " --> pdb=" O ARG C1275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS C1269 " --> pdb=" O MET C1260 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 2775 through 2778 removed outlier: 4.835A pdb=" N GLY C2778 " --> pdb=" O HIS C2788 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 4178 through 4184 removed outlier: 3.591A pdb=" N PHE C4195 " --> pdb=" O GLY C4179 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 4580 through 4584 Processing sheet with id= 41, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.604A pdb=" N PHE D 48 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 52 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.865A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.648A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N HIS D 105 " --> pdb=" O MET D 150 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.008A pdb=" N ASP D 134 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 288 through 291 removed outlier: 4.771A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL D 285 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N LEU D 259 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'D' and resid 313 through 318 removed outlier: 7.916A pdb=" N SER D 313 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 348 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'D' and resid 714 through 717 removed outlier: 3.784A pdb=" N TRP D 686 " --> pdb=" O TYR D 714 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 716 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL D 684 " --> pdb=" O PHE D 716 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 743 through 750 removed outlier: 3.510A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 748 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 838 through 841 removed outlier: 5.726A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D1088 " --> pdb=" O ILE D1153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE D1153 " --> pdb=" O TRP D1088 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'D' and resid 891 through 894 removed outlier: 3.638A pdb=" N GLY D 894 " --> pdb=" O HIS D 904 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 3.644A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D1237 " --> pdb=" O ARG D1076 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 2775 through 2778 removed outlier: 4.823A pdb=" N GLY D2778 " --> pdb=" O HIS D2788 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'D' and resid 4178 through 4184 removed outlier: 3.605A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 4580 through 4584 4293 hydrogen bonds defined for protein. 12846 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: 64.80 Time building geometry restraints manager: 41.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 19795 1.32 - 1.44: 30125 1.44 - 1.57: 67270 1.57 - 1.69: 24 1.69 - 1.82: 998 Bond restraints: 118212 Sorted by residual: bond pdb=" C UNK A3450 " pdb=" N UNK A3451 " ideal model delta sigma weight residual 1.329 1.471 -0.142 1.40e-02 5.10e+03 1.02e+02 bond pdb=" C UNK A3449 " pdb=" N UNK A3450 " ideal model delta sigma weight residual 1.329 1.469 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" C ARG D4892 " pdb=" N ALA D4893 " ideal model delta sigma weight residual 1.335 1.250 0.084 1.36e-02 5.41e+03 3.85e+01 bond pdb=" O2B ACP C5101 " pdb=" PB ACP C5101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O2B ACP A5101 " pdb=" PB ACP A5101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.63e+01 ... (remaining 118207 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.87: 1901 104.87 - 112.67: 63466 112.67 - 120.48: 45667 120.48 - 128.28: 49414 128.28 - 136.09: 787 Bond angle restraints: 161235 Sorted by residual: angle pdb=" C GLU D4869 " pdb=" CA GLU D4869 " pdb=" CB GLU D4869 " ideal model delta sigma weight residual 116.54 105.04 11.50 1.15e+00 7.56e-01 1.00e+02 angle pdb=" O VAL D4891 " pdb=" C VAL D4891 " pdb=" N ARG D4892 " ideal model delta sigma weight residual 121.87 131.18 -9.31 9.70e-01 1.06e+00 9.21e+01 angle pdb=" C VAL C3751 " pdb=" N SER C3752 " pdb=" CA SER C3752 " ideal model delta sigma weight residual 120.82 107.66 13.16 1.47e+00 4.63e-01 8.01e+01 angle pdb=" C SER B3668 " pdb=" N PHE B3669 " pdb=" CA PHE B3669 " ideal model delta sigma weight residual 122.26 109.58 12.68 1.59e+00 3.96e-01 6.36e+01 angle pdb=" C UNK A3450 " pdb=" N UNK A3451 " pdb=" CA UNK A3451 " ideal model delta sigma weight residual 121.70 107.89 13.81 1.80e+00 3.09e-01 5.89e+01 ... (remaining 161230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 67521 27.47 - 54.95: 2722 54.95 - 82.42: 195 82.42 - 109.89: 16 109.89 - 137.36: 2 Dihedral angle restraints: 70456 sinusoidal: 22502 harmonic: 47954 Sorted by residual: dihedral pdb=" C ASP B4868 " pdb=" N ASP B4868 " pdb=" CA ASP B4868 " pdb=" CB ASP B4868 " ideal model delta harmonic sigma weight residual -122.60 -142.33 19.73 0 2.50e+00 1.60e-01 6.23e+01 dihedral pdb=" N ASP B4868 " pdb=" C ASP B4868 " pdb=" CA ASP B4868 " pdb=" CB ASP B4868 " ideal model delta harmonic sigma weight residual 122.80 140.10 -17.30 0 2.50e+00 1.60e-01 4.79e+01 dihedral pdb=" CD ARG D4892 " pdb=" NE ARG D4892 " pdb=" CZ ARG D4892 " pdb=" NH1 ARG D4892 " ideal model delta sinusoidal sigma weight residual 0.00 49.50 -49.50 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 70453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 18779 0.139 - 0.278: 97 0.278 - 0.416: 11 0.416 - 0.555: 0 0.555 - 0.694: 1 Chirality restraints: 18888 Sorted by residual: chirality pdb=" CA ASP B4868 " pdb=" N ASP B4868 " pdb=" C ASP B4868 " pdb=" CB ASP B4868 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA LYS D4875 " pdb=" N LYS D4875 " pdb=" C LYS D4875 " pdb=" CB LYS D4875 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB VAL B3751 " pdb=" CA VAL B3751 " pdb=" CG1 VAL B3751 " pdb=" CG2 VAL B3751 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 18885 not shown) Planarity restraints: 21196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D4892 " 0.829 9.50e-02 1.11e+02 3.71e-01 8.38e+01 pdb=" NE ARG D4892 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG D4892 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D4892 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D4892 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C4864 " -0.023 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C ASN C4864 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN C4864 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS C4865 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B3667 " -0.020 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C HIS B3667 " 0.075 2.00e-02 2.50e+03 pdb=" O HIS B3667 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B3668 " -0.026 2.00e-02 2.50e+03 ... (remaining 21193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1172 2.63 - 3.20: 104414 3.20 - 3.77: 176302 3.77 - 4.33: 211903 4.33 - 4.90: 343132 Nonbonded interactions: 836923 Sorted by model distance: nonbonded pdb=" O SER B4866 " pdb=" CG GLU B4867 " model vdw 2.069 3.440 nonbonded pdb=" O2B ACP D5101 " pdb=" O2G ACP D5101 " model vdw 2.069 3.040 nonbonded pdb=" O HIS B4812 " pdb=" ND1 HIS B4812 " model vdw 2.129 2.520 nonbonded pdb=" O GLU D4869 " pdb=" O ASP D4870 " model vdw 2.162 3.040 nonbonded pdb=" O UNK A3549 " pdb=" C UNK A3550 " model vdw 2.177 3.270 ... (remaining 836918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 162 or resid 164 throug \ h 167 or resid 170 through 749 or resid 751 through 754 or resid 756 through 365 \ 4 or (resid 3655 and (name N or name CA or name C or name O or name CB )) or res \ id 3656 through 3660 or (resid 3661 and (name N or name CA or name C or name O o \ r name CB )) or resid 3662 through 3664 or (resid 3665 and (name N or name CA or \ name C or name O or name CB )) or resid 3666 through 3760 or (resid 3761 and (n \ ame N or name CA or name C or name O or name CB )) or resid 3762 through 4025 or \ (resid 4026 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 027 through 4180 or resid 4182 through 4587 or resid 4626 through 4629 or (resid \ 4630 through 4631 and (name N or name CA or name C or name O or name CB )) or r \ esid 4632 through 4633 or (resid 4634 and (name N or name CA or name C or name O \ or name CB )) or resid 4635 through 4638 or (resid 4639 through 4640 and (name \ N or name CA or name C or name O or name CB )) or resid 4641 through 4763 or (re \ sid 4764 through 4765 and (name N or name CA or name C or name O or name CB )) o \ r resid 4766 through 4811 or resid 4813 through 4815 or resid 4817 through 4900 \ or resid 4902 through 4954 or (resid 4955 and (name N or name CA or name C or na \ me O or name CB )) or resid 4956 through 4980 or resid 4982 through 4983 or resi \ d 4985 through 5037 or resid 5101 through 5103)) selection = (chain 'B' and (resid 12 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 162 or resid 164 throug \ h 167 or resid 170 through 747 or (resid 748 and (name N or name CA or name C or \ name O or name CB )) or resid 749 or resid 751 through 754 or resid 756 through \ 3772 or (resid 3773 and (name N or name CA or name C or name O or name CB )) or \ resid 3774 through 4025 or (resid 4026 and (name N or name CA or name C or name \ O or name CB )) or resid 4027 through 4180 or resid 4182 through 4580 or (resid \ 4581 and (name N or name CA or name C or name O or name CB )) or resid 4582 thr \ ough 4587 or resid 4626 through 4629 or (resid 4630 through 4631 and (name N or \ name CA or name C or name O or name CB )) or resid 4632 through 4748 or (resid 4 \ 749 and (name N or name CA or name C or name O or name CB )) or resid 4750 throu \ gh 4754 or (resid 4755 through 4757 and (name N or name CA or name C or name O o \ r name CB )) or resid 4758 through 4811 or resid 4813 through 4815 or resid 4817 \ through 4863 or (resid 4864 and (name N or name CA or name C or name O or name \ CB )) or resid 4865 through 4900 or resid 4902 through 4907 or (resid 4908 and ( \ name N or name CA or name C or name O or name CB )) or resid 4909 through 4980 o \ r resid 4982 through 4983 or resid 4985 through 5037 or resid 5101 through 5103) \ ) selection = (chain 'C' and (resid 12 through 75 or (resid 76 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 162 or resid 164 throug \ h 167 or resid 170 through 747 or (resid 748 and (name N or name CA or name C or \ name O or name CB )) or resid 749 or resid 751 through 754 or resid 756 through \ 1784 or resid 1791 through 2820 or resid 2868 through 3612 or resid 3639 throug \ h 3654 or (resid 3655 and (name N or name CA or name C or name O or name CB )) o \ r resid 3656 through 3660 or (resid 3661 and (name N or name CA or name C or nam \ e O or name CB )) or resid 3662 through 3664 or (resid 3665 and (name N or name \ CA or name C or name O or name CB )) or resid 3666 through 3760 or (resid 3761 a \ nd (name N or name CA or name C or name O or name CB )) or resid 3762 through 37 \ 72 or (resid 3773 and (name N or name CA or name C or name O or name CB )) or re \ sid 3774 through 4025 or (resid 4026 and (name N or name CA or name C or name O \ or name CB )) or resid 4027 through 4180 or resid 4182 through 4580 or (resid 45 \ 81 and (name N or name CA or name C or name O or name CB )) or resid 4582 throug \ h 4630 or (resid 4631 and (name N or name CA or name C or name O or name CB )) o \ r resid 4632 through 4633 or (resid 4634 and (name N or name CA or name C or nam \ e O or name CB )) or resid 4635 through 4638 or (resid 4639 through 4640 and (na \ me N or name CA or name C or name O or name CB )) or resid 4641 through 4754 or \ (resid 4755 through 4757 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4758 through 4811 or resid 4813 through 4815 or resid 4817 through 48 \ 63 or (resid 4864 and (name N or name CA or name C or name O or name CB )) or re \ sid 4865 through 4900 or resid 4902 through 4907 or (resid 4908 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4909 through 4954 or (resid 49 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 4956 throug \ h 4980 or resid 4982 through 4983 or resid 4985 through 5037 or resid 5101 throu \ gh 5103)) selection = (chain 'D' and (resid 12 through 162 or resid 164 through 167 or resid 170 throu \ gh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 or resid 751 through 754 or resid 756 through 3654 or (resid 3655 and \ (name N or name CA or name C or name O or name CB )) or resid 3656 through 3660 \ or (resid 3661 and (name N or name CA or name C or name O or name CB )) or resi \ d 3662 through 3664 or (resid 3665 and (name N or name CA or name C or name O or \ name CB )) or resid 3666 through 3760 or (resid 3761 and (name N or name CA or \ name C or name O or name CB )) or resid 3762 through 3772 or (resid 3773 and (na \ me N or name CA or name C or name O or name CB )) or resid 3774 through 4180 or \ resid 4182 through 4580 or (resid 4581 and (name N or name CA or name C or name \ O or name CB )) or resid 4582 through 4629 or (resid 4630 through 4631 and (name \ N or name CA or name C or name O or name CB )) or resid 4632 through 4633 or (r \ esid 4634 and (name N or name CA or name C or name O or name CB )) or resid 4635 \ through 4637 or (resid 4638 through 4640 and (name N or name CA or name C or na \ me O or name CB )) or resid 4641 through 4811 or resid 4813 through 4815 or resi \ d 4817 through 4900 or resid 4902 through 4907 or (resid 4908 and (name N or nam \ e CA or name C or name O or name CB )) or resid 4909 through 4980 or resid 4982 \ through 4983 or resid 4985 through 5037 or resid 5101 through 5103)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 Mg 5 5.21 5 S 625 5.16 5 C 73496 2.51 5 N 20570 2.21 5 O 21345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.110 Extract box with map and model: 17.140 Check model and map are aligned: 1.250 Convert atoms to be neutral: 0.730 Process input model: 290.280 Find NCS groups from input model: 12.580 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.142 118212 Z= 0.205 Angle : 0.643 14.274 161235 Z= 0.362 Chirality : 0.039 0.694 18888 Planarity : 0.005 0.371 21196 Dihedral : 13.931 137.363 39246 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.77 % Favored : 92.01 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.08), residues: 12775 helix: 1.77 (0.07), residues: 5687 sheet: -0.52 (0.19), residues: 799 loop : -1.83 (0.08), residues: 6289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1243 time to evaluate : 8.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 36 residues processed: 1322 average time/residue: 0.9818 time to fit residues: 2396.4924 Evaluate side-chains 972 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 936 time to evaluate : 8.687 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.8722 time to fit residues: 69.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1928 GLN A1953 HIS A2041 HIS ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN A3809 ASN A3850 GLN ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3994 HIS ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4714 ASN ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B 938 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN B1691 GLN B1693 GLN ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 HIS ** B2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2041 HIS ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2161 GLN ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3845 ASN ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3895 HIS ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4714 ASN ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 GLN C1928 GLN C1953 HIS ** C2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2041 HIS ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2161 GLN ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3845 ASN ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4714 ASN ** C4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4973 HIS ** C4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1691 GLN D1928 GLN D1953 HIS ** D2029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 HIS ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN D3845 ASN ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4714 ASN ** D4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.436 118212 Z= 2.739 Angle : 3.049 40.210 161235 Z= 1.577 Chirality : 0.120 0.675 18888 Planarity : 0.021 0.206 21196 Dihedral : 12.718 123.860 17398 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 116.33 Ramachandran Plot: Outliers : 4.10 % Allowed : 23.86 % Favored : 72.04 % Rotamer Outliers : 14.08 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.21 % Twisted General : 2.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.05 (0.05), residues: 12775 helix: -4.03 (0.04), residues: 5557 sheet: -2.24 (0.19), residues: 701 loop : -4.31 (0.06), residues: 6517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2033 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1384 poor density : 649 time to evaluate : 8.852 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 outliers start: 1384 outliers final: 766 residues processed: 2002 average time/residue: 0.9747 time to fit residues: 3624.5963 Evaluate side-chains 1376 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 766 poor density : 610 time to evaluate : 8.914 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 766 outliers final: 10 residues processed: 766 average time/residue: 0.8221 time to fit residues: 1215.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4973 HIS ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 ASN ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2029 GLN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3960 GLN ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4803 HIS ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 ASN ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2029 GLN ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4728 HIS C4803 HIS ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2029 GLN ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2441 HIS D2773 ASN ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3850 GLN D3889 GLN ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4728 HIS D4803 HIS D4886 HIS ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.449 118212 Z= 2.710 Angle : 2.998 36.932 161235 Z= 1.549 Chirality : 0.119 0.695 18888 Planarity : 0.021 0.214 21196 Dihedral : 14.148 122.725 17398 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 127.48 Ramachandran Plot: Outliers : 3.40 % Allowed : 35.21 % Favored : 61.39 % Rotamer Outliers : 10.30 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.42 % Twisted General : 4.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.94 (0.05), residues: 12775 helix: -4.62 (0.03), residues: 5597 sheet: -3.23 (0.18), residues: 712 loop : -4.88 (0.06), residues: 6466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1013 poor density : 609 time to evaluate : 8.746 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 outliers start: 1013 outliers final: 726 residues processed: 1594 average time/residue: 0.8863 time to fit residues: 2622.4075 Evaluate side-chains 1298 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 726 poor density : 572 time to evaluate : 8.835 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 726 outliers final: 6 residues processed: 726 average time/residue: 0.8849 time to fit residues: 1248.5606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1645 ASN ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** A4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1693 GLN ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4691 GLN ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 HIS ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4043 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.8720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.494 118212 Z= 2.728 Angle : 3.043 36.785 161235 Z= 1.566 Chirality : 0.121 0.751 18888 Planarity : 0.021 0.234 21196 Dihedral : 14.837 130.261 17398 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 133.44 Ramachandran Plot: Outliers : 3.23 % Allowed : 39.14 % Favored : 57.63 % Rotamer Outliers : 9.23 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.45 % Twisted General : 5.84 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.20 (0.05), residues: 12775 helix: -4.72 (0.03), residues: 5630 sheet: -3.57 (0.17), residues: 663 loop : -5.11 (0.06), residues: 6482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 907 poor density : 567 time to evaluate : 10.620 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 outliers start: 907 outliers final: 655 residues processed: 1454 average time/residue: 0.9121 time to fit residues: 2457.1737 Evaluate side-chains 1197 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 655 poor density : 542 time to evaluate : 9.005 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 655 outliers final: 2 residues processed: 655 average time/residue: 0.8326 time to fit residues: 1054.0331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 GLN ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4973 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 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 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** 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 576 ASN ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4005 GLN ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.481 118212 Z= 2.732 Angle : 3.033 35.825 161235 Z= 1.565 Chirality : 0.122 0.718 18888 Planarity : 0.021 0.249 21196 Dihedral : 15.201 135.170 17398 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 135.10 Ramachandran Plot: Outliers : 3.15 % Allowed : 40.95 % Favored : 55.89 % Rotamer Outliers : 6.60 % Cbeta Deviations : 0.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.80 % Twisted General : 6.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.33 (0.05), residues: 12775 helix: -4.75 (0.03), residues: 5636 sheet: -3.67 (0.18), residues: 668 loop : -5.26 (0.06), residues: 6471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 649 poor density : 559 time to evaluate : 8.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 649 outliers final: 528 residues processed: 1196 average time/residue: 0.8996 time to fit residues: 1994.7580 Evaluate side-chains 1048 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 528 poor density : 520 time to evaluate : 8.691 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 528 outliers final: 2 residues processed: 528 average time/residue: 0.8334 time to fit residues: 853.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 ASN ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3761 GLN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3978 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A4947 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS B 904 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1949 GLN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2773 ASN ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3889 GLN ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 79 GLN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2253 HIS ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4886 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 HIS ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2773 ASN ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.9376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.470 118212 Z= 2.738 Angle : 3.044 36.725 161235 Z= 1.570 Chirality : 0.124 0.990 18888 Planarity : 0.021 0.274 21196 Dihedral : 15.416 131.841 17398 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 135.13 Ramachandran Plot: Outliers : 3.18 % Allowed : 42.33 % Favored : 54.49 % Rotamer Outliers : 4.90 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.80 % Twisted General : 6.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.42 (0.05), residues: 12775 helix: -4.75 (0.03), residues: 5681 sheet: -3.97 (0.17), residues: 649 loop : -5.35 (0.05), residues: 6445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 482 poor density : 563 time to evaluate : 8.632 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 outliers start: 482 outliers final: 382 residues processed: 1037 average time/residue: 0.9995 time to fit residues: 1928.7150 Evaluate side-chains 909 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 527 time to evaluate : 8.953 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 382 outliers final: 1 residues processed: 382 average time/residue: 0.8792 time to fit residues: 656.2620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2773 ASN ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2933 ASN ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2007 ASN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4728 HIS ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 938 HIS ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2007 ASN ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2007 ASN ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.9561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.471 118212 Z= 2.745 Angle : 3.061 36.642 161235 Z= 1.579 Chirality : 0.126 1.399 18888 Planarity : 0.021 0.221 21196 Dihedral : 15.587 117.702 17398 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 135.12 Ramachandran Plot: Outliers : 3.15 % Allowed : 42.92 % Favored : 53.93 % Rotamer Outliers : 2.52 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.30 % Twisted General : 7.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.46 (0.05), residues: 12775 helix: -4.77 (0.03), residues: 5674 sheet: -3.99 (0.17), residues: 606 loop : -5.39 (0.05), residues: 6495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 556 time to evaluate : 8.984 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 outliers start: 248 outliers final: 194 residues processed: 803 average time/residue: 0.9842 time to fit residues: 1462.4188 Evaluate side-chains 712 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 518 time to evaluate : 8.920 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 194 outliers final: 1 residues processed: 194 average time/residue: 0.8993 time to fit residues: 344.5400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3889 GLN ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1158 ASN ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3850 GLN ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 911 HIS ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1158 ASN ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2253 HIS ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS D 911 HIS ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 ASN ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3978 GLN D4005 GLN ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4805 ASN ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.9723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.468 118212 Z= 2.754 Angle : 3.083 35.581 161235 Z= 1.592 Chirality : 0.129 2.301 18888 Planarity : 0.021 0.247 21196 Dihedral : 15.790 128.926 17398 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 135.41 Ramachandran Plot: Outliers : 3.26 % Allowed : 43.42 % Favored : 53.32 % Rotamer Outliers : 0.85 % Cbeta Deviations : 1.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.81 % Twisted General : 7.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.49 (0.05), residues: 12775 helix: -4.77 (0.03), residues: 5611 sheet: -4.03 (0.17), residues: 637 loop : -5.43 (0.05), residues: 6527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 550 time to evaluate : 8.624 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 outliers start: 84 outliers final: 48 residues processed: 632 average time/residue: 0.9812 time to fit residues: 1143.1377 Evaluate side-chains 564 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 516 time to evaluate : 8.561 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.8973 time to fit residues: 93.7766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 GLN ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3699 HIS ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4946 GLN ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2933 ASN B3699 HIS ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4078 GLN ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2773 ASN ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3699 HIS ** C3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 ASN ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3699 HIS ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4078 GLN ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4805 ASN ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.9857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.474 118212 Z= 2.762 Angle : 3.093 36.737 161235 Z= 1.598 Chirality : 0.130 1.749 18888 Planarity : 0.022 0.306 21196 Dihedral : 15.936 138.752 17398 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 135.54 Ramachandran Plot: Outliers : 3.33 % Allowed : 43.94 % Favored : 52.73 % Rotamer Outliers : 0.05 % Cbeta Deviations : 1.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.98 % Twisted General : 7.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.52 (0.04), residues: 12775 helix: -4.78 (0.03), residues: 5640 sheet: -4.04 (0.17), residues: 651 loop : -5.46 (0.05), residues: 6484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 552 time to evaluate : 8.445 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 outliers start: 5 outliers final: 1 residues processed: 556 average time/residue: 0.9643 time to fit residues: 992.1336 Evaluate side-chains 520 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 519 time to evaluate : 8.951 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8299 time to fit residues: 13.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2169 GLN ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4005 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4728 HIS ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 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 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2032 GLN ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4805 ASN ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.9959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.470 118212 Z= 2.769 Angle : 3.109 37.070 161235 Z= 1.608 Chirality : 0.133 3.188 18888 Planarity : 0.022 0.259 21196 Dihedral : 16.043 147.123 17398 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 136.05 Ramachandran Plot: Outliers : 3.38 % Allowed : 44.34 % Favored : 52.28 % Rotamer Outliers : 0.02 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.99 % Twisted General : 7.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.54 (0.04), residues: 12775 helix: -4.78 (0.03), residues: 5618 sheet: -4.05 (0.17), residues: 675 loop : -5.49 (0.05), residues: 6482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25550 Ramachandran restraints generated. 12775 Oldfield, 0 Emsley, 12775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 541 time to evaluate : 8.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 542 average time/residue: 0.9439 time to fit residues: 944.3532 Evaluate side-chains 512 residues out of total 11192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 8.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.1160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS ** B1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1825 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 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 576 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3889 GLN ** C3896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 938 HIS ** D1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2253 HIS ** D2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4805 ASN ** D4832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062655 restraints weight = 674549.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061713 restraints weight = 1004913.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062368 restraints weight = 769187.141| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 1.0059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.475 118212 Z= 2.767 Angle : 3.112 35.993 161235 Z= 1.609 Chirality : 0.132 2.178 18888 Planarity : 0.022 0.252 21196 Dihedral : 16.121 154.148 17398 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 136.08 Ramachandran Plot: Outliers : 3.40 % Allowed : 44.50 % Favored : 52.10 % Rotamer Outliers : 0.03 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.50 % Twisted General : 7.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.55 (0.04), residues: 12775 helix: -4.79 (0.03), residues: 5599 sheet: -4.05 (0.17), residues: 654 loop : -5.50 (0.05), residues: 6522 =============================================================================== Job complete usr+sys time: 56148.53 seconds wall clock time: 956 minutes 0.74 seconds (57360.74 seconds total)