Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 08:44:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umz_26610/07_2023/7umz_26610_neut_updated.pdb" } resolution = 3.09 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 20 5.49 5 Mg 13 5.21 5 S 652 5.16 5 C 70228 2.51 5 N 19638 2.21 5 O 20882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2209": "OE1" <-> "OE2" Residue "A GLU 2296": "OE1" <-> "OE2" Residue "A GLU 2449": "OE1" <-> "OE2" Residue "A GLU 4116": "OE1" <-> "OE2" Residue "A GLU 4165": "OE1" <-> "OE2" Residue "A GLU 4244": "OE1" <-> "OE2" Residue "A GLU 4640": "OE1" <-> "OE2" Residue "A GLU 4676": "OE1" <-> "OE2" Residue "A GLU 4690": "OE1" <-> "OE2" Residue "A GLU 4739": "OE1" <-> "OE2" Residue "A GLU 4902": "OE1" <-> "OE2" Residue "A GLU 5002": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2209": "OE1" <-> "OE2" Residue "B GLU 2296": "OE1" <-> "OE2" Residue "B GLU 2449": "OE1" <-> "OE2" Residue "B GLU 4116": "OE1" <-> "OE2" Residue "B GLU 4165": "OE1" <-> "OE2" Residue "B GLU 4244": "OE1" <-> "OE2" Residue "B GLU 4676": "OE1" <-> "OE2" Residue "B GLU 4690": "OE1" <-> "OE2" Residue "B GLU 4739": "OE1" <-> "OE2" Residue "B GLU 4902": "OE1" <-> "OE2" Residue "B GLU 4942": "OE1" <-> "OE2" Residue "B GLU 5002": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2209": "OE1" <-> "OE2" Residue "C GLU 2296": "OE1" <-> "OE2" Residue "C GLU 2449": "OE1" <-> "OE2" Residue "C GLU 3879": "OE1" <-> "OE2" Residue "C GLU 4116": "OE1" <-> "OE2" Residue "C GLU 4165": "OE1" <-> "OE2" Residue "C GLU 4244": "OE1" <-> "OE2" Residue "C TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4676": "OE1" <-> "OE2" Residue "C GLU 4690": "OE1" <-> "OE2" Residue "C GLU 4739": "OE1" <-> "OE2" Residue "C GLU 4902": "OE1" <-> "OE2" Residue "C GLU 5002": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 1044": "NH1" <-> "NH2" Residue "D GLU 2209": "OE1" <-> "OE2" Residue "D GLU 2296": "OE1" <-> "OE2" Residue "D GLU 2449": "OE1" <-> "OE2" Residue "D GLU 3872": "OE1" <-> "OE2" Residue "D GLU 4116": "OE1" <-> "OE2" Residue "D GLU 4165": "OE1" <-> "OE2" Residue "D GLU 4244": "OE1" <-> "OE2" Residue "D GLU 4676": "OE1" <-> "OE2" Residue "D GLU 4690": "OE1" <-> "OE2" Residue "D GLU 4739": "OE1" <-> "OE2" Residue "D GLU 4902": "OE1" <-> "OE2" Residue "D GLU 4942": "OE1" <-> "OE2" Residue "D GLU 5002": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 111437 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 27761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3927, 27761 Classifications: {'peptide': 3927} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1081} Link IDs: {'PTRANS': 141, 'TRANS': 3785} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2809 Unresolved non-hydrogen angles: 3939 Unresolved non-hydrogen dihedrals: 1826 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 33, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 8, 'HIS:plan': 12, 'PHE:plan': 15, 'GLU:plan': 62, 'ASP:plan': 27, 'UNK:plan-1': 798} Unresolved non-hydrogen planarities: 1673 Chain: "B" Number of atoms: 27785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3927, 27785 Classifications: {'peptide': 3927} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1073} Link IDs: {'PTRANS': 141, 'TRANS': 3785} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2783 Unresolved non-hydrogen angles: 3903 Unresolved non-hydrogen dihedrals: 1805 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 32, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 8, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 63, 'ASP:plan': 23, 'UNK:plan-1': 798} Unresolved non-hydrogen planarities: 1658 Chain: "C" Number of atoms: 27693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3927, 27693 Classifications: {'peptide': 3927} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1097} Link IDs: {'PTRANS': 141, 'TRANS': 3785} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2879 Unresolved non-hydrogen angles: 4027 Unresolved non-hydrogen dihedrals: 1882 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 35, 'TYR:plan': 12, 'ASN:plan1': 14, 'TRP:plan': 8, 'HIS:plan': 13, 'PHE:plan': 16, 'GLU:plan': 65, 'ASP:plan': 25, 'UNK:plan-1': 798} Unresolved non-hydrogen planarities: 1723 Chain: "D" Number of atoms: 27677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3927, 27677 Classifications: {'peptide': 3927} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1098} Link IDs: {'PTRANS': 141, 'TRANS': 3785} Chain breaks: 23 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2896 Unresolved non-hydrogen angles: 4045 Unresolved non-hydrogen dihedrals: 1901 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 36, 'TYR:plan': 13, 'ASN:plan1': 15, 'TRP:plan': 8, 'HIS:plan': 12, 'PHE:plan': 17, 'GLU:plan': 67, 'ASP:plan': 25, 'UNK:plan-1': 798} Unresolved non-hydrogen planarities: 1747 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 129 Unusual residues: {' MG': 4, ' ZN': 1, 'ACP': 1, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 128 Unusual residues: {' MG': 3, ' ZN': 1, 'ACP': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 128 Unusual residues: {' MG': 3, ' ZN': 1, 'ACP': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 128 Unusual residues: {' MG': 3, ' ZN': 1, 'ACP': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27093 SG CYS A4958 157.050 174.724 88.324 1.00 38.51 S ATOM 27118 SG CYS A4961 159.679 175.458 91.850 1.00 47.22 S ATOM 54878 SG CYS B4958 174.754 157.708 88.314 1.00 38.51 S ATOM 54903 SG CYS B4961 175.475 155.053 91.871 1.00 47.22 S ATOM 82571 SG CYS C4958 157.691 140.010 88.313 1.00 38.51 S ATOM 82596 SG CYS C4961 155.041 139.300 91.880 1.00 47.22 S ATOM A07WO SG CYS D4958 140.004 157.061 88.309 1.00 38.51 S ATOM A07XD SG CYS D4961 139.296 159.739 91.892 1.00 47.22 S Time building chain proxies: 38.02, per 1000 atoms: 0.34 Number of scatterers: 111437 At special positions: 0 Unit cell: (315.62, 315.62, 193.5, 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 652 16.00 P 20 15.00 Mg 13 11.99 O 20882 8.00 N 19638 7.00 C 70228 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: 32.75 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal 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 A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " Number of angles added : 8 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 29720 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: 460 helices and 68 sheets defined 54.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.63 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.784A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.579A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.921A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 422 removed outlier: 3.675A pdb=" N GLN A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.511A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.692A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.530A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 494 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 6.368A pdb=" N PHE A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 507' Processing helix chain 'A' and resid 508 through 531 removed outlier: 4.563A pdb=" N ALA A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.651A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.237A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.378A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.039A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 removed outlier: 4.512A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.666A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.581A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 890 removed outlier: 3.677A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 933 removed outlier: 3.811A pdb=" N LEU A 933 " --> pdb=" O LEU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 951 removed outlier: 5.689A pdb=" N LYS A 951 " --> pdb=" O GLU A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 961 removed outlier: 3.680A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 956 through 961' Processing helix chain 'A' and resid 978 through 1003 removed outlier: 3.996A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1039 Processing helix chain 'A' and resid 1041 through 1050 Processing helix chain 'A' and resid 1574 through 1580 removed outlier: 3.691A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1574 through 1580' Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.210A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 4.139A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 removed outlier: 4.323A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA A1701 " --> pdb=" O ALA A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 6.650A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 removed outlier: 4.317A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 4.304A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 4.121A pdb=" N LEU A1807 " --> pdb=" O PRO A1803 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1868 removed outlier: 4.699A pdb=" N GLN A1861 " --> pdb=" O GLU A1857 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A1862 " --> pdb=" O ASP A1858 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS A1864 " --> pdb=" O LYS A1860 " (cutoff:3.500A) Proline residue: A1868 - end of helix Processing helix chain 'A' and resid 1925 through 1930 removed outlier: 5.739A pdb=" N LYS A1930 " --> pdb=" O LEU A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1984 removed outlier: 7.046A pdb=" N LEU A1937 " --> pdb=" O GLU A1933 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A1980 " --> pdb=" O ARG A1976 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N MET A1981 " --> pdb=" O TYR A1977 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA A1983 " --> pdb=" O LEU A1979 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 1998 Processing helix chain 'A' and resid 2001 through 2011 Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 3.896A pdb=" N ARG A2028 " --> pdb=" O PRO A2024 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 4.004A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.523A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.459A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 3.625A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2189 removed outlier: 3.636A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2194 through 2202 removed outlier: 4.102A pdb=" N MET A2198 " --> pdb=" O HIS A2194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A2202 " --> pdb=" O MET A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2216 Processing helix chain 'A' and resid 2218 through 2226 removed outlier: 5.125A pdb=" N PHE A2225 " --> pdb=" O LYS A2221 " (cutoff:3.500A) Proline residue: A2226 - end of helix Processing helix chain 'A' and resid 2227 through 2244 removed outlier: 6.481A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2254 removed outlier: 4.135A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2264 removed outlier: 3.659A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.664A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 removed outlier: 3.834A pdb=" N ALA A2287 " --> pdb=" O ASN A2283 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A2288 " --> pdb=" O ASN A2284 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA A2289 " --> pdb=" O GLU A2285 " (cutoff:3.500A) Processing helix chain 'A' and resid 2293 through 2309 removed outlier: 5.125A pdb=" N GLN A2308 " --> pdb=" O GLY A2304 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.731A pdb=" N LEU A2314 " --> pdb=" O CYS A2310 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A2316 " --> pdb=" O MET A2312 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A2317 " --> pdb=" O LEU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2341 removed outlier: 5.025A pdb=" N GLY A2328 " --> pdb=" O ASN A2324 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A2329 " --> pdb=" O PRO A2325 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG A2330 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR A2331 " --> pdb=" O GLY A2327 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL A2341 " --> pdb=" O PHE A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 4.040A 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 Processing helix chain 'A' and resid 2375 through 2390 removed outlier: 4.724A pdb=" N ALA A2379 " --> pdb=" O GLY A2375 " (cutoff:3.500A) Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 Processing helix chain 'A' and resid 2441 through 2447 removed outlier: 3.736A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2448 through 2462 removed outlier: 3.806A pdb=" N VAL A2461 " --> pdb=" O LEU A2457 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2463 through 2473 removed outlier: 7.016A pdb=" N VAL A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 3645 through 3662 removed outlier: 4.049A pdb=" N ALA A3649 " --> pdb=" O PRO A3645 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3681 removed outlier: 4.238A pdb=" N ALA A3680 " --> pdb=" O ASP A3676 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3740 removed outlier: 5.291A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU A3737 " --> pdb=" O CYS A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 3.675A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A3772 " --> pdb=" O SER A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.700A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 6.886A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3856 removed outlier: 3.649A pdb=" N ALA A3853 " --> pdb=" O ARG A3849 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A3854 " --> pdb=" O GLN A3850 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3871 Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 4.068A pdb=" N THR A3881 " --> pdb=" O ASP A3877 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A3882 " --> pdb=" O ASP A3878 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 3.774A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.654A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4004 removed outlier: 3.628A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A3991 " --> pdb=" O ASP A3987 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.624A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 4.971A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 3.851A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4099 removed outlier: 3.772A pdb=" N SER A4099 " --> pdb=" O LYS A4095 " (cutoff:3.500A) Processing helix chain 'A' and resid 4107 through 4115 removed outlier: 4.220A pdb=" N LEU A4111 " --> pdb=" O GLU A4107 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4129 Processing helix chain 'A' and resid 4134 through 4154 removed outlier: 4.004A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A4154 " --> pdb=" O LEU A4150 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.559A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.912A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4540 through 4559 removed outlier: 4.214A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.381A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4637 through 4683 Proline residue: A4641 - end of helix removed outlier: 4.265A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4709 removed outlier: 3.781A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Proline residue: A4709 - end of helix Processing helix chain 'A' and resid 4719 through 4729 Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 3.504A pdb=" N GLY A4742 " --> pdb=" O ALA A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4750 removed outlier: 3.756A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4765 through 4771 removed outlier: 4.254A pdb=" N MET A4769 " --> pdb=" O LEU A4765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.775A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4805 removed outlier: 3.824A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A4805 " --> pdb=" O LEU A4801 " (cutoff:3.500A) Processing helix chain 'A' and resid 4807 through 4820 removed outlier: 4.907A pdb=" N ALA A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.900A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.622A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.960A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4928 through 4957 removed outlier: 3.658A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.927A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 5.636A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'A' and resid 4685 through 4690 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.784A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.579A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.921A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 422 removed outlier: 3.719A pdb=" N GLN B 399 " --> pdb=" O GLN B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.509A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.691A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.530A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 494 " --> pdb=" O CYS B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 6.369A pdb=" N PHE B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 507' Processing helix chain 'B' and resid 508 through 531 removed outlier: 4.562A pdb=" N ALA B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.652A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 4.236A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.379A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.038A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 4.511A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 3.667A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 3.582A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 890 removed outlier: 3.677A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 933 removed outlier: 3.812A pdb=" N LEU B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 removed outlier: 5.688A pdb=" N LYS B 951 " --> pdb=" O GLU B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 961 removed outlier: 3.680A pdb=" N MET B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N MET B 961 " --> pdb=" O LYS B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 956 through 961' Processing helix chain 'B' and resid 978 through 1003 removed outlier: 3.996A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1039 Processing helix chain 'B' and resid 1041 through 1050 Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 3.692A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1574 through 1580' Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.210A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 Processing helix chain 'B' and resid 1678 through 1690 removed outlier: 4.139A pdb=" N ASP B1690 " --> pdb=" O CYS B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1701 removed outlier: 4.322A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ALA B1701 " --> pdb=" O ALA B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 6.650A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 4.317A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 4.304A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 4.121A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1868 removed outlier: 4.699A pdb=" N GLN B1861 " --> pdb=" O GLU B1857 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B1862 " --> pdb=" O ASP B1858 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS B1864 " --> pdb=" O LYS B1860 " (cutoff:3.500A) Proline residue: B1868 - end of helix Processing helix chain 'B' and resid 1925 through 1930 removed outlier: 5.739A pdb=" N LYS B1930 " --> pdb=" O LEU B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1984 removed outlier: 7.047A pdb=" N LEU B1937 " --> pdb=" O GLU B1933 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B1980 " --> pdb=" O ARG B1976 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N MET B1981 " --> pdb=" O TYR B1977 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG B1982 " --> pdb=" O ALA B1978 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA B1983 " --> pdb=" O LEU B1979 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 1998 Processing helix chain 'B' and resid 2001 through 2011 Processing helix chain 'B' and resid 2024 through 2043 removed outlier: 3.896A pdb=" N ARG B2028 " --> pdb=" O PRO B2024 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 4.003A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.524A 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: 5.459A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 3.625A pdb=" N THR B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2189 removed outlier: 3.636A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS B2189 " --> pdb=" O ILE B2185 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2202 removed outlier: 4.102A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B2202 " --> pdb=" O MET B2198 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2216 Processing helix chain 'B' and resid 2218 through 2226 removed outlier: 5.126A pdb=" N PHE B2225 " --> pdb=" O LYS B2221 " (cutoff:3.500A) Proline residue: B2226 - end of helix Processing helix chain 'B' and resid 2227 through 2244 removed outlier: 6.480A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2254 removed outlier: 4.384A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2255 through 2264 removed outlier: 3.659A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 3.665A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2290 removed outlier: 4.677A pdb=" N ALA B2287 " --> pdb=" O ASN B2283 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B2288 " --> pdb=" O ASN B2284 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B2289 " --> pdb=" O GLU B2285 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2283 through 2290' Processing helix chain 'B' and resid 2293 through 2309 removed outlier: 5.125A pdb=" N GLN B2308 " --> pdb=" O GLY B2304 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.731A pdb=" N LEU B2314 " --> pdb=" O CYS B2310 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B2316 " --> pdb=" O MET B2312 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY B2317 " --> pdb=" O LEU B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2341 removed outlier: 5.024A pdb=" N GLY B2328 " --> pdb=" O ASN B2324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B2329 " --> pdb=" O PRO B2325 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG B2330 " --> pdb=" O CYS B2326 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B2341 " --> pdb=" O PHE B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 4.040A 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 removed outlier: 4.725A pdb=" N ALA B2379 " --> pdb=" O GLY B2375 " (cutoff:3.500A) Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 Processing helix chain 'B' and resid 2441 through 2447 removed outlier: 3.737A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B2446 " --> pdb=" O LEU B2442 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2462 removed outlier: 3.806A pdb=" N VAL B2461 " --> pdb=" O LEU B2457 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2463 through 2473 removed outlier: 7.016A pdb=" N VAL B2467 " --> pdb=" O LEU B2463 " (cutoff:3.500A) Proline residue: B2473 - end of helix Processing helix chain 'B' and resid 3645 through 3662 removed outlier: 6.351A pdb=" N ALA B3649 " --> pdb=" O PRO B3645 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B3662 " --> pdb=" O LYS B3658 " (cutoff:3.500A) Processing helix chain 'B' and resid 3668 through 3681 removed outlier: 6.442A pdb=" N ARG B3672 " --> pdb=" O SER B3668 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B3680 " --> pdb=" O ASP B3676 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 Processing helix chain 'B' and resid 3719 through 3740 removed outlier: 5.292A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU B3737 " --> pdb=" O CYS B3733 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 3.675A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B3772 " --> pdb=" O SER B3768 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 3.700A pdb=" N CYS B3786 " --> pdb=" O MET B3782 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 6.886A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3856 removed outlier: 3.902A pdb=" N ALA B3853 " --> pdb=" O ARG B3849 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B3854 " --> pdb=" O GLN B3850 " (cutoff:3.500A) Processing helix chain 'B' and resid 3864 through 3871 removed outlier: 5.107A pdb=" N ARG B3868 " --> pdb=" O THR B3864 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN B3869 " --> pdb=" O VAL B3865 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N ASN B3870 " --> pdb=" O ILE B3866 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLY B3871 " --> pdb=" O ASN B3867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3864 through 3871' Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 4.740A pdb=" N THR B3881 " --> pdb=" O ASP B3877 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B3882 " --> pdb=" O ASP B3878 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 3.777A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.655A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4004 removed outlier: 3.627A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B3991 " --> pdb=" O ASP B3987 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.624A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4052 removed outlier: 4.972A pdb=" N ARG B4042 " --> pdb=" O GLY B4038 " (cutoff:3.500A) Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 3.835A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4099 removed outlier: 3.771A pdb=" N SER B4099 " --> pdb=" O LYS B4095 " (cutoff:3.500A) Processing helix chain 'B' and resid 4107 through 4115 removed outlier: 4.220A pdb=" N LEU B4111 " --> pdb=" O GLU B4107 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4129 Processing helix chain 'B' and resid 4134 through 4154 removed outlier: 4.005A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL B4154 " --> pdb=" O LEU B4150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.559A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.913A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4540 through 4559 removed outlier: 4.214A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 4.381A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4637 through 4683 Proline residue: B4641 - end of helix removed outlier: 4.064A pdb=" N TRP B4644 " --> pdb=" O GLU B4640 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix Processing helix chain 'B' and resid 4696 through 4709 removed outlier: 4.028A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Proline residue: B4709 - end of helix Processing helix chain 'B' and resid 4719 through 4729 Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 3.503A pdb=" N GLY B4742 " --> pdb=" O ALA B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4750 removed outlier: 3.756A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4765 through 4771 removed outlier: 4.254A pdb=" N MET B4769 " --> pdb=" O LEU B4765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B4771 " --> pdb=" O TRP B4767 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4787 removed outlier: 5.774A pdb=" N ASN B4787 " --> pdb=" O ILE B4783 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4805 removed outlier: 3.825A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B4805 " --> pdb=" O LEU B4801 " (cutoff:3.500A) Processing helix chain 'B' and resid 4807 through 4820 removed outlier: 4.906A pdb=" N ALA B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.901A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.622A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.955A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4928 through 4957 removed outlier: 3.659A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.928A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4999 removed outlier: 5.657A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 5.289A 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 5033 Processing helix chain 'B' and resid 4685 through 4690 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.784A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 84 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.579A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 256' Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.921A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 422 removed outlier: 3.719A pdb=" N GLN C 399 " --> pdb=" O GLN C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 3.510A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.692A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.530A pdb=" N LEU C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 494 " --> pdb=" O CYS C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 6.370A pdb=" N PHE C 503 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C 507 " --> pdb=" O PHE C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 499 through 507' Processing helix chain 'C' and resid 508 through 531 removed outlier: 4.563A pdb=" N ALA C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.652A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 4.237A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.378A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 4.039A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 593 removed outlier: 4.512A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 3.666A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 3.582A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 890 removed outlier: 3.677A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY C 890 " --> pdb=" O ARG C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 933 removed outlier: 3.811A pdb=" N LEU C 933 " --> pdb=" O LEU C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 951 removed outlier: 5.688A pdb=" N LYS C 951 " --> pdb=" O GLU C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 961 removed outlier: 3.680A pdb=" N MET C 960 " --> pdb=" O PRO C 956 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 956 through 961' Processing helix chain 'C' and resid 978 through 1003 removed outlier: 3.995A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1039 Processing helix chain 'C' and resid 1041 through 1050 Processing helix chain 'C' and resid 1574 through 1580 removed outlier: 3.691A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) removed outlier: 4.961A 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 1649 through 1657 removed outlier: 4.211A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.138A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1701 removed outlier: 4.322A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA C1701 " --> pdb=" O ALA C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 6.650A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 removed outlier: 4.317A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 4.305A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 4.121A pdb=" N LEU C1807 " --> pdb=" O PRO C1803 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1868 removed outlier: 4.699A pdb=" N GLN C1861 " --> pdb=" O GLU C1857 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE C1862 " --> pdb=" O ASP C1858 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS C1864 " --> pdb=" O LYS C1860 " (cutoff:3.500A) Proline residue: C1868 - end of helix Processing helix chain 'C' and resid 1925 through 1930 removed outlier: 5.739A pdb=" N LYS C1930 " --> pdb=" O LEU C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1984 removed outlier: 7.047A pdb=" N LEU C1937 " --> pdb=" O GLU C1933 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU C1980 " --> pdb=" O ARG C1976 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET C1981 " --> pdb=" O TYR C1977 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG C1982 " --> pdb=" O ALA C1978 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C1983 " --> pdb=" O LEU C1979 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1990 through 1998 Processing helix chain 'C' and resid 2001 through 2011 Processing helix chain 'C' and resid 2024 through 2043 removed outlier: 3.897A pdb=" N ARG C2028 " --> pdb=" O PRO C2024 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 4.003A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.524A 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: 5.459A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 3.625A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2189 removed outlier: 3.637A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS C2189 " --> pdb=" O ILE C2185 " (cutoff:3.500A) Processing helix chain 'C' and resid 2194 through 2202 removed outlier: 4.102A pdb=" N MET C2198 " --> pdb=" O HIS C2194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C2202 " --> pdb=" O MET C2198 " (cutoff:3.500A) Processing helix chain 'C' and resid 2203 through 2216 Processing helix chain 'C' and resid 2218 through 2226 removed outlier: 5.125A pdb=" N PHE C2225 " --> pdb=" O LYS C2221 " (cutoff:3.500A) Proline residue: C2226 - end of helix Processing helix chain 'C' and resid 2227 through 2244 removed outlier: 6.480A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2254 removed outlier: 4.384A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2255 through 2264 removed outlier: 3.660A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 3.665A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2283 through 2290 removed outlier: 3.768A pdb=" N ALA C2287 " --> pdb=" O ASN C2283 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU C2288 " --> pdb=" O ASN C2284 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C2289 " --> pdb=" O GLU C2285 " (cutoff:3.500A) Processing helix chain 'C' and resid 2293 through 2309 removed outlier: 5.125A pdb=" N GLN C2308 " --> pdb=" O GLY C2304 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.732A pdb=" N LEU C2314 " --> pdb=" O CYS C2310 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS C2316 " --> pdb=" O MET C2312 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY C2317 " --> pdb=" O LEU C2313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2341 removed outlier: 5.025A pdb=" N GLY C2328 " --> pdb=" O ASN C2324 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C2329 " --> pdb=" O PRO C2325 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG C2330 " --> pdb=" O CYS C2326 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR C2331 " --> pdb=" O GLY C2327 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL C2341 " --> pdb=" O PHE C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 4.039A 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 removed outlier: 4.724A pdb=" N ALA C2379 " --> pdb=" O GLY C2375 " (cutoff:3.500A) Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 Processing helix chain 'C' and resid 2441 through 2447 removed outlier: 3.736A pdb=" N ALA C2445 " --> pdb=" O HIS C2441 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C2446 " --> pdb=" O LEU C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2448 through 2462 removed outlier: 3.806A pdb=" N VAL C2461 " --> pdb=" O LEU C2457 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2463 through 2473 removed outlier: 7.016A pdb=" N VAL C2467 " --> pdb=" O LEU C2463 " (cutoff:3.500A) Proline residue: C2473 - end of helix Processing helix chain 'C' and resid 3645 through 3662 removed outlier: 4.080A pdb=" N ALA C3649 " --> pdb=" O PRO C3645 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C3662 " --> pdb=" O LYS C3658 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3681 removed outlier: 5.899A pdb=" N ARG C3672 " --> pdb=" O SER C3668 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C3680 " --> pdb=" O ASP C3676 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 Processing helix chain 'C' and resid 3719 through 3740 removed outlier: 5.291A pdb=" N GLU C3736 " --> pdb=" O SER C3732 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU C3737 " --> pdb=" O CYS C3733 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 3.674A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C3772 " --> pdb=" O SER C3768 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 3.699A pdb=" N CYS C3786 " --> pdb=" O MET C3782 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 6.886A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3856 removed outlier: 3.542A pdb=" N ALA C3853 " --> pdb=" O ARG C3849 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU C3854 " --> pdb=" O GLN C3850 " (cutoff:3.500A) Processing helix chain 'C' and resid 3864 through 3871 removed outlier: 3.930A pdb=" N ARG C3868 " --> pdb=" O THR C3864 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN C3869 " --> pdb=" O VAL C3865 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASN C3870 " --> pdb=" O ILE C3866 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY C3871 " --> pdb=" O ASN C3867 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3864 through 3871' Processing helix chain 'C' and resid 3877 through 3893 Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 3.774A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C3904 " --> pdb=" O GLN C3900 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.655A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4004 removed outlier: 3.628A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C3991 " --> pdb=" O ASP C3987 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.624A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4052 removed outlier: 4.970A pdb=" N ARG C4042 " --> pdb=" O GLY C4038 " (cutoff:3.500A) Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 3.838A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4099 removed outlier: 3.772A pdb=" N SER C4099 " --> pdb=" O LYS C4095 " (cutoff:3.500A) Processing helix chain 'C' and resid 4107 through 4115 removed outlier: 4.220A pdb=" N LEU C4111 " --> pdb=" O GLU C4107 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4129 Processing helix chain 'C' and resid 4134 through 4154 removed outlier: 4.005A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL C4154 " --> pdb=" O LEU C4150 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.558A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 3.963A 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: 3.913A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4540 through 4559 removed outlier: 4.213A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.381A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4637 through 4683 Proline residue: C4641 - end of helix removed outlier: 4.259A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix Processing helix chain 'C' and resid 4696 through 4709 removed outlier: 3.781A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Proline residue: C4709 - end of helix Processing helix chain 'C' and resid 4719 through 4729 Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 3.504A pdb=" N GLY C4742 " --> pdb=" O ALA C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4745 through 4750 removed outlier: 3.756A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4765 through 4771 removed outlier: 4.253A pdb=" N MET C4769 " --> pdb=" O LEU C4765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4787 removed outlier: 5.775A pdb=" N ASN C4787 " --> pdb=" O ILE C4783 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4805 removed outlier: 3.825A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN C4805 " --> pdb=" O LEU C4801 " (cutoff:3.500A) Processing helix chain 'C' and resid 4807 through 4820 removed outlier: 4.906A pdb=" N ALA C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C4820 " --> pdb=" O ILE C4816 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.900A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.621A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.954A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4928 through 4957 removed outlier: 3.659A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.928A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4999 removed outlier: 5.697A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 5.288A 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 5033 Processing helix chain 'C' and resid 4685 through 4690 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.785A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.579A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 256' Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.920A pdb=" N THR D 312 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 422 removed outlier: 3.676A pdb=" N GLN D 399 " --> pdb=" O GLN D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 3.510A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.692A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.530A pdb=" N LEU D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D 493 " --> pdb=" O ASN D 489 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 494 " --> pdb=" O CYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 6.369A pdb=" N PHE D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU D 505 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA D 507 " --> pdb=" O PHE D 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 507' Processing helix chain 'D' and resid 508 through 531 removed outlier: 4.562A pdb=" N ALA D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 3.652A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 4.236A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 4.379A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.039A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 removed outlier: 4.513A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.666A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 3.582A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 890 removed outlier: 3.677A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY D 890 " --> pdb=" O ARG D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 933 removed outlier: 3.811A pdb=" N LEU D 933 " --> pdb=" O LEU D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 951 removed outlier: 5.689A pdb=" N LYS D 951 " --> pdb=" O GLU D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 961 removed outlier: 3.679A pdb=" N MET D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 956 through 961' Processing helix chain 'D' and resid 978 through 1003 removed outlier: 3.995A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1039 Processing helix chain 'D' and resid 1041 through 1050 Processing helix chain 'D' and resid 1574 through 1580 removed outlier: 3.691A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1574 through 1580' Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.211A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 Processing helix chain 'D' and resid 1678 through 1690 removed outlier: 4.138A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 4.322A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 removed outlier: 6.649A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.318A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 4.304A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 4.121A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D1812 " --> pdb=" O ARG D1808 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1868 removed outlier: 4.699A pdb=" N GLN D1861 " --> pdb=" O GLU D1857 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D1862 " --> pdb=" O ASP D1858 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D1864 " --> pdb=" O LYS D1860 " (cutoff:3.500A) Proline residue: D1868 - end of helix Processing helix chain 'D' and resid 1925 through 1930 removed outlier: 5.740A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1984 removed outlier: 7.047A pdb=" N LEU D1937 " --> pdb=" O GLU D1933 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU D1980 " --> pdb=" O ARG D1976 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N MET D1981 " --> pdb=" O TYR D1977 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ARG D1982 " --> pdb=" O ALA D1978 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ALA D1983 " --> pdb=" O LEU D1979 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 1998 Processing helix chain 'D' and resid 2001 through 2011 Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 3.897A pdb=" N ARG D2028 " --> pdb=" O PRO D2024 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 4.003A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.523A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.459A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 3.625A pdb=" N THR D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2189 removed outlier: 3.637A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS D2189 " --> pdb=" O ILE D2185 " (cutoff:3.500A) Processing helix chain 'D' and resid 2194 through 2202 removed outlier: 4.103A pdb=" N MET D2198 " --> pdb=" O HIS D2194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D2202 " --> pdb=" O MET D2198 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2216 Processing helix chain 'D' and resid 2218 through 2226 removed outlier: 5.126A pdb=" N PHE D2225 " --> pdb=" O LYS D2221 " (cutoff:3.500A) Proline residue: D2226 - end of helix Processing helix chain 'D' and resid 2227 through 2244 removed outlier: 6.481A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2254 removed outlier: 4.384A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2255 through 2264 removed outlier: 3.660A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.664A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2283 through 2290 removed outlier: 4.583A pdb=" N ALA D2287 " --> pdb=" O ASN D2283 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D2288 " --> pdb=" O ASN D2284 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA D2289 " --> pdb=" O GLU D2285 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2283 through 2290' Processing helix chain 'D' and resid 2293 through 2309 removed outlier: 5.125A pdb=" N GLN D2308 " --> pdb=" O GLY D2304 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.730A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS D2316 " --> pdb=" O MET D2312 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY D2317 " --> pdb=" O LEU D2313 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2341 removed outlier: 5.025A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D2329 " --> pdb=" O PRO D2325 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG D2330 " --> pdb=" O CYS D2326 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR D2331 " --> pdb=" O GLY D2327 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL D2341 " --> pdb=" O PHE D2337 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 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 Processing helix chain 'D' and resid 2375 through 2390 removed outlier: 4.724A pdb=" N ALA D2379 " --> pdb=" O GLY D2375 " (cutoff:3.500A) Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 Processing helix chain 'D' and resid 2441 through 2447 removed outlier: 3.736A pdb=" N ALA D2445 " --> pdb=" O HIS D2441 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY D2446 " --> pdb=" O LEU D2442 " (cutoff:3.500A) Processing helix chain 'D' and resid 2448 through 2462 removed outlier: 3.806A pdb=" N VAL D2461 " --> pdb=" O LEU D2457 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2463 through 2473 removed outlier: 7.016A pdb=" N VAL D2467 " --> pdb=" O LEU D2463 " (cutoff:3.500A) Proline residue: D2473 - end of helix Processing helix chain 'D' and resid 3645 through 3662 removed outlier: 3.961A pdb=" N ALA D3649 " --> pdb=" O PRO D3645 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D3662 " --> pdb=" O LYS D3658 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3681 removed outlier: 4.239A pdb=" N ALA D3680 " --> pdb=" O ASP D3676 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3740 removed outlier: 5.292A pdb=" N GLU D3736 " --> pdb=" O SER D3732 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU D3737 " --> pdb=" O CYS D3733 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.675A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D3772 " --> pdb=" O SER D3768 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 3.699A pdb=" N CYS D3786 " --> pdb=" O MET D3782 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 6.887A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3856 removed outlier: 3.546A pdb=" N ALA D3853 " --> pdb=" O ARG D3849 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU D3854 " --> pdb=" O GLN D3850 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) Processing helix chain 'D' and resid 3864 through 3871 removed outlier: 4.549A pdb=" N ARG D3868 " --> pdb=" O THR D3864 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN D3869 " --> pdb=" O VAL D3865 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASN D3870 " --> pdb=" O ILE D3866 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY D3871 " --> pdb=" O ASN D3867 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3864 through 3871' Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 4.005A pdb=" N THR D3881 " --> pdb=" O ASP D3877 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN D3882 " --> pdb=" O ASP D3878 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 3.776A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.655A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4004 removed outlier: 3.628A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D3991 " --> pdb=" O ASP D3987 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.624A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 removed outlier: 4.972A pdb=" N ARG D4042 " --> pdb=" O GLY D4038 " (cutoff:3.500A) Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 3.843A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4099 removed outlier: 3.772A pdb=" N SER D4099 " --> pdb=" O LYS D4095 " (cutoff:3.500A) Processing helix chain 'D' and resid 4107 through 4115 removed outlier: 4.220A pdb=" N LEU D4111 " --> pdb=" O GLU D4107 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4129 Processing helix chain 'D' and resid 4134 through 4154 removed outlier: 4.005A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL D4154 " --> pdb=" O LEU D4150 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.558A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.913A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4540 through 4559 removed outlier: 4.213A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.381A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4637 through 4683 Proline residue: D4641 - end of helix removed outlier: 4.261A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 3.781A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix Processing helix chain 'D' and resid 4719 through 4729 Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 3.503A pdb=" N GLY D4742 " --> pdb=" O ALA D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4745 through 4750 removed outlier: 3.756A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4765 through 4771 removed outlier: 4.254A pdb=" N MET D4769 " --> pdb=" O LEU D4765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D4771 " --> pdb=" O TRP D4767 " (cutoff:3.500A) Processing helix chain 'D' and resid 4772 through 4787 removed outlier: 5.775A pdb=" N ASN D4787 " --> pdb=" O ILE D4783 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4805 removed outlier: 3.824A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN D4805 " --> pdb=" O LEU D4801 " (cutoff:3.500A) Processing helix chain 'D' and resid 4807 through 4820 removed outlier: 4.906A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D4820 " --> pdb=" O ILE D4816 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.900A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.622A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.955A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4928 through 4957 removed outlier: 3.658A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.928A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 5.633A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 Processing helix chain 'D' and resid 4685 through 4690 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.067A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 11.658A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 14.412A 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: 6.900A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 135 through 139 Processing sheet with id= 4, first strand: chain 'A' and resid 148 through 152 Processing sheet with id= 5, first strand: chain 'A' and resid 229 through 233 Processing sheet with id= 6, first strand: chain 'A' and resid 260 through 264 removed outlier: 16.359A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 660 through 669 removed outlier: 8.075A pdb=" N GLY A 660 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP A 662 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 681 through 685 removed outlier: 6.636A pdb=" N HIS A 681 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A1646 " --> pdb=" O ILE A1641 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 786 through 790 removed outlier: 6.054A pdb=" N VAL A 787 " --> pdb=" O CYS A1630 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 838 through 841 removed outlier: 5.713A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 892 through 895 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'A' and resid 1135 through 1139 removed outlier: 3.613A pdb=" N GLY A1135 " --> pdb=" O HIS A1133 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY A1129 " --> pdb=" O PHE A1139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1123 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1269 through 1272 removed outlier: 5.124A pdb=" N ARG A1470 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A1471 " --> pdb=" O SER A1486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A1486 " --> pdb=" O ALA A1471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A1484 " --> pdb=" O THR A1473 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A1475 " --> pdb=" O ASN A1482 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN A1482 " --> pdb=" O THR A1475 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1284 through 1289 removed outlier: 5.810A pdb=" N GLU A1285 " --> pdb=" O MET A1462 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS A1458 " --> pdb=" O LEU A1289 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 4.900A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 4580 through 4584 Processing sheet with id= 17, first strand: chain 'A' and resid 109 through 112 removed outlier: 5.518A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.068A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 14.411A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.900A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 135 through 139 Processing sheet with id= 21, first strand: chain 'B' and resid 148 through 152 Processing sheet with id= 22, first strand: chain 'B' and resid 229 through 233 Processing sheet with id= 23, first strand: chain 'B' and resid 260 through 264 removed outlier: 16.358A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 660 through 669 removed outlier: 8.074A pdb=" N GLY B 660 " --> pdb=" O LEU B 750 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 681 through 685 removed outlier: 6.636A pdb=" N HIS B 681 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B1646 " --> pdb=" O ILE B1641 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 786 through 790 removed outlier: 6.054A pdb=" N VAL B 787 " --> pdb=" O CYS B1630 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 838 through 841 removed outlier: 5.712A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 892 through 895 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'B' and resid 1135 through 1139 removed outlier: 3.613A pdb=" N GLY B1135 " --> pdb=" O HIS B1133 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY B1129 " --> pdb=" O PHE B1139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B1123 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N VAL B1072 " --> pdb=" O SER B1241 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B1241 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 1269 through 1272 removed outlier: 5.123A pdb=" N ARG B1470 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B1471 " --> pdb=" O SER B1486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B1486 " --> pdb=" O ALA B1471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS B1484 " --> pdb=" O THR B1473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B1475 " --> pdb=" O ASN B1482 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN B1482 " --> pdb=" O THR B1475 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1284 through 1289 removed outlier: 5.809A pdb=" N GLU B1285 " --> pdb=" O MET B1462 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B1458 " --> pdb=" O LEU B1289 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 4.898A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 4580 through 4584 Processing sheet with id= 34, first strand: chain 'B' and resid 109 through 112 removed outlier: 5.518A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.068A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 11.656A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 14.411A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.901A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 135 through 139 Processing sheet with id= 38, first strand: chain 'C' and resid 148 through 152 Processing sheet with id= 39, first strand: chain 'C' and resid 229 through 233 Processing sheet with id= 40, first strand: chain 'C' and resid 260 through 264 removed outlier: 16.359A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 660 through 669 removed outlier: 8.074A pdb=" N GLY C 660 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP C 662 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 681 through 685 removed outlier: 6.635A pdb=" N HIS C 681 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C1646 " --> pdb=" O ILE C1641 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 786 through 790 removed outlier: 6.055A pdb=" N VAL C 787 " --> pdb=" O CYS C1630 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 838 through 841 removed outlier: 5.712A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 892 through 895 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'C' and resid 1135 through 1139 removed outlier: 3.614A pdb=" N GLY C1135 " --> pdb=" O HIS C1133 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY C1129 " --> pdb=" O PHE C1139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C1123 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N VAL C1072 " --> pdb=" O SER C1241 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER C1241 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 1269 through 1272 removed outlier: 5.123A pdb=" N ARG C1470 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C1471 " --> pdb=" O SER C1486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C1486 " --> pdb=" O ALA C1471 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C1484 " --> pdb=" O THR C1473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C1475 " --> pdb=" O ASN C1482 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C1482 " --> pdb=" O THR C1475 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 1284 through 1289 removed outlier: 5.809A pdb=" N GLU C1285 " --> pdb=" O MET C1462 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS C1458 " --> pdb=" O LEU C1289 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 4.899A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 4580 through 4584 Processing sheet with id= 51, first strand: chain 'C' and resid 109 through 112 removed outlier: 5.518A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.068A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 11.657A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 14.412A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.900A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'D' and resid 135 through 139 Processing sheet with id= 55, first strand: chain 'D' and resid 148 through 152 Processing sheet with id= 56, first strand: chain 'D' and resid 229 through 233 Processing sheet with id= 57, first strand: chain 'D' and resid 260 through 264 removed outlier: 16.359A pdb=" N LEU D 280 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LEU D 293 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 660 through 669 removed outlier: 8.073A pdb=" N GLY D 660 " --> pdb=" O LEU D 750 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP D 662 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'D' and resid 681 through 685 removed outlier: 6.635A pdb=" N HIS D 681 " --> pdb=" O SER D 784 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D1646 " --> pdb=" O ILE D1641 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 786 through 790 removed outlier: 6.055A pdb=" N VAL D 787 " --> pdb=" O CYS D1630 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 838 through 841 removed outlier: 5.713A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 892 through 895 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'D' and resid 1135 through 1139 removed outlier: 3.613A pdb=" N GLY D1135 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY D1129 " --> pdb=" O PHE D1139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 1269 through 1272 removed outlier: 5.123A pdb=" N ARG D1470 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D1471 " --> pdb=" O SER D1486 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D1486 " --> pdb=" O ALA D1471 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS D1484 " --> pdb=" O THR D1473 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D1475 " --> pdb=" O ASN D1482 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN D1482 " --> pdb=" O THR D1475 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 1284 through 1289 removed outlier: 5.809A pdb=" N GLU D1285 " --> pdb=" O MET D1462 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS D1458 " --> pdb=" O LEU D1289 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 4.900A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 4580 through 4584 Processing sheet with id= 68, first strand: chain 'D' and resid 109 through 112 removed outlier: 5.518A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) 4678 hydrogen bonds defined for protein. 13986 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: 59.33 Time building geometry restraints manager: 36.15 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: 19858 1.32 - 1.45: 27861 1.45 - 1.57: 64588 1.57 - 1.70: 34 1.70 - 1.82: 1024 Bond restraints: 113365 Sorted by residual: bond pdb=" O3A ACP C5101 " pdb=" PB ACP C5101 " ideal model delta sigma weight residual 1.698 1.590 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O3A ACP D5101 " pdb=" PB ACP D5101 " ideal model delta sigma weight residual 1.698 1.590 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O2B ACP A5101 " pdb=" PB ACP A5101 " ideal model delta sigma weight residual 1.507 1.602 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O2B ACP B5101 " pdb=" PB ACP B5101 " ideal model delta sigma weight residual 1.507 1.602 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 ACP B5101 " pdb=" N9 ACP B5101 " ideal model delta sigma weight residual 1.364 1.281 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 113360 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.31: 3726 107.31 - 114.88: 66028 114.88 - 122.45: 68369 122.45 - 130.02: 15685 130.02 - 137.59: 654 Bond angle restraints: 154462 Sorted by residual: angle pdb=" N VAL A3874 " pdb=" CA VAL A3874 " pdb=" C VAL A3874 " ideal model delta sigma weight residual 113.22 103.38 9.84 1.23e+00 6.61e-01 6.41e+01 angle pdb=" N LYS B3873 " pdb=" CA LYS B3873 " pdb=" C LYS B3873 " ideal model delta sigma weight residual 114.39 105.27 9.12 1.45e+00 4.76e-01 3.96e+01 angle pdb=" CA GLN D2308 " pdb=" CB GLN D2308 " pdb=" CG GLN D2308 " ideal model delta sigma weight residual 114.10 126.37 -12.27 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLN C2308 " pdb=" CB GLN C2308 " pdb=" CG GLN C2308 " ideal model delta sigma weight residual 114.10 126.36 -12.26 2.00e+00 2.50e-01 3.76e+01 angle pdb=" CA GLN B2308 " pdb=" CB GLN B2308 " pdb=" CG GLN B2308 " ideal model delta sigma weight residual 114.10 126.36 -12.26 2.00e+00 2.50e-01 3.76e+01 ... (remaining 154457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 65545 35.92 - 71.84: 2176 71.84 - 107.75: 162 107.75 - 143.67: 8 143.67 - 179.59: 7 Dihedral angle restraints: 67898 sinusoidal: 22218 harmonic: 45680 Sorted by residual: dihedral pdb=" CA ALA B3680 " pdb=" C ALA B3680 " pdb=" N GLY B3681 " pdb=" CA GLY B3681 " ideal model delta harmonic sigma weight residual 180.00 151.57 28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ALA A3680 " pdb=" C ALA A3680 " pdb=" N GLY A3681 " pdb=" CA GLY A3681 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ALA D3680 " pdb=" C ALA D3680 " pdb=" N GLY D3681 " pdb=" CA GLY D3681 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 67895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 15357 0.059 - 0.117: 2260 0.117 - 0.176: 395 0.176 - 0.234: 61 0.234 - 0.293: 14 Chirality restraints: 18087 Sorted by residual: chirality pdb=" CA PHE A4077 " pdb=" N PHE A4077 " pdb=" C PHE A4077 " pdb=" CB PHE A4077 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE A4181 " pdb=" N ILE A4181 " pdb=" C ILE A4181 " pdb=" CB ILE A4181 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ILE D4181 " pdb=" N ILE D4181 " pdb=" C ILE D4181 " pdb=" CB ILE D4181 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 18084 not shown) Planarity restraints: 20349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C5107 " -0.256 2.00e-02 2.50e+03 2.48e-01 6.15e+02 pdb=" C42 LBN C5107 " 0.280 2.00e-02 2.50e+03 pdb=" C5 LBN C5107 " 0.214 2.00e-02 2.50e+03 pdb=" C8 LBN C5107 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A5107 " -0.094 2.00e-02 2.50e+03 2.09e-01 4.37e+02 pdb=" C42 LBN A5107 " 0.279 2.00e-02 2.50e+03 pdb=" C5 LBN A5107 " -0.281 2.00e-02 2.50e+03 pdb=" C8 LBN A5107 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C5106 " 0.092 2.00e-02 2.50e+03 1.90e-01 3.60e+02 pdb=" C42 LBN C5106 " -0.254 2.00e-02 2.50e+03 pdb=" C5 LBN C5106 " 0.251 2.00e-02 2.50e+03 pdb=" C8 LBN C5106 " -0.089 2.00e-02 2.50e+03 ... (remaining 20346 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6896 2.74 - 3.28: 113788 3.28 - 3.82: 178480 3.82 - 4.36: 190125 4.36 - 4.90: 331514 Nonbonded interactions: 820803 Sorted by model distance: nonbonded pdb=" O1G ACP B5101 " pdb="MG MG B5105 " model vdw 2.198 2.170 nonbonded pdb=" N ASP D4092 " pdb=" OD1 ASP D4092 " model vdw 2.226 2.520 nonbonded pdb=" N ASP B4092 " pdb=" OD1 ASP B4092 " model vdw 2.227 2.520 nonbonded pdb=" N ASP C4092 " pdb=" OD1 ASP C4092 " model vdw 2.227 2.520 nonbonded pdb=" O LEU A2257 " pdb=" OG SER A2261 " model vdw 2.236 2.440 ... (remaining 820798 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 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 277 or (resid 278 and (name N o \ r name CA or name C or name O or name CB )) or resid 279 through 356 or (resid 3 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 358 through \ 509 or (resid 510 through 512 and (name N or name CA or name C or name O or nam \ e CB )) or resid 513 through 553 or (resid 554 and (name N or name CA or name C \ or name O or name CB )) or resid 555 through 651 or (resid 652 through 654 and ( \ name N or name CA or name C or name O or name CB )) or resid 655 through 658 or \ (resid 659 and (name N or name CA or name C or name O or name CB )) or resid 660 \ through 662 or (resid 663 through 665 and (name N or name CA or name C or name \ O or name CB )) or resid 666 through 734 or (resid 735 and (name N or name CA or \ name C or name O or name CB )) or resid 736 through 777 or (resid 778 and (name \ N or name CA or name C or name O or name CB )) or resid 779 through 812 or (res \ id 813 through 814 and (name N or name CA or name C or name O or name CB )) or r \ esid 815 through 918 or (resid 919 and (name N or name CA or name C or name O or \ name CB )) or resid 920 through 964 or (resid 965 through 966 and (name N or na \ me CA or name C or name O or name CB )) or resid 967 through 1028 or (resid 1029 \ through 1030 and (name N or name CA or name C or name O or name CB )) or resid \ 1031 or (resid 1032 through 1033 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1034 through 1035 or (resid 1036 through 1037 and (name N or \ name CA or name C or name O or name CB )) or resid 1038 through 1043 or (resid 1 \ 044 and (name N or name CA or name C or name O or name CB )) or resid 1045 or (r \ esid 1046 through 1047 and (name N or name CA or name C or name O or name CB )) \ or resid 1048 through 1442 or (resid 1443 through 1444 and (name N or name CA or \ name C or name O or name CB )) or resid 1445 through 1457 or (resid 1458 throug \ h 1459 and (name N or name CA or name C or name O or name CB )) or resid 1460 th \ rough 1464 or (resid 1465 and (name N or name CA or name C or name O or name CB \ )) or resid 1466 through 1473 or (resid 1474 through 1476 and (name N or name CA \ or name C or name O or name CB )) or (resid 1477 through 1484 and (name N or na \ me CA or name C or name O or name CB )) or resid 1485 through 2027 or (resid 202 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 2029 through \ 2044 or (resid 2045 and (name N or name CA or name C or name O or name CB )) or \ resid 2046 through 2439 or (resid 2440 through 2441 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2442 through 3660 or (resid 3661 and (nam \ e N or name CA or name C or name O or name CB )) or resid 3662 through 3681 or ( \ resid 3682 through 3693 and (name N or name CA or name C or name O or name CB )) \ or resid 3694 through 3736 or (resid 3737 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 3738 through 3750 and (name N or name CA or name C \ or name O or name CB )) or resid 3751 through 4077 or (resid 4078 through 4080 \ and (name N or name CA or name C or name O or name CB )) or resid 4081 through 4 \ 101 or (resid 4102 through 4103 and (name N or name CA or name C or name O or na \ me CB )) or resid 4104 through 4863 or (resid 4864 and (name N or name CA or nam \ e C or name O or name CB )) or resid 4865 through 5037 or resid 5101 through 510 \ 5 or (resid 5107 and (name C1 or name C10 or name C11 or name C12 or name C15 or \ name C18 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or n \ ame C42 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or nam \ e O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name O \ 8 or name P1 )))) selection = (chain 'B' and (resid 12 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 258 or (resid 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 through 277 or (resid 2 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 279 through \ 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) or r \ esid 358 through 509 or (resid 510 through 512 and (name N or name CA or name C \ or name O or name CB )) or resid 513 through 553 or (resid 554 and (name N or na \ me CA or name C or name O or name CB )) or resid 555 through 658 or (resid 659 a \ nd (name N or name CA or name C or name O or name CB )) or resid 660 through 662 \ or (resid 663 through 665 and (name N or name CA or name C or name O or name CB \ )) or resid 666 through 734 or (resid 735 and (name N or name CA or name C or n \ ame O or name CB )) or resid 736 through 812 or (resid 813 through 814 and (name \ N or name CA or name C or name O or name CB )) or resid 815 through 876 or (res \ id 877 through 883 and (name N or name CA or name C or name O or name CB )) or r \ esid 884 through 918 or (resid 919 and (name N or name CA or name C or name O or \ name CB )) or resid 920 through 964 or (resid 965 through 966 and (name N or na \ me CA or name C or name O or name CB )) or resid 967 through 990 or (resid 991 a \ nd (name N or name CA or name C or name O or name CB )) or resid 992 or (resid 9 \ 93 through 1003 and (name N or name CA or name C or name O or name CB )) or (res \ id 1004 through 1027 and (name N or name CA or name C or name O or name CB )) or \ resid 1028 through 1031 or (resid 1032 through 1033 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1034 through 1035 or (resid 1036 through \ 1037 and (name N or name CA or name C or name O or name CB )) or resid 1038 thro \ ugh 1043 or (resid 1044 and (name N or name CA or name C or name O or name CB )) \ or resid 1045 or (resid 1046 through 1047 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1048 through 1220 or (resid 1221 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1222 through 1274 or (resid 1275 \ through 1277 and (name N or name CA or name C or name O or name CB )) or resid \ 1278 through 1442 or (resid 1443 through 1444 and (name N or name CA or name C o \ r name O or name CB )) or resid 1445 through 1457 or (resid 1458 through 1459 an \ d (name N or name CA or name C or name O or name CB )) or resid 1460 through 146 \ 4 or (resid 1465 and (name N or name CA or name C or name O or name CB )) or res \ id 1466 through 1473 or (resid 1474 through 1476 and (name N or name CA or name \ C or name O or name CB )) or resid 1477 through 1582 or (resid 1583 through 1585 \ and (name N or name CA or name C or name O or name CB )) or resid 1586 through \ 1758 or (resid 1759 and (name N or name CA or name C or name O or name CB )) or \ resid 1760 through 1870 or (resid 1871 and (name N or name CA or name C or name \ O or name CB )) or resid 1872 through 2027 or (resid 2028 and (name N or name CA \ or name C or name O or name CB )) or resid 2029 through 2044 or (resid 2045 and \ (name N or name CA or name C or name O or name CB )) or resid 2046 through 4078 \ or (resid 4079 through 4080 and (name N or name CA or name C or name O or name \ CB )) or resid 4081 or (resid 4082 through 4083 and (name N or name CA or name C \ or name O or name CB )) or resid 4084 through 4086 or (resid 4087 and (name N o \ r name CA or name C or name O or name CB )) or resid 4088 or (resid 4089 through \ 4093 and (name N or name CA or name C or name O or name CB )) or resid 4094 thr \ ough 4097 or (resid 4098 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4099 through 4635 or (resid 4636 and (name N or name CA or name C or \ name O or name CB )) or resid 4637 through 4870 or (resid 4871 and (name N or na \ me CA or name C or name O or name CB )) or resid 4872 through 5037 or resid 5101 \ through 5105 or (resid 5107 and (name C1 or name C10 or name C11 or name C12 or \ name C15 or name C18 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name C4 or name C40 or n \ ame C41 or name C42 or name C5 or name C6 or name C7 or name C8 or name C9 or na \ me N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name \ O7 or name O8 or name P1 )))) selection = (chain 'C' and (resid 12 through 651 or (resid 652 through 654 and (name N or na \ me CA or name C or name O or name CB )) or resid 655 through 658 or (resid 659 a \ nd (name N or name CA or name C or name O or name CB )) or resid 660 through 662 \ or (resid 663 through 665 and (name N or name CA or name C or name O or name CB \ )) or resid 666 through 777 or (resid 778 and (name N or name CA or name C or n \ ame O or name CB )) or resid 779 through 812 or (resid 813 through 814 and (name \ N or name CA or name C or name O or name CB )) or resid 815 through 918 or (res \ id 919 and (name N or name CA or name C or name O or name CB )) or resid 920 thr \ ough 965 or (resid 966 and (name N or name CA or name C or name O or name CB )) \ or resid 967 through 1031 or (resid 1032 through 1033 and (name N or name CA or \ name C or name O or name CB )) or resid 1034 through 1220 or (resid 1221 and (na \ me N or name CA or name C or name O or name CB )) or resid 1222 through 1442 or \ (resid 1443 through 1444 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1445 through 1583 or (resid 1584 through 1585 and (name N or name CA \ or name C or name O or name CB )) or resid 1586 through 2027 or (resid 2028 and \ (name N or name CA or name C or name O or name CB )) or resid 2029 through 2044 \ or (resid 2045 and (name N or name CA or name C or name O or name CB )) or resid \ 2046 through 2439 or (resid 2440 through 2441 and (name N or name CA or name C \ or name O or name CB )) or resid 2442 through 3660 or (resid 3661 and (name N or \ name CA or name C or name O or name CB )) or resid 3662 through 4078 or (resid \ 4079 through 4080 and (name N or name CA or name C or name O or name CB )) or re \ sid 4081 or (resid 4082 through 4083 and (name N or name CA or name C or name O \ or name CB )) or resid 4084 through 4086 or (resid 4087 and (name N or name CA o \ r name C or name O or name CB )) or resid 4088 or (resid 4089 through 4093 and ( \ name N or name CA or name C or name O or name CB )) or resid 4094 through 4097 o \ r (resid 4098 and (name N or name CA or name C or name O or name CB )) or resid \ 4099 through 4635 or (resid 4636 and (name N or name CA or name C or name O or n \ ame CB )) or resid 4637 through 4870 or (resid 4871 and (name N or name CA or na \ me C or name O or name CB )) or resid 4872 through 5037 or resid 5101 through 51 \ 05 or (resid 5107 and (name C1 or name C10 or name C11 or name C12 or name C15 o \ r name C18 or name C25 or name C26 or name C27 or name C28 or name C29 or name C \ 3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or \ name C42 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or na \ me O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name \ O8 or name P1 )))) selection = (chain 'D' and (resid 12 through 188 or (resid 189 and (name N or name CA or nam \ e C or name O or name CB )) or resid 190 through 277 or (resid 278 and (name N o \ r name CA or name C or name O or name CB )) or resid 279 through 356 or (resid 3 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 358 through \ 509 or (resid 510 through 512 and (name N or name CA or name C or name O or nam \ e CB )) or resid 513 through 553 or (resid 554 and (name N or name CA or name C \ or name O or name CB )) or resid 555 through 651 or (resid 652 through 654 and ( \ name N or name CA or name C or name O or name CB )) or resid 655 through 734 or \ (resid 735 and (name N or name CA or name C or name O or name CB )) or resid 736 \ through 777 or (resid 778 and (name N or name CA or name C or name O or name CB \ )) or resid 779 through 828 or (resid 829 and (name N or name CA or name C or n \ ame O or name CB )) or resid 830 through 1043 or (resid 1044 and (name N or name \ CA or name C or name O or name CB )) or resid 1045 or (resid 1046 through 1047 \ and (name N or name CA or name C or name O or name CB )) or resid 1048 through 1 \ 457 or (resid 1458 through 1459 and (name N or name CA or name C or name O or na \ me CB )) or resid 1460 through 1482 or (resid 1483 through 1484 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1485 through 2439 or (resid 24 \ 40 through 2441 and (name N or name CA or name C or name O or name CB )) or resi \ d 2442 through 3660 or (resid 3661 and (name N or name CA or name C or name O or \ name CB )) or resid 3662 through 4078 or (resid 4079 through 4080 and (name N o \ r name CA or name C or name O or name CB )) or resid 4081 or (resid 4082 through \ 4083 and (name N or name CA or name C or name O or name CB )) or resid 4084 thr \ ough 4086 or (resid 4087 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4088 or (resid 4089 through 4093 and (name N or name CA or name C or \ name O or name CB )) or resid 4094 through 4097 or (resid 4098 and (name N or na \ me CA or name C or name O or name CB )) or resid 4099 through 4635 or (resid 463 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 4637 through \ 4870 or (resid 4871 and (name N or name CA or name C or name O or name CB )) or \ resid 4872 through 5037 or resid 5101 through 5105 or (resid 5107 and (name C1 \ or name C10 or name C11 or name C12 or name C15 or name C18 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C4 or name C40 or name C41 or name C42 or name C5 or name C6 \ or name C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or \ name O4 or name O5 or name O6 or name O7 or name O8 or name P1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 39.240 Check model and map are aligned: 1.440 Set scattering table: 0.760 Process input model: 242.750 Find NCS groups from input model: 10.850 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 303.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.004 0.108 113365 Z= 0.285 Angle : 0.871 16.950 154462 Z= 0.478 Chirality : 0.045 0.293 18087 Planarity : 0.006 0.248 20349 Dihedral : 17.349 179.588 38166 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.10 % Favored : 93.27 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.07), residues: 12368 helix: 0.79 (0.07), residues: 5664 sheet: -0.37 (0.16), residues: 1032 loop : -2.34 (0.07), residues: 5672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1953 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1722 time to evaluate : 8.467 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 outliers start: 231 outliers final: 50 residues processed: 1892 average time/residue: 0.9221 time to fit residues: 3057.0378 Evaluate side-chains 1103 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1053 time to evaluate : 8.625 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.9109 time to fit residues: 92.6801 ------------------------------------------------------------------------------- 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 105 HIS A 151 HIS A 278 GLN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 593 HIS ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 HIS ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2032 GLN A2035 HIS ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 ASN A3667 HIS A3683 GLN A3771 HIS A3814 GLN ** A3895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3970 GLN A3994 HIS A4109 GLN A4120 ASN A4216 GLN ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4832 HIS A4864 ASN ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 105 HIS B 151 HIS B 278 GLN B 308 HIS B 413 GLN B 593 HIS ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 HIS ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 HIS B 877 ASN ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 HIS B1458 HIS B1614 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN B2035 HIS ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2193 GLN ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2351 ASN B3814 GLN ** B3895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3970 GLN B3994 HIS B4109 GLN B4120 ASN B4216 GLN B4650 HIS ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5003 HIS C 12 GLN C 57 ASN C 105 HIS C 151 HIS ** C 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN C 593 HIS ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 HIS ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 HIS ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1614 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2032 GLN C2035 HIS ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2193 GLN ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2351 ASN C3771 HIS C3814 GLN C3867 ASN ** C3895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3970 GLN C3994 HIS C4109 GLN C4120 ASN C4216 GLN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4832 HIS ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 79 GLN D 105 HIS D 151 HIS D 308 HIS D 405 HIS D 413 GLN D 593 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 HIS ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 848 HIS ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 HIS ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1614 GLN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2032 GLN D2035 HIS ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2193 GLN ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2351 ASN D3771 HIS D3814 GLN ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3970 GLN D3994 HIS D4109 GLN D4216 GLN ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.697 113365 Z= 3.862 Angle : 2.907 46.671 154462 Z= 1.535 Chirality : 0.188 1.362 18087 Planarity : 0.021 0.478 20349 Dihedral : 11.956 178.175 16824 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 42.59 Ramachandran Plot: Outliers : 3.02 % Allowed : 14.89 % Favored : 82.10 % Rotamer Outliers : 16.53 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 1.23 % 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: -5.38 (0.06), residues: 12368 helix: -3.48 (0.05), residues: 5684 sheet: -2.26 (0.13), residues: 1216 loop : -3.95 (0.07), residues: 5468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2551 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1607 poor density : 944 time to evaluate : 8.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1607 outliers final: 943 residues processed: 2383 average time/residue: 0.8775 time to fit residues: 3746.5052 Evaluate side-chains 1851 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 943 poor density : 908 time to evaluate : 8.676 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 943 outliers final: 22 residues processed: 943 average time/residue: 0.7646 time to fit residues: 1381.8721 ------------------------------------------------------------------------------- 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 ASN ** A1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1696 HIS ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2268 GLN A2351 ASN ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3895 HIS A4650 HIS ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1598 GLN B1696 HIS ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2268 GLN B2351 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3895 HIS ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 ASN ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1598 GLN C1696 HIS ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2268 GLN ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3895 HIS C4650 HIS ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 ASN D 974 HIS ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1598 GLN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2032 GLN ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2268 GLN D2351 ASN ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3895 HIS D4650 HIS D4832 HIS ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.671 113365 Z= 3.851 Angle : 2.873 41.691 154462 Z= 1.521 Chirality : 0.186 1.575 18087 Planarity : 0.020 0.458 20349 Dihedral : 13.035 171.387 16824 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 47.28 Ramachandran Plot: Outliers : 2.85 % Allowed : 21.59 % Favored : 75.57 % Rotamer Outliers : 17.47 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.09 % Twisted General : 2.27 % 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: -6.29 (0.05), residues: 12368 helix: -4.04 (0.04), residues: 5744 sheet: -3.08 (0.12), residues: 1404 loop : -4.58 (0.06), residues: 5220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2582 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1698 poor density : 884 time to evaluate : 8.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1698 outliers final: 1018 residues processed: 2412 average time/residue: 0.9255 time to fit residues: 3965.8594 Evaluate side-chains 1894 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1018 poor density : 876 time to evaluate : 8.717 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1018 outliers final: 29 residues processed: 1018 average time/residue: 0.8159 time to fit residues: 1569.3522 ------------------------------------------------------------------------------- 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1598 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 ASN ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 ASN ** B1165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2351 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C1165 ASN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 79 GLN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN D1165 ASN ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2351 ASN ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.671 113365 Z= 3.868 Angle : 2.891 39.743 154462 Z= 1.530 Chirality : 0.185 1.546 18087 Planarity : 0.021 0.440 20349 Dihedral : 13.366 172.285 16824 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 49.34 Ramachandran Plot: Outliers : 2.72 % Allowed : 23.89 % Favored : 73.39 % Rotamer Outliers : 16.96 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 2.58 % 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: -6.54 (0.05), residues: 12368 helix: -4.18 (0.04), residues: 5696 sheet: -3.30 (0.12), residues: 1380 loop : -4.76 (0.06), residues: 5292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2497 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1648 poor density : 849 time to evaluate : 8.663 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 outliers start: 1648 outliers final: 1024 residues processed: 2335 average time/residue: 0.8870 time to fit residues: 3662.1455 Evaluate side-chains 1926 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1024 poor density : 902 time to evaluate : 8.688 Switching outliers to nearest non-outliers outliers start: 1024 outliers final: 37 residues processed: 1024 average time/residue: 0.7926 time to fit residues: 1538.0531 ------------------------------------------------------------------------------- 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2011 HIS ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2011 HIS ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2011 HIS ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2284 ASN ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2011 HIS ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2284 ASN ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.670 113365 Z= 3.872 Angle : 2.891 40.191 154462 Z= 1.531 Chirality : 0.186 1.680 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.481 178.433 16824 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 2.81 % Allowed : 24.78 % Favored : 72.41 % Rotamer Outliers : 15.28 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 2.77 % 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: -6.69 (0.05), residues: 12368 helix: -4.24 (0.04), residues: 5668 sheet: -3.43 (0.12), residues: 1352 loop : -4.92 (0.06), residues: 5348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2336 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1485 poor density : 851 time to evaluate : 8.692 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 outliers start: 1485 outliers final: 933 residues processed: 2193 average time/residue: 0.8850 time to fit residues: 3461.4994 Evaluate side-chains 1810 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 933 poor density : 877 time to evaluate : 8.705 Switching outliers to nearest non-outliers outliers start: 933 outliers final: 36 residues processed: 933 average time/residue: 0.7812 time to fit residues: 1385.7712 ------------------------------------------------------------------------------- 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: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 923 GLN ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN B1127 HIS B1296 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 GLN ** C2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2284 ASN ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2284 ASN ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.8601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.668 113365 Z= 3.876 Angle : 2.903 37.821 154462 Z= 1.535 Chirality : 0.186 1.813 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.536 175.792 16824 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 50.71 Ramachandran Plot: Outliers : 2.71 % Allowed : 25.38 % Favored : 71.91 % Rotamer Outliers : 12.06 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 2.85 % 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: -6.79 (0.05), residues: 12368 helix: -4.28 (0.04), residues: 5672 sheet: -3.55 (0.12), residues: 1344 loop : -4.98 (0.06), residues: 5352 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2015 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1172 poor density : 843 time to evaluate : 8.809 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 outliers start: 1172 outliers final: 687 residues processed: 1911 average time/residue: 0.8780 time to fit residues: 3010.9423 Evaluate side-chains 1535 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 687 poor density : 848 time to evaluate : 8.693 Switching outliers to nearest non-outliers outliers start: 687 outliers final: 33 residues processed: 687 average time/residue: 0.7960 time to fit residues: 1050.4092 ------------------------------------------------------------------------------- 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: 4.9990 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3830 GLN ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3830 GLN ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.669 113365 Z= 3.881 Angle : 2.909 37.267 154462 Z= 1.539 Chirality : 0.193 3.743 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.561 177.904 16824 Min Nonbonded Distance : 1.338 Molprobity Statistics. All-atom Clashscore : 50.86 Ramachandran Plot: Outliers : 2.77 % Allowed : 25.82 % Favored : 71.41 % Rotamer Outliers : 10.12 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.21 % Twisted General : 2.95 % 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: -6.83 (0.05), residues: 12368 helix: -4.30 (0.04), residues: 5656 sheet: -3.60 (0.12), residues: 1312 loop : -5.03 (0.06), residues: 5400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1806 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 984 poor density : 822 time to evaluate : 8.165 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 outliers start: 984 outliers final: 542 residues processed: 1699 average time/residue: 0.8793 time to fit residues: 2675.3430 Evaluate side-chains 1379 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 542 poor density : 837 time to evaluate : 8.110 Switching outliers to nearest non-outliers outliers start: 542 outliers final: 33 residues processed: 542 average time/residue: 0.7529 time to fit residues: 786.8036 ------------------------------------------------------------------------------- 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: 5.9990 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 405 HIS ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4120 ASN ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.669 113365 Z= 3.884 Angle : 2.915 36.918 154462 Z= 1.542 Chirality : 0.193 3.559 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.588 178.815 16824 Min Nonbonded Distance : 0.534 Molprobity Statistics. All-atom Clashscore : 51.42 Ramachandran Plot: Outliers : 2.74 % Allowed : 26.21 % Favored : 71.05 % Rotamer Outliers : 7.73 % Cbeta Deviations : 1.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.56 % Twisted General : 2.98 % 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: -6.87 (0.05), residues: 12368 helix: -4.29 (0.04), residues: 5648 sheet: -3.69 (0.12), residues: 1388 loop : -5.07 (0.06), residues: 5332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 751 poor density : 820 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 751 outliers final: 449 residues processed: 1496 average time/residue: 0.9138 time to fit residues: 2434.4558 Evaluate side-chains 1277 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 449 poor density : 828 time to evaluate : 8.813 Switching outliers to nearest non-outliers outliers start: 449 outliers final: 35 residues processed: 449 average time/residue: 0.7911 time to fit residues: 687.6623 ------------------------------------------------------------------------------- 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: 4.9990 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 405 HIS ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1127 HIS ** A1296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2284 ASN ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS C 495 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1231 GLN ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4120 ASN ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.670 113365 Z= 3.887 Angle : 2.924 36.999 154462 Z= 1.547 Chirality : 0.193 3.464 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.636 178.681 16824 Min Nonbonded Distance : 0.749 Molprobity Statistics. All-atom Clashscore : 51.58 Ramachandran Plot: Outliers : 2.73 % Allowed : 26.54 % Favored : 70.73 % Rotamer Outliers : 5.63 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.45 % Twisted General : 2.99 % 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: -6.88 (0.05), residues: 12368 helix: -4.29 (0.04), residues: 5632 sheet: -3.69 (0.12), residues: 1324 loop : -5.08 (0.06), residues: 5412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 547 poor density : 817 time to evaluate : 8.672 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 outliers start: 547 outliers final: 274 residues processed: 1300 average time/residue: 0.9330 time to fit residues: 2150.5591 Evaluate side-chains 1082 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 808 time to evaluate : 8.730 Switching outliers to nearest non-outliers outliers start: 274 outliers final: 35 residues processed: 274 average time/residue: 0.7703 time to fit residues: 417.1226 ------------------------------------------------------------------------------- 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: 5.9990 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 405 HIS A 495 ASN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN B1598 GLN ** B2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1231 GLN ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.8933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.670 113365 Z= 3.887 Angle : 2.928 37.240 154462 Z= 1.547 Chirality : 0.193 3.412 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.697 178.770 16824 Min Nonbonded Distance : 0.808 Molprobity Statistics. All-atom Clashscore : 51.88 Ramachandran Plot: Outliers : 2.74 % Allowed : 26.91 % Favored : 70.35 % Rotamer Outliers : 2.82 % Cbeta Deviations : 1.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.09 % Twisted General : 3.06 % 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: -6.88 (0.05), residues: 12368 helix: -4.29 (0.04), residues: 5628 sheet: -3.59 (0.12), residues: 1272 loop : -5.12 (0.06), residues: 5468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24736 Ramachandran restraints generated. 12368 Oldfield, 0 Emsley, 12368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 806 time to evaluate : 8.924 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 outliers start: 274 outliers final: 136 residues processed: 1040 average time/residue: 0.9563 time to fit residues: 1751.7624 Evaluate side-chains 936 residues out of total 10876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 800 time to evaluate : 8.742 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 35 residues processed: 136 average time/residue: 0.8202 time to fit residues: 219.4272 ------------------------------------------------------------------------------- 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: 5.9990 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 405 HIS ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN ** A2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN ** B2011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1231 GLN ** C2011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.163399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122383 restraints weight = 198413.971| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.79 r_work: 0.2883 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.8965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.060 0.670 113365 Z= 3.887 Angle : 2.930 36.524 154462 Z= 1.549 Chirality : 0.193 3.371 18087 Planarity : 0.021 0.438 20349 Dihedral : 13.707 178.719 16824 Min Nonbonded Distance : 0.810 Molprobity Statistics. All-atom Clashscore : 51.66 Ramachandran Plot: Outliers : 2.74 % Allowed : 26.99 % Favored : 70.27 % Rotamer Outliers : 2.86 % Cbeta Deviations : 1.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 3.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.90 (0.05), residues: 12368 helix: -4.30 (0.04), residues: 5664 sheet: -3.65 (0.12), residues: 1256 loop : -5.13 (0.06), residues: 5448 =============================================================================== Job complete usr+sys time: 64699.97 seconds wall clock time: 1107 minutes 18.79 seconds (66438.79 seconds total)