Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 05:17:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2023/8hr7_34962.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 601 5.16 5 C 77620 2.51 5 N 21081 2.21 5 O 22360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 760": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 572": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "F GLU 354": "OE1" <-> "OE2" Residue "F GLU 671": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 229": "OE1" <-> "OE2" Residue "G GLU 566": "OE1" <-> "OE2" Residue "G GLU 736": "OE1" <-> "OE2" Residue "I GLU 354": "OE1" <-> "OE2" Residue "I GLU 736": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 566": "OE1" <-> "OE2" Residue "J GLU 736": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "K GLU 736": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 608": "OE1" <-> "OE2" Residue "L GLU 678": "OE1" <-> "OE2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "M GLU 289": "OE1" <-> "OE2" Residue "M GLU 704": "OE1" <-> "OE2" Residue "M GLU 785": "OE1" <-> "OE2" Residue "N GLU 472": "OE1" <-> "OE2" Residue "N GLU 760": "OE1" <-> "OE2" Residue "N GLU 785": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 545": "OE1" <-> "OE2" Residue "O GLU 638": "OE1" <-> "OE2" Residue "P GLU 890": "OE1" <-> "OE2" Residue "Q TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 471": "OE1" <-> "OE2" Residue "Q GLU 526": "OE1" <-> "OE2" Residue "Q GLU 534": "OE1" <-> "OE2" Residue "R GLU 209": "OE1" <-> "OE2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 714": "OE1" <-> "OE2" Residue "S GLU 209": "OE1" <-> "OE2" Residue "S GLU 279": "OE1" <-> "OE2" Residue "S GLU 517": "OE1" <-> "OE2" Residue "T GLU 202": "OE1" <-> "OE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 121662 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "B" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 6244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6244 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 41, 'TRANS': 732} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6217 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 41, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6239 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 733} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "I" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6273 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 6361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6361 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 43, 'TRANS': 742} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "O" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "P" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "Q" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "R" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "S" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "T" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Time building chain proxies: 43.32, per 1000 atoms: 0.36 Number of scatterers: 121662 At special positions: 0 Unit cell: (217.36, 303.68, 214.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 601 16.00 O 22360 8.00 N 21081 7.00 C 77620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 35.71 Conformation dependent library (CDL) restraints added in 13.2 seconds 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28866 Finding SS restraints... Secondary structure from input PDB file: 737 helices and 88 sheets defined 62.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.663A pdb=" N TYR A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.572A pdb=" N MET A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 169 removed outlier: 3.745A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.232A pdb=" N TYR A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 removed outlier: 4.067A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.503A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.589A pdb=" N LEU A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.537A pdb=" N ASP A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.569A pdb=" N ASP A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.971A pdb=" N GLY A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.080A pdb=" N PHE A 441 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.928A pdb=" N LEU A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS A 447 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.530A pdb=" N TYR A 465 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.524A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 4.216A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.530A pdb=" N ILE A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.881A pdb=" N ARG A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 636 removed outlier: 3.686A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 705 through 722 removed outlier: 4.289A pdb=" N ALA A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.747A pdb=" N GLY A 726 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 727 " --> pdb=" O GLU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 727' Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.905A pdb=" N ASN A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 770 through 791 removed outlier: 3.507A pdb=" N ILE A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.656A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.674A pdb=" N SER A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 889 through 897 removed outlier: 4.663A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 25 through 41 removed outlier: 4.037A pdb=" N SER B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 91 through 103 removed outlier: 4.644A pdb=" N SER B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.613A pdb=" N SER B 123 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.622A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.774A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 224 Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.713A pdb=" N ALA B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.517A pdb=" N ALA B 241 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 242 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 331 through 343 Processing helix chain 'B' and resid 362 through 385 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.982A pdb=" N LEU B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 456 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.541A pdb=" N LEU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.604A pdb=" N GLY B 535 " --> pdb=" O CYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 574 through 593 removed outlier: 3.510A pdb=" N LYS B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 619 Processing helix chain 'B' and resid 632 through 647 removed outlier: 4.219A pdb=" N THR B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'B' and resid 662 through 671 removed outlier: 3.534A pdb=" N ALA B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.619A pdb=" N TRP B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 771 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.875A pdb=" N ARG B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.658A pdb=" N THR C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 45 through 63 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.544A pdb=" N THR C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.804A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 162 through 171 removed outlier: 4.041A pdb=" N LEU C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.601A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 200 through 224 removed outlier: 3.564A pdb=" N ARG C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 4.184A pdb=" N ASN C 242 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.115A pdb=" N GLU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 309 Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.572A pdb=" N MET C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 456 through 462 Processing helix chain 'C' and resid 476 through 479 removed outlier: 3.505A pdb=" N LEU C 479 " --> pdb=" O PRO C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 553 through 566 Processing helix chain 'C' and resid 574 through 593 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 632 through 648 removed outlier: 3.767A pdb=" N ARG C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.639A pdb=" N SER C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 670 removed outlier: 3.741A pdb=" N ALA C 670 " --> pdb=" O ARG C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 700 Processing helix chain 'C' and resid 718 through 722 removed outlier: 3.692A pdb=" N GLU C 721 " --> pdb=" O ASN C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 729 removed outlier: 3.623A pdb=" N TRP C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 771 removed outlier: 3.542A pdb=" N LEU C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 793 removed outlier: 4.266A pdb=" N VAL C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 790 " --> pdb=" O VAL C 786 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.761A pdb=" N LEU D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.536A pdb=" N THR D 17 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 41 Processing helix chain 'D' and resid 45 through 62 Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.869A pdb=" N ARG D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.549A pdb=" N THR D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.502A pdb=" N SER D 123 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.607A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 4.108A pdb=" N SER D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 removed outlier: 3.561A pdb=" N ALA D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 224 removed outlier: 3.724A pdb=" N VAL D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 removed outlier: 4.268A pdb=" N ASN D 242 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 285 through 311 Processing helix chain 'D' and resid 331 through 343 removed outlier: 3.814A pdb=" N LEU D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 385 removed outlier: 4.062A pdb=" N LYS D 368 " --> pdb=" O ASN D 364 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 384 " --> pdb=" O TYR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.521A pdb=" N VAL D 400 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 489 removed outlier: 4.562A pdb=" N LEU D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 553 through 568 removed outlier: 3.649A pdb=" N ARG D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 593 removed outlier: 3.622A pdb=" N LYS D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 613 through 618 Processing helix chain 'D' and resid 632 through 647 Processing helix chain 'D' and resid 650 through 662 Processing helix chain 'D' and resid 662 through 669 Processing helix chain 'D' and resid 681 through 700 removed outlier: 3.626A pdb=" N ALA D 697 " --> pdb=" O MET D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 722 Processing helix chain 'D' and resid 723 through 729 Processing helix chain 'D' and resid 756 through 771 Processing helix chain 'D' and resid 775 through 793 removed outlier: 3.545A pdb=" N VAL D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 45 through 63 removed outlier: 3.703A pdb=" N ARG E 63 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 94 through 103 removed outlier: 3.562A pdb=" N SER E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.506A pdb=" N LEU E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 185 through 196 removed outlier: 3.512A pdb=" N LYS E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 224 removed outlier: 3.553A pdb=" N VAL E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.523A pdb=" N ALA E 232 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.160A pdb=" N ASN E 242 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 279 Processing helix chain 'E' and resid 285 through 310 Processing helix chain 'E' and resid 330 through 343 Processing helix chain 'E' and resid 362 through 385 removed outlier: 3.664A pdb=" N LYS E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS E 384 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 407 removed outlier: 3.540A pdb=" N LEU E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 456 removed outlier: 4.090A pdb=" N MET E 452 " --> pdb=" O ILE E 448 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.627A pdb=" N GLY E 461 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 479 Processing helix chain 'E' and resid 480 through 489 removed outlier: 3.553A pdb=" N VAL E 486 " --> pdb=" O PRO E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 531 through 536 removed outlier: 3.647A pdb=" N GLY E 535 " --> pdb=" O CYS E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 3.938A pdb=" N ARG E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 568 removed outlier: 3.556A pdb=" N ARG E 568 " --> pdb=" O TRP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 593 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 613 through 619 Processing helix chain 'E' and resid 632 through 647 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 662 through 670 Processing helix chain 'E' and resid 681 through 700 Processing helix chain 'E' and resid 723 through 729 Processing helix chain 'E' and resid 756 through 771 Processing helix chain 'E' and resid 775 through 793 Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 8 through 18 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 45 through 63 removed outlier: 3.711A pdb=" N ARG F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 107 through 118 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.583A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'F' and resid 171 through 184 removed outlier: 3.530A pdb=" N ALA F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.597A pdb=" N LYS F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 224 removed outlier: 3.578A pdb=" N VAL F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.116A pdb=" N ASN F 242 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 285 through 310 removed outlier: 3.539A pdb=" N TRP F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'F' and resid 362 through 385 removed outlier: 3.778A pdb=" N MET F 366 " --> pdb=" O ASP F 362 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.546A pdb=" N VAL F 400 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 456 removed outlier: 3.544A pdb=" N LEU F 449 " --> pdb=" O GLN F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 476 through 479 Processing helix chain 'F' and resid 480 through 489 Processing helix chain 'F' and resid 505 through 520 Processing helix chain 'F' and resid 531 through 536 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 553 through 568 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 593 removed outlier: 3.748A pdb=" N ALA F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 585 " --> pdb=" O ALA F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 613 through 619 Processing helix chain 'F' and resid 632 through 647 removed outlier: 3.551A pdb=" N ARG F 641 " --> pdb=" O TYR F 637 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 643 " --> pdb=" O ARG F 639 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 647 " --> pdb=" O LEU F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.532A pdb=" N LEU F 653 " --> pdb=" O MET F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 681 through 699 removed outlier: 3.656A pdb=" N ARG F 699 " --> pdb=" O LYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 removed outlier: 3.554A pdb=" N TRP F 727 " --> pdb=" O HIS F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 756 through 770 Processing helix chain 'F' and resid 775 through 793 removed outlier: 3.934A pdb=" N ARG F 781 " --> pdb=" O ALA F 777 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 785 " --> pdb=" O ARG F 781 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL F 786 " --> pdb=" O LYS F 782 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 790 " --> pdb=" O VAL F 786 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 25 through 41 removed outlier: 3.520A pdb=" N SER G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 62 removed outlier: 3.540A pdb=" N LYS G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 120 through 124 removed outlier: 3.545A pdb=" N SER G 123 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 removed outlier: 3.558A pdb=" N ASP G 141 " --> pdb=" O PRO G 137 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 171 removed outlier: 3.599A pdb=" N TRP G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 184 removed outlier: 3.757A pdb=" N ALA G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 196 Processing helix chain 'G' and resid 200 through 224 Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 236 through 241 removed outlier: 3.563A pdb=" N LEU G 240 " --> pdb=" O PRO G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 removed outlier: 3.567A pdb=" N LYS G 279 " --> pdb=" O GLY G 275 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP G 280 " --> pdb=" O LEU G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 310 removed outlier: 4.306A pdb=" N ASP G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 343 removed outlier: 3.642A pdb=" N LEU G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE G 338 " --> pdb=" O TYR G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 385 Processing helix chain 'G' and resid 396 through 406 removed outlier: 3.732A pdb=" N LEU G 406 " --> pdb=" O ASP G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 456 removed outlier: 3.864A pdb=" N MET G 452 " --> pdb=" O ILE G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 462 removed outlier: 3.958A pdb=" N GLY G 461 " --> pdb=" O ARG G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 490 Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 531 through 536 removed outlier: 3.566A pdb=" N GLY G 535 " --> pdb=" O CYS G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 553 through 568 Processing helix chain 'G' and resid 573 through 593 removed outlier: 4.229A pdb=" N ALA G 577 " --> pdb=" O LEU G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 610 through 612 No H-bonds generated for 'chain 'G' and resid 610 through 612' Processing helix chain 'G' and resid 613 through 619 removed outlier: 3.540A pdb=" N GLY G 618 " --> pdb=" O ALA G 614 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 619 " --> pdb=" O GLU G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 632 through 647 removed outlier: 3.681A pdb=" N GLU G 638 " --> pdb=" O LEU G 634 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA G 640 " --> pdb=" O GLU G 636 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG G 641 " --> pdb=" O TYR G 637 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR G 647 " --> pdb=" O LEU G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 661 Processing helix chain 'G' and resid 662 through 671 Processing helix chain 'G' and resid 681 through 700 removed outlier: 3.661A pdb=" N LYS G 695 " --> pdb=" O ALA G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 722 removed outlier: 3.703A pdb=" N GLU G 721 " --> pdb=" O ASN G 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 723 through 729 removed outlier: 3.553A pdb=" N GLY G 729 " --> pdb=" O PHE G 725 " (cutoff:3.500A) Processing helix chain 'G' and resid 756 through 771 Processing helix chain 'G' and resid 775 through 793 removed outlier: 3.756A pdb=" N ARG G 781 " --> pdb=" O ALA G 777 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL G 786 " --> pdb=" O LYS G 782 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 791 " --> pdb=" O ASN G 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 25 through 41 removed outlier: 3.566A pdb=" N PHE I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 63 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'I' and resid 106 through 118 removed outlier: 4.460A pdb=" N ILE I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.605A pdb=" N TRP I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 185 removed outlier: 3.789A pdb=" N SER I 185 " --> pdb=" O LYS I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 196 removed outlier: 3.644A pdb=" N ASP I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 224 removed outlier: 3.512A pdb=" N GLY I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 233 removed outlier: 4.052A pdb=" N ALA I 232 " --> pdb=" O GLU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 242 removed outlier: 3.548A pdb=" N LEU I 240 " --> pdb=" O PRO I 237 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN I 242 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 285 through 309 Processing helix chain 'I' and resid 331 through 343 Processing helix chain 'I' and resid 362 through 385 Processing helix chain 'I' and resid 396 through 405 removed outlier: 3.557A pdb=" N ASN I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 456 removed outlier: 3.655A pdb=" N ILE I 448 " --> pdb=" O ASN I 444 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I 449 " --> pdb=" O GLN I 445 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 453 " --> pdb=" O LEU I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 462 removed outlier: 3.660A pdb=" N THR I 460 " --> pdb=" O PRO I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 478 No H-bonds generated for 'chain 'I' and resid 476 through 478' Processing helix chain 'I' and resid 479 through 490 removed outlier: 4.380A pdb=" N LEU I 483 " --> pdb=" O LEU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 553 through 568 removed outlier: 3.521A pdb=" N ARG I 568 " --> pdb=" O TRP I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 593 Processing helix chain 'I' and resid 599 through 609 removed outlier: 4.241A pdb=" N MET I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 632 through 647 removed outlier: 4.006A pdb=" N ARG I 641 " --> pdb=" O TYR I 637 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU I 642 " --> pdb=" O GLU I 638 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU I 643 " --> pdb=" O ARG I 639 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL I 644 " --> pdb=" O ALA I 640 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR I 647 " --> pdb=" O LEU I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 661 removed outlier: 4.015A pdb=" N LEU I 653 " --> pdb=" O MET I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 670 Processing helix chain 'I' and resid 681 through 699 removed outlier: 3.540A pdb=" N LYS I 695 " --> pdb=" O ALA I 691 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 697 " --> pdb=" O MET I 693 " (cutoff:3.500A) Processing helix chain 'I' and resid 718 through 721 removed outlier: 3.681A pdb=" N GLU I 721 " --> pdb=" O ASN I 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 718 through 721' Processing helix chain 'I' and resid 722 through 729 removed outlier: 4.338A pdb=" N ARG I 726 " --> pdb=" O HIS I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 771 Processing helix chain 'I' and resid 775 through 793 removed outlier: 3.687A pdb=" N ARG I 781 " --> pdb=" O ALA I 777 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS I 782 " --> pdb=" O ASP I 778 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL I 786 " --> pdb=" O LYS I 782 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG I 791 " --> pdb=" O ASN I 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 8 through 18 Processing helix chain 'J' and resid 25 through 41 Processing helix chain 'J' and resid 45 through 62 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 94 through 103 removed outlier: 3.640A pdb=" N THR J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 120 through 124 removed outlier: 3.520A pdb=" N SER J 123 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 146 removed outlier: 3.703A pdb=" N TYR J 142 " --> pdb=" O THR J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 171 removed outlier: 4.020A pdb=" N TRP J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 185 removed outlier: 3.544A pdb=" N LEU J 176 " --> pdb=" O PRO J 172 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 196 removed outlier: 3.789A pdb=" N ILE J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 224 Processing helix chain 'J' and resid 236 through 241 Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 285 through 310 removed outlier: 3.633A pdb=" N LEU J 291 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN J 308 " --> pdb=" O THR J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 343 Processing helix chain 'J' and resid 362 through 385 Processing helix chain 'J' and resid 396 through 405 Processing helix chain 'J' and resid 436 through 456 Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 476 through 479 Processing helix chain 'J' and resid 480 through 489 Processing helix chain 'J' and resid 505 through 520 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 553 through 568 removed outlier: 3.544A pdb=" N ARG J 568 " --> pdb=" O TRP J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 593 removed outlier: 3.512A pdb=" N ARG J 586 " --> pdb=" O ILE J 582 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 609 removed outlier: 3.609A pdb=" N MET J 609 " --> pdb=" O GLN J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 612 No H-bonds generated for 'chain 'J' and resid 610 through 612' Processing helix chain 'J' and resid 615 through 619 Processing helix chain 'J' and resid 632 through 647 removed outlier: 3.718A pdb=" N GLU J 638 " --> pdb=" O LEU J 634 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA J 640 " --> pdb=" O GLU J 636 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG J 641 " --> pdb=" O TYR J 637 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU J 643 " --> pdb=" O ARG J 639 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL J 644 " --> pdb=" O ALA J 640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR J 647 " --> pdb=" O LEU J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 662 Processing helix chain 'J' and resid 662 through 671 removed outlier: 3.535A pdb=" N GLU J 671 " --> pdb=" O LYS J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 681 through 699 removed outlier: 3.521A pdb=" N LYS J 695 " --> pdb=" O ALA J 691 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG J 699 " --> pdb=" O LYS J 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 721 Processing helix chain 'J' and resid 722 through 729 removed outlier: 4.270A pdb=" N ARG J 726 " --> pdb=" O HIS J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 756 through 771 Processing helix chain 'J' and resid 775 through 793 removed outlier: 3.508A pdb=" N ARG J 781 " --> pdb=" O ALA J 777 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL J 786 " --> pdb=" O LYS J 782 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY J 790 " --> pdb=" O VAL J 786 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 8 through 18 removed outlier: 3.594A pdb=" N THR K 17 " --> pdb=" O TYR K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 45 through 63 Processing helix chain 'K' and resid 68 through 80 removed outlier: 3.712A pdb=" N GLU K 78 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 102 removed outlier: 3.605A pdb=" N THR K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 120 through 124 removed outlier: 3.500A pdb=" N SER K 123 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.769A pdb=" N CYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU K 169 " --> pdb=" O TRP K 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 184 removed outlier: 3.579A pdb=" N ALA K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 200 through 224 Processing helix chain 'K' and resid 229 through 234 removed outlier: 3.814A pdb=" N ALA K 232 " --> pdb=" O GLU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 242 removed outlier: 4.008A pdb=" N ASN K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 280 Processing helix chain 'K' and resid 285 through 313 removed outlier: 3.754A pdb=" N TRP K 293 " --> pdb=" O GLU K 289 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP K 311 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE K 312 " --> pdb=" O GLN K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.760A pdb=" N LEU K 335 " --> pdb=" O GLU K 331 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY K 343 " --> pdb=" O LYS K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 385 removed outlier: 3.782A pdb=" N ALA K 383 " --> pdb=" O GLU K 379 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS K 384 " --> pdb=" O TYR K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 407 removed outlier: 3.529A pdb=" N ASP K 402 " --> pdb=" O SER K 398 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU K 406 " --> pdb=" O ASP K 402 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL K 407 " --> pdb=" O ASN K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 456 removed outlier: 3.688A pdb=" N ALA K 447 " --> pdb=" O LYS K 443 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET K 452 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU K 453 " --> pdb=" O LEU K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 462 Processing helix chain 'K' and resid 476 through 479 Processing helix chain 'K' and resid 480 through 490 removed outlier: 3.562A pdb=" N LYS K 489 " --> pdb=" O ARG K 485 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER K 490 " --> pdb=" O VAL K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 520 removed outlier: 3.540A pdb=" N ARG K 511 " --> pdb=" O ILE K 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE K 513 " --> pdb=" O GLY K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 535 Processing helix chain 'K' and resid 537 through 542 Processing helix chain 'K' and resid 553 through 568 removed outlier: 3.556A pdb=" N ARG K 568 " --> pdb=" O TRP K 564 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 593 removed outlier: 3.789A pdb=" N ALA K 577 " --> pdb=" O LEU K 573 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 610 through 612 No H-bonds generated for 'chain 'K' and resid 610 through 612' Processing helix chain 'K' and resid 615 through 619 removed outlier: 3.800A pdb=" N GLY K 618 " --> pdb=" O GLU K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 647 removed outlier: 3.819A pdb=" N ARG K 641 " --> pdb=" O TYR K 637 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL K 644 " --> pdb=" O ALA K 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 662 removed outlier: 3.538A pdb=" N SER K 662 " --> pdb=" O GLN K 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 671 removed outlier: 3.538A pdb=" N GLU K 671 " --> pdb=" O LYS K 667 " (cutoff:3.500A) Processing helix chain 'K' and resid 681 through 700 Processing helix chain 'K' and resid 718 through 722 Processing helix chain 'K' and resid 723 through 729 removed outlier: 3.652A pdb=" N GLY K 729 " --> pdb=" O PHE K 725 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 771 Processing helix chain 'K' and resid 775 through 793 removed outlier: 3.535A pdb=" N VAL K 786 " --> pdb=" O LYS K 782 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY K 790 " --> pdb=" O VAL K 786 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG K 791 " --> pdb=" O ASN K 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.565A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 41 Processing helix chain 'L' and resid 45 through 63 Processing helix chain 'L' and resid 68 through 80 removed outlier: 3.780A pdb=" N ARG L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 105 removed outlier: 3.517A pdb=" N THR L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 118 removed outlier: 4.529A pdb=" N ILE L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 124 removed outlier: 3.737A pdb=" N SER L 123 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN L 124 " --> pdb=" O PRO L 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 124' Processing helix chain 'L' and resid 136 through 146 removed outlier: 3.588A pdb=" N TYR L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 171 removed outlier: 3.715A pdb=" N TRP L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 184 removed outlier: 3.820A pdb=" N ALA L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 196 Processing helix chain 'L' and resid 200 through 224 removed outlier: 3.669A pdb=" N VAL L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 234 Processing helix chain 'L' and resid 236 through 241 Processing helix chain 'L' and resid 265 through 280 Processing helix chain 'L' and resid 285 through 310 removed outlier: 3.668A pdb=" N GLN L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP L 310 " --> pdb=" O LEU L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 343 removed outlier: 3.848A pdb=" N LEU L 335 " --> pdb=" O GLU L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 385 removed outlier: 3.854A pdb=" N MET L 366 " --> pdb=" O ASP L 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN L 367 " --> pdb=" O PRO L 363 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS L 368 " --> pdb=" O ASN L 364 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 383 " --> pdb=" O GLU L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 405 Processing helix chain 'L' and resid 436 through 456 removed outlier: 3.503A pdb=" N ASP L 441 " --> pdb=" O LEU L 437 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE L 448 " --> pdb=" O ASN L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 462 removed outlier: 3.550A pdb=" N GLY L 461 " --> pdb=" O ARG L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 478 No H-bonds generated for 'chain 'L' and resid 476 through 478' Processing helix chain 'L' and resid 479 through 490 removed outlier: 4.477A pdb=" N LEU L 483 " --> pdb=" O LEU L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 520 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 553 through 568 Processing helix chain 'L' and resid 574 through 593 Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 610 through 612 No H-bonds generated for 'chain 'L' and resid 610 through 612' Processing helix chain 'L' and resid 613 through 617 removed outlier: 3.565A pdb=" N GLU L 617 " --> pdb=" O ALA L 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 632 through 647 removed outlier: 3.557A pdb=" N GLU L 636 " --> pdb=" O LEU L 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR L 647 " --> pdb=" O LEU L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 681 through 700 Processing helix chain 'L' and resid 718 through 722 removed outlier: 3.680A pdb=" N GLU L 721 " --> pdb=" O ASN L 718 " (cutoff:3.500A) Processing helix chain 'L' and resid 723 through 729 removed outlier: 3.659A pdb=" N TRP L 727 " --> pdb=" O HIS L 723 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 771 Processing helix chain 'L' and resid 775 through 793 removed outlier: 3.578A pdb=" N LYS L 782 " --> pdb=" O ASP L 778 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 17 removed outlier: 3.544A pdb=" N THR M 17 " --> pdb=" O TYR M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 41 removed outlier: 3.500A pdb=" N SER M 31 " --> pdb=" O GLU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 64 Processing helix chain 'M' and resid 68 through 80 removed outlier: 4.066A pdb=" N ARG M 74 " --> pdb=" O VAL M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 103 removed outlier: 3.614A pdb=" N SER M 103 " --> pdb=" O GLN M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 118 Processing helix chain 'M' and resid 120 through 124 removed outlier: 3.601A pdb=" N SER M 123 " --> pdb=" O GLY M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 146 removed outlier: 3.506A pdb=" N ASP M 141 " --> pdb=" O PRO M 137 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR M 142 " --> pdb=" O THR M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 171 removed outlier: 3.902A pdb=" N LEU M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 185 removed outlier: 3.959A pdb=" N SER M 185 " --> pdb=" O LYS M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 196 Processing helix chain 'M' and resid 200 through 224 removed outlier: 3.546A pdb=" N VAL M 221 " --> pdb=" O ILE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 234 removed outlier: 3.560A pdb=" N ALA M 232 " --> pdb=" O GLU M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 242 removed outlier: 3.716A pdb=" N ASN M 242 " --> pdb=" O GLN M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 279 Processing helix chain 'M' and resid 285 through 311 removed outlier: 3.599A pdb=" N ASP M 311 " --> pdb=" O VAL M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 Processing helix chain 'M' and resid 332 through 343 removed outlier: 4.335A pdb=" N SER M 336 " --> pdb=" O LYS M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 385 removed outlier: 3.625A pdb=" N HIS M 384 " --> pdb=" O TYR M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 405 Processing helix chain 'M' and resid 436 through 456 Processing helix chain 'M' and resid 457 through 462 Processing helix chain 'M' and resid 476 through 479 Processing helix chain 'M' and resid 480 through 490 Processing helix chain 'M' and resid 505 through 520 Processing helix chain 'M' and resid 531 through 535 Processing helix chain 'M' and resid 537 through 542 Processing helix chain 'M' and resid 553 through 568 Processing helix chain 'M' and resid 573 through 593 removed outlier: 3.701A pdb=" N ALA M 577 " --> pdb=" O LEU M 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 609 removed outlier: 3.592A pdb=" N MET M 609 " --> pdb=" O GLN M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 633 through 646 removed outlier: 3.882A pdb=" N VAL M 644 " --> pdb=" O ALA M 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 650 through 662 removed outlier: 3.600A pdb=" N GLN M 658 " --> pdb=" O LYS M 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 662 through 671 Processing helix chain 'M' and resid 681 through 700 removed outlier: 3.691A pdb=" N VAL M 686 " --> pdb=" O ASP M 682 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU M 688 " --> pdb=" O ALA M 684 " (cutoff:3.500A) Processing helix chain 'M' and resid 718 through 722 removed outlier: 3.796A pdb=" N GLU M 721 " --> pdb=" O ASN M 718 " (cutoff:3.500A) Processing helix chain 'M' and resid 723 through 729 Processing helix chain 'M' and resid 756 through 771 Processing helix chain 'M' and resid 775 through 793 removed outlier: 3.683A pdb=" N ARG M 781 " --> pdb=" O ALA M 777 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS M 782 " --> pdb=" O ASP M 778 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL M 786 " --> pdb=" O LYS M 782 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG M 791 " --> pdb=" O ASN M 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 25 through 41 removed outlier: 3.700A pdb=" N GLU N 39 " --> pdb=" O LEU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 63 Processing helix chain 'N' and resid 68 through 80 removed outlier: 3.809A pdb=" N ARG N 74 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 103 Processing helix chain 'N' and resid 107 through 118 Processing helix chain 'N' and resid 120 through 124 removed outlier: 3.561A pdb=" N SER N 123 " --> pdb=" O GLY N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 146 removed outlier: 3.940A pdb=" N TYR N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.770A pdb=" N CYS N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 184 Processing helix chain 'N' and resid 185 through 196 removed outlier: 3.550A pdb=" N LYS N 189 " --> pdb=" O SER N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 224 Processing helix chain 'N' and resid 236 through 243 removed outlier: 3.606A pdb=" N ASN N 242 " --> pdb=" O GLN N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 280 Processing helix chain 'N' and resid 285 through 310 removed outlier: 4.405A pdb=" N LEU N 291 " --> pdb=" O GLY N 287 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP N 310 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 343 removed outlier: 3.946A pdb=" N LEU N 335 " --> pdb=" O GLU N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 385 removed outlier: 3.819A pdb=" N ALA N 383 " --> pdb=" O GLU N 379 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS N 384 " --> pdb=" O TYR N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 405 Processing helix chain 'N' and resid 436 through 456 removed outlier: 3.540A pdb=" N ILE N 448 " --> pdb=" O ASN N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 462 Processing helix chain 'N' and resid 476 through 479 Processing helix chain 'N' and resid 480 through 489 removed outlier: 3.500A pdb=" N LYS N 489 " --> pdb=" O ARG N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 520 Processing helix chain 'N' and resid 531 through 535 Processing helix chain 'N' and resid 537 through 542 Processing helix chain 'N' and resid 553 through 568 Processing helix chain 'N' and resid 571 through 573 No H-bonds generated for 'chain 'N' and resid 571 through 573' Processing helix chain 'N' and resid 574 through 593 removed outlier: 3.541A pdb=" N LYS N 590 " --> pdb=" O ARG N 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 609 removed outlier: 3.587A pdb=" N MET N 609 " --> pdb=" O GLN N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 610 through 612 No H-bonds generated for 'chain 'N' and resid 610 through 612' Processing helix chain 'N' and resid 613 through 619 removed outlier: 3.644A pdb=" N GLY N 618 " --> pdb=" O ALA N 614 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU N 619 " --> pdb=" O GLU N 615 " (cutoff:3.500A) Processing helix chain 'N' and resid 632 through 645 removed outlier: 3.685A pdb=" N ALA N 640 " --> pdb=" O GLU N 636 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 643 " --> pdb=" O ARG N 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 661 Processing helix chain 'N' and resid 662 through 671 Processing helix chain 'N' and resid 681 through 699 Processing helix chain 'N' and resid 718 through 722 Processing helix chain 'N' and resid 723 through 729 Processing helix chain 'N' and resid 756 through 772 Processing helix chain 'N' and resid 775 through 793 removed outlier: 3.522A pdb=" N VAL N 786 " --> pdb=" O LYS N 782 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY N 790 " --> pdb=" O VAL N 786 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG N 791 " --> pdb=" O ASN N 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 51 removed outlier: 3.964A pdb=" N ASP O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL O 42 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU O 43 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 95 removed outlier: 3.547A pdb=" N PHE O 85 " --> pdb=" O GLY O 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 137 removed outlier: 3.781A pdb=" N MET O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 168 removed outlier: 4.002A pdb=" N LYS O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU O 167 " --> pdb=" O GLY O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.799A pdb=" N PHE O 177 " --> pdb=" O LYS O 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER O 178 " --> pdb=" O PRO O 174 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP O 179 " --> pdb=" O GLU O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 211 removed outlier: 4.042A pdb=" N ILE O 199 " --> pdb=" O ASP O 195 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU O 201 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU O 202 " --> pdb=" O GLU O 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 240 removed outlier: 3.521A pdb=" N VAL O 233 " --> pdb=" O ALA O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 268 removed outlier: 3.611A pdb=" N TYR O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 268 " --> pdb=" O LYS O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 277 Processing helix chain 'O' and resid 279 through 302 Processing helix chain 'O' and resid 312 through 318 Processing helix chain 'O' and resid 344 through 356 removed outlier: 3.838A pdb=" N GLU O 354 " --> pdb=" O ASP O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 361 through 373 removed outlier: 3.738A pdb=" N VAL O 368 " --> pdb=" O ALA O 364 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 395 removed outlier: 3.550A pdb=" N SER O 395 " --> pdb=" O TYR O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 425 removed outlier: 3.510A pdb=" N LEU O 416 " --> pdb=" O SER O 412 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY O 423 " --> pdb=" O ASN O 419 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER O 424 " --> pdb=" O ALA O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 433 removed outlier: 4.242A pdb=" N TYR O 430 " --> pdb=" O LEU O 426 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG O 431 " --> pdb=" O SER O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 458 Processing helix chain 'O' and resid 472 through 490 removed outlier: 3.812A pdb=" N ILE O 480 " --> pdb=" O ARG O 476 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR O 481 " --> pdb=" O ASN O 477 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 503 Processing helix chain 'O' and resid 505 through 514 removed outlier: 3.626A pdb=" N SER O 509 " --> pdb=" O CYS O 505 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN O 512 " --> pdb=" O VAL O 508 " (cutoff:3.500A) Processing helix chain 'O' and resid 525 through 538 removed outlier: 4.032A pdb=" N GLU O 529 " --> pdb=" O ARG O 525 " (cutoff:3.500A) Processing helix chain 'O' and resid 546 through 560 Processing helix chain 'O' and resid 563 through 567 removed outlier: 3.551A pdb=" N ILE O 567 " --> pdb=" O ASP O 564 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 606 Processing helix chain 'O' and resid 622 through 636 removed outlier: 3.586A pdb=" N ILE O 632 " --> pdb=" O ALA O 628 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER O 633 " --> pdb=" O ILE O 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA O 634 " --> pdb=" O ALA O 630 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS O 635 " --> pdb=" O ASP O 631 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG O 636 " --> pdb=" O ILE O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 646 removed outlier: 3.639A pdb=" N PHE O 646 " --> pdb=" O ILE O 642 " (cutoff:3.500A) Processing helix chain 'O' and resid 701 through 716 removed outlier: 3.687A pdb=" N GLU O 705 " --> pdb=" O ASP O 701 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP O 708 " --> pdb=" O THR O 704 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA O 709 " --> pdb=" O GLU O 705 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU O 714 " --> pdb=" O ILE O 710 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP O 716 " --> pdb=" O LYS O 712 " (cutoff:3.500A) Processing helix chain 'O' and resid 719 through 724 removed outlier: 3.508A pdb=" N ILE O 723 " --> pdb=" O ASN O 719 " (cutoff:3.500A) Processing helix chain 'O' and resid 725 through 727 No H-bonds generated for 'chain 'O' and resid 725 through 727' Processing helix chain 'O' and resid 730 through 746 removed outlier: 3.913A pdb=" N ASN O 746 " --> pdb=" O TYR O 742 " (cutoff:3.500A) Processing helix chain 'O' and resid 746 through 751 removed outlier: 4.217A pdb=" N ASP O 750 " --> pdb=" O ASN O 746 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN O 751 " --> pdb=" O ASN O 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 746 through 751' Processing helix chain 'O' and resid 770 through 786 removed outlier: 4.673A pdb=" N VAL O 786 " --> pdb=" O PHE O 782 " (cutoff:3.500A) Processing helix chain 'O' and resid 786 through 791 removed outlier: 4.028A pdb=" N SER O 791 " --> pdb=" O LEU O 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 814 through 830 removed outlier: 3.536A pdb=" N LYS O 819 " --> pdb=" O ASP O 815 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 830 " --> pdb=" O GLU O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 834 through 839 removed outlier: 3.769A pdb=" N HIS O 839 " --> pdb=" O TRP O 835 " (cutoff:3.500A) Processing helix chain 'O' and resid 839 through 846 removed outlier: 3.533A pdb=" N ILE O 846 " --> pdb=" O PHE O 842 " (cutoff:3.500A) Processing helix chain 'O' and resid 867 through 883 removed outlier: 3.793A pdb=" N SER O 873 " --> pdb=" O ASN O 869 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY O 883 " --> pdb=" O ASP O 879 " (cutoff:3.500A) Processing helix chain 'O' and resid 890 through 898 removed outlier: 3.856A pdb=" N TYR O 894 " --> pdb=" O GLU O 890 " (cutoff:3.500A) Processing helix chain 'O' and resid 915 through 919 removed outlier: 4.132A pdb=" N ASN O 918 " --> pdb=" O THR O 915 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 removed outlier: 3.864A pdb=" N THR P 27 " --> pdb=" O PRO P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 49 Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'P' and resid 111 through 115 Processing helix chain 'P' and resid 121 through 141 removed outlier: 3.679A pdb=" N MET P 132 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS P 136 " --> pdb=" O MET P 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 169 removed outlier: 3.503A pdb=" N LYS P 148 " --> pdb=" O ASN P 144 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN P 159 " --> pdb=" O ASN P 155 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY P 163 " --> pdb=" O GLN P 159 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU P 167 " --> pdb=" O GLY P 163 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP P 169 " --> pdb=" O HIS P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 3.856A pdb=" N SER P 178 " --> pdb=" O PRO P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 189 removed outlier: 3.771A pdb=" N ASP P 188 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR P 189 " --> pdb=" O GLN P 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 185 through 189' Processing helix chain 'P' and resid 195 through 212 removed outlier: 3.894A pdb=" N ILE P 199 " --> pdb=" O ASP P 195 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU P 201 " --> pdb=" O SER P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 240 removed outlier: 4.238A pdb=" N VAL P 233 " --> pdb=" O ALA P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 268 removed outlier: 3.611A pdb=" N TYR P 257 " --> pdb=" O ASP P 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 267 " --> pdb=" O GLY P 263 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN P 268 " --> pdb=" O LYS P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 277 Processing helix chain 'P' and resid 279 through 302 removed outlier: 3.741A pdb=" N GLU P 291 " --> pdb=" O GLY P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 305 No H-bonds generated for 'chain 'P' and resid 303 through 305' Processing helix chain 'P' and resid 312 through 318 Processing helix chain 'P' and resid 343 through 357 Processing helix chain 'P' and resid 361 through 373 Processing helix chain 'P' and resid 375 through 395 Processing helix chain 'P' and resid 412 through 425 removed outlier: 3.869A pdb=" N ALA P 420 " --> pdb=" O LEU P 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY P 423 " --> pdb=" O ASN P 419 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET P 425 " --> pdb=" O LEU P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 431 Processing helix chain 'P' and resid 442 through 458 removed outlier: 4.190A pdb=" N CYS P 447 " --> pdb=" O MET P 443 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS P 448 " --> pdb=" O ASP P 444 " (cutoff:3.500A) Processing helix chain 'P' and resid 462 through 466 removed outlier: 3.543A pdb=" N TYR P 465 " --> pdb=" O THR P 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 466 " --> pdb=" O GLY P 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 462 through 466' Processing helix chain 'P' and resid 473 through 490 removed outlier: 3.608A pdb=" N CYS P 478 " --> pdb=" O ALA P 474 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER P 479 " --> pdb=" O LEU P 475 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN P 485 " --> pdb=" O TYR P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 493 through 514 removed outlier: 3.742A pdb=" N PHE P 497 " --> pdb=" O SER P 493 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN P 499 " --> pdb=" O SER P 495 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU P 502 " --> pdb=" O LEU P 498 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS P 505 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 507 " --> pdb=" O VAL P 503 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL P 508 " --> pdb=" O GLY P 504 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER P 509 " --> pdb=" O CYS P 505 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN P 513 " --> pdb=" O SER P 509 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE P 514 " --> pdb=" O ILE P 510 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 539 removed outlier: 3.882A pdb=" N GLU P 529 " --> pdb=" O ARG P 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 537 " --> pdb=" O SER P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 546 through 558 removed outlier: 3.502A pdb=" N ASN P 552 " --> pdb=" O SER P 548 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG P 553 " --> pdb=" O HIS P 549 " (cutoff:3.500A) Processing helix chain 'P' and resid 563 through 567 removed outlier: 3.884A pdb=" N LYS P 566 " --> pdb=" O ASN P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 592 through 596 removed outlier: 3.937A pdb=" N THR P 595 " --> pdb=" O ASN P 592 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU P 596 " --> pdb=" O ILE P 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 592 through 596' Processing helix chain 'P' and resid 597 through 608 Processing helix chain 'P' and resid 621 through 636 removed outlier: 4.279A pdb=" N LEU P 625 " --> pdb=" O SER P 621 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER P 633 " --> pdb=" O ILE P 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS P 635 " --> pdb=" O ASP P 631 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG P 636 " --> pdb=" O ILE P 632 " (cutoff:3.500A) Processing helix chain 'P' and resid 642 through 646 removed outlier: 4.243A pdb=" N PHE P 646 " --> pdb=" O THR P 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 701 through 721 removed outlier: 4.132A pdb=" N GLU P 705 " --> pdb=" O ASP P 701 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE P 706 " --> pdb=" O ASP P 702 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER P 707 " --> pdb=" O ALA P 703 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN P 719 " --> pdb=" O GLN P 715 " (cutoff:3.500A) Processing helix chain 'P' and resid 723 through 727 removed outlier: 3.620A pdb=" N ILE P 727 " --> pdb=" O GLU P 724 " (cutoff:3.500A) Processing helix chain 'P' and resid 730 through 752 removed outlier: 3.629A pdb=" N ARG P 740 " --> pdb=" O LYS P 736 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN P 746 " --> pdb=" O TYR P 742 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN P 747 " --> pdb=" O PHE P 743 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL P 748 " --> pdb=" O ASN P 744 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA P 749 " --> pdb=" O LEU P 745 " (cutoff:3.500A) Processing helix chain 'P' and resid 770 through 789 removed outlier: 3.774A pdb=" N VAL P 779 " --> pdb=" O MET P 775 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL P 786 " --> pdb=" O PHE P 782 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU P 787 " --> pdb=" O LEU P 783 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL P 788 " --> pdb=" O HIS P 784 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU P 789 " --> pdb=" O ALA P 785 " (cutoff:3.500A) Processing helix chain 'P' and resid 814 through 831 removed outlier: 3.685A pdb=" N LYS P 827 " --> pdb=" O ILE P 823 " (cutoff:3.500A) Processing helix chain 'P' and resid 834 through 839 removed outlier: 3.610A pdb=" N THR P 838 " --> pdb=" O THR P 834 " (cutoff:3.500A) Processing helix chain 'P' and resid 841 through 846 Processing helix chain 'P' and resid 857 through 861 removed outlier: 3.874A pdb=" N ILE P 861 " --> pdb=" O VAL P 858 " (cutoff:3.500A) Processing helix chain 'P' and resid 866 through 883 removed outlier: 3.868A pdb=" N LYS P 870 " --> pdb=" O LYS P 866 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 878 " --> pdb=" O PHE P 874 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP P 879 " --> pdb=" O ASN P 875 " (cutoff:3.500A) Processing helix chain 'P' and resid 888 through 898 removed outlier: 3.776A pdb=" N ASN P 898 " --> pdb=" O TYR P 894 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 51 removed outlier: 3.718A pdb=" N ARG Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP Q 39 " --> pdb=" O LYS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 95 removed outlier: 3.511A pdb=" N ASN Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 115 Processing helix chain 'Q' and resid 121 through 141 Processing helix chain 'Q' and resid 145 through 169 removed outlier: 3.631A pdb=" N GLN Q 149 " --> pdb=" O ASP Q 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN Q 152 " --> pdb=" O LYS Q 148 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS Q 165 " --> pdb=" O GLN Q 161 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU Q 166 " --> pdb=" O ARG Q 162 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Q 167 " --> pdb=" O GLY Q 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Q 169 " --> pdb=" O HIS Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 180 removed outlier: 3.614A pdb=" N PHE Q 177 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER Q 178 " --> pdb=" O PRO Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 211 Processing helix chain 'Q' and resid 229 through 241 Processing helix chain 'Q' and resid 253 through 267 removed outlier: 3.850A pdb=" N TYR Q 257 " --> pdb=" O ASP Q 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU Q 267 " --> pdb=" O GLY Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 277 removed outlier: 4.342A pdb=" N GLU Q 275 " --> pdb=" O LYS Q 271 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 300 removed outlier: 3.577A pdb=" N LEU Q 293 " --> pdb=" O MET Q 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN Q 295 " --> pdb=" O GLU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 312 through 318 Processing helix chain 'Q' and resid 343 through 356 removed outlier: 3.541A pdb=" N GLU Q 354 " --> pdb=" O ASP Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 3.588A pdb=" N TYR Q 367 " --> pdb=" O ASP Q 363 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Q 368 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 375 through 394 removed outlier: 3.534A pdb=" N LEU Q 383 " --> pdb=" O LEU Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 412 through 425 removed outlier: 3.934A pdb=" N ALA Q 420 " --> pdb=" O LEU Q 416 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY Q 423 " --> pdb=" O ASN Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 433 Processing helix chain 'Q' and resid 442 through 458 removed outlier: 3.547A pdb=" N LYS Q 448 " --> pdb=" O ASP Q 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE Q 451 " --> pdb=" O CYS Q 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP Q 457 " --> pdb=" O TYR Q 453 " (cutoff:3.500A) Processing helix chain 'Q' and resid 462 through 466 Processing helix chain 'Q' and resid 472 through 490 removed outlier: 4.252A pdb=" N SER Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE Q 480 " --> pdb=" O ARG Q 476 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Q 481 " --> pdb=" O ASN Q 477 " (cutoff:3.500A) Processing helix chain 'Q' and resid 493 through 515 removed outlier: 3.586A pdb=" N GLN Q 499 " --> pdb=" O SER Q 495 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL Q 508 " --> pdb=" O GLY Q 504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 540 removed outlier: 3.672A pdb=" N SER Q 540 " --> pdb=" O VAL Q 536 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 559 removed outlier: 4.154A pdb=" N ARG Q 553 " --> pdb=" O HIS Q 549 " (cutoff:3.500A) Processing helix chain 'Q' and resid 563 through 567 Processing helix chain 'Q' and resid 592 through 596 removed outlier: 3.991A pdb=" N THR Q 595 " --> pdb=" O ASN Q 592 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU Q 596 " --> pdb=" O ILE Q 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 592 through 596' Processing helix chain 'Q' and resid 597 through 606 Processing helix chain 'Q' and resid 622 through 636 removed outlier: 3.506A pdb=" N SER Q 633 " --> pdb=" O ILE Q 629 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG Q 636 " --> pdb=" O ILE Q 632 " (cutoff:3.500A) Processing helix chain 'Q' and resid 639 through 645 Processing helix chain 'Q' and resid 701 through 718 removed outlier: 3.754A pdb=" N GLU Q 705 " --> pdb=" O ASP Q 701 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE Q 706 " --> pdb=" O ASP Q 702 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER Q 707 " --> pdb=" O ALA Q 703 " (cutoff:3.500A) Processing helix chain 'Q' and resid 720 through 725 removed outlier: 3.729A pdb=" N ILE Q 725 " --> pdb=" O ASN Q 721 " (cutoff:3.500A) Processing helix chain 'Q' and resid 730 through 752 removed outlier: 3.816A pdb=" N TRP Q 738 " --> pdb=" O ILE Q 734 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE Q 743 " --> pdb=" O SER Q 739 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN Q 747 " --> pdb=" O PHE Q 743 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL Q 748 " --> pdb=" O ASN Q 744 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS Q 752 " --> pdb=" O VAL Q 748 " (cutoff:3.500A) Processing helix chain 'Q' and resid 770 through 791 removed outlier: 3.964A pdb=" N GLU Q 789 " --> pdb=" O ALA Q 785 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER Q 791 " --> pdb=" O LEU Q 787 " (cutoff:3.500A) Processing helix chain 'Q' and resid 814 through 831 Processing helix chain 'Q' and resid 834 through 839 Processing helix chain 'Q' and resid 839 through 846 removed outlier: 3.943A pdb=" N PHE Q 843 " --> pdb=" O HIS Q 839 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 856 Processing helix chain 'Q' and resid 866 through 883 removed outlier: 4.012A pdb=" N LYS Q 870 " --> pdb=" O LYS Q 866 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER Q 873 " --> pdb=" O ASN Q 869 " (cutoff:3.500A) Processing helix chain 'Q' and resid 888 through 898 Processing helix chain 'R' and resid 34 through 51 removed outlier: 3.501A pdb=" N ASP R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR R 51 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 94 removed outlier: 3.758A pdb=" N SER R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 140 removed outlier: 3.578A pdb=" N THR R 124 " --> pdb=" O PRO R 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 165 removed outlier: 4.047A pdb=" N ARG R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY R 163 " --> pdb=" O GLN R 159 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 196 through 211 Processing helix chain 'R' and resid 229 through 241 Processing helix chain 'R' and resid 253 through 267 removed outlier: 3.823A pdb=" N TYR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 277 removed outlier: 3.581A pdb=" N GLU R 277 " --> pdb=" O LEU R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 302 removed outlier: 3.616A pdb=" N GLU R 291 " --> pdb=" O GLY R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 307 Processing helix chain 'R' and resid 312 through 318 Processing helix chain 'R' and resid 344 through 354 removed outlier: 4.306A pdb=" N GLU R 354 " --> pdb=" O ASP R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 374 removed outlier: 3.750A pdb=" N TYR R 367 " --> pdb=" O ASP R 363 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 368 " --> pdb=" O ALA R 364 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN R 374 " --> pdb=" O GLU R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 395 removed outlier: 3.883A pdb=" N HIS R 392 " --> pdb=" O THR R 388 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA R 393 " --> pdb=" O LYS R 389 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR R 394 " --> pdb=" O LYS R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 425 removed outlier: 3.974A pdb=" N GLY R 423 " --> pdb=" O ASN R 419 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER R 424 " --> pdb=" O ALA R 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 425 through 433 removed outlier: 4.412A pdb=" N ARG R 431 " --> pdb=" O SER R 427 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 456 removed outlier: 3.621A pdb=" N GLN R 456 " --> pdb=" O THR R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 462 through 466 Processing helix chain 'R' and resid 472 through 490 removed outlier: 4.533A pdb=" N ILE R 480 " --> pdb=" O ARG R 476 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR R 481 " --> pdb=" O ASN R 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS R 490 " --> pdb=" O VAL R 486 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 503 Processing helix chain 'R' and resid 506 through 515 Processing helix chain 'R' and resid 525 through 539 removed outlier: 4.000A pdb=" N GLU R 529 " --> pdb=" O ARG R 525 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 537 " --> pdb=" O SER R 533 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET R 539 " --> pdb=" O TYR R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 546 through 560 removed outlier: 3.887A pdb=" N TRP R 550 " --> pdb=" O SER R 546 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 567 Processing helix chain 'R' and resid 597 through 608 removed outlier: 3.745A pdb=" N ALA R 603 " --> pdb=" O LEU R 599 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 636 removed outlier: 3.525A pdb=" N ILE R 632 " --> pdb=" O ALA R 628 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER R 633 " --> pdb=" O ILE R 629 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG R 636 " --> pdb=" O ILE R 632 " (cutoff:3.500A) Processing helix chain 'R' and resid 701 through 723 removed outlier: 3.511A pdb=" N PHE R 706 " --> pdb=" O ASP R 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 750 removed outlier: 3.645A pdb=" N ASN R 746 " --> pdb=" O TYR R 742 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN R 747 " --> pdb=" O PHE R 743 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP R 750 " --> pdb=" O ASN R 746 " (cutoff:3.500A) Processing helix chain 'R' and resid 770 through 791 removed outlier: 4.237A pdb=" N PHE R 782 " --> pdb=" O ASN R 778 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU R 789 " --> pdb=" O ALA R 785 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER R 791 " --> pdb=" O LEU R 787 " (cutoff:3.500A) Processing helix chain 'R' and resid 814 through 829 Processing helix chain 'R' and resid 834 through 839 Processing helix chain 'R' and resid 839 through 846 removed outlier: 3.821A pdb=" N ILE R 846 " --> pdb=" O PHE R 842 " (cutoff:3.500A) Processing helix chain 'R' and resid 848 through 852 removed outlier: 3.515A pdb=" N LEU R 851 " --> pdb=" O CYS R 848 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS R 852 " --> pdb=" O PRO R 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 848 through 852' Processing helix chain 'R' and resid 866 through 883 removed outlier: 4.065A pdb=" N LYS R 870 " --> pdb=" O LYS R 866 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER R 873 " --> pdb=" O ASN R 869 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY R 883 " --> pdb=" O ASP R 879 " (cutoff:3.500A) Processing helix chain 'R' and resid 888 through 898 Processing helix chain 'S' and resid 35 through 49 removed outlier: 3.979A pdb=" N GLU S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE S 45 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 95 removed outlier: 3.991A pdb=" N ILE S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN S 87 " --> pdb=" O THR S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 141 removed outlier: 3.660A pdb=" N THR S 124 " --> pdb=" O PRO S 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET S 132 " --> pdb=" O ARG S 128 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL S 133 " --> pdb=" O LEU S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 162 Processing helix chain 'S' and resid 163 through 169 removed outlier: 4.033A pdb=" N LEU S 167 " --> pdb=" O GLY S 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR S 168 " --> pdb=" O LEU S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 180 removed outlier: 4.407A pdb=" N SER S 178 " --> pdb=" O PRO S 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 189 removed outlier: 4.031A pdb=" N ASP S 188 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 189 " --> pdb=" O GLN S 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 185 through 189' Processing helix chain 'S' and resid 195 through 211 removed outlier: 3.736A pdb=" N ILE S 199 " --> pdb=" O ASP S 195 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU S 202 " --> pdb=" O GLU S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 240 removed outlier: 3.749A pdb=" N LEU S 234 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU S 235 " --> pdb=" O TRP S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 253 through 269 removed outlier: 3.603A pdb=" N TYR S 266 " --> pdb=" O ARG S 262 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU S 267 " --> pdb=" O GLY S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 271 through 277 removed outlier: 4.300A pdb=" N GLU S 275 " --> pdb=" O LYS S 271 " (cutoff:3.500A) Processing helix chain 'S' and resid 279 through 302 removed outlier: 3.587A pdb=" N GLU S 285 " --> pdb=" O VAL S 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG S 286 " --> pdb=" O ARG S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 318 Processing helix chain 'S' and resid 343 through 357 Processing helix chain 'S' and resid 361 through 373 removed outlier: 3.570A pdb=" N LEU S 372 " --> pdb=" O VAL S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 375 through 395 removed outlier: 3.533A pdb=" N LEU S 383 " --> pdb=" O LEU S 379 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR S 394 " --> pdb=" O LYS S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 423 removed outlier: 4.104A pdb=" N GLY S 423 " --> pdb=" O ASN S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 425 through 433 removed outlier: 3.976A pdb=" N ILE S 429 " --> pdb=" O MET S 425 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR S 430 " --> pdb=" O LEU S 426 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG S 431 " --> pdb=" O SER S 427 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 458 removed outlier: 3.502A pdb=" N CYS S 447 " --> pdb=" O MET S 443 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS S 455 " --> pdb=" O PHE S 451 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN S 456 " --> pdb=" O THR S 452 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP S 457 " --> pdb=" O TYR S 453 " (cutoff:3.500A) Processing helix chain 'S' and resid 473 through 490 removed outlier: 4.092A pdb=" N SER S 479 " --> pdb=" O LEU S 475 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE S 480 " --> pdb=" O ARG S 476 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR S 481 " --> pdb=" O ASN S 477 " (cutoff:3.500A) Processing helix chain 'S' and resid 494 through 503 Processing helix chain 'S' and resid 505 through 515 removed outlier: 4.409A pdb=" N SER S 509 " --> pdb=" O CYS S 505 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE S 510 " --> pdb=" O GLY S 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 525 through 539 removed outlier: 3.892A pdb=" N GLU S 529 " --> pdb=" O ARG S 525 " (cutoff:3.500A) Processing helix chain 'S' and resid 546 through 561 removed outlier: 3.821A pdb=" N TRP S 550 " --> pdb=" O SER S 546 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA S 551 " --> pdb=" O ALA S 547 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER S 561 " --> pdb=" O VAL S 557 " (cutoff:3.500A) Processing helix chain 'S' and resid 563 through 567 Processing helix chain 'S' and resid 597 through 606 removed outlier: 3.950A pdb=" N MET S 604 " --> pdb=" O ALA S 600 " (cutoff:3.500A) Processing helix chain 'S' and resid 622 through 631 removed outlier: 3.753A pdb=" N ILE S 629 " --> pdb=" O LEU S 625 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA S 630 " --> pdb=" O ILE S 626 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP S 631 " --> pdb=" O GLY S 627 " (cutoff:3.500A) Processing helix chain 'S' and resid 631 through 636 removed outlier: 4.394A pdb=" N CYS S 635 " --> pdb=" O ASP S 631 " (cutoff:3.500A) Processing helix chain 'S' and resid 705 through 717 removed outlier: 4.004A pdb=" N ALA S 709 " --> pdb=" O GLU S 705 " (cutoff:3.500A) Processing helix chain 'S' and resid 718 through 720 No H-bonds generated for 'chain 'S' and resid 718 through 720' Processing helix chain 'S' and resid 722 through 727 removed outlier: 3.835A pdb=" N ILE S 725 " --> pdb=" O GLU S 722 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE S 727 " --> pdb=" O GLU S 724 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 752 removed outlier: 4.970A pdb=" N TRP S 738 " --> pdb=" O ILE S 734 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER S 739 " --> pdb=" O GLY S 735 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN S 746 " --> pdb=" O TYR S 742 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN S 747 " --> pdb=" O PHE S 743 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL S 748 " --> pdb=" O ASN S 744 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA S 749 " --> pdb=" O LEU S 745 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP S 750 " --> pdb=" O ASN S 746 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN S 751 " --> pdb=" O ASN S 747 " (cutoff:3.500A) Processing helix chain 'S' and resid 753 through 756 removed outlier: 4.015A pdb=" N LEU S 756 " --> pdb=" O LYS S 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 753 through 756' Processing helix chain 'S' and resid 770 through 793 removed outlier: 3.525A pdb=" N VAL S 788 " --> pdb=" O HIS S 784 " (cutoff:3.500A) Processing helix chain 'S' and resid 814 through 831 removed outlier: 3.841A pdb=" N GLU S 826 " --> pdb=" O LYS S 822 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS S 827 " --> pdb=" O ILE S 823 " (cutoff:3.500A) Processing helix chain 'S' and resid 834 through 839 Processing helix chain 'S' and resid 839 through 847 removed outlier: 3.831A pdb=" N SER S 847 " --> pdb=" O PHE S 843 " (cutoff:3.500A) Processing helix chain 'S' and resid 851 through 856 removed outlier: 4.146A pdb=" N PHE S 856 " --> pdb=" O HIS S 852 " (cutoff:3.500A) Processing helix chain 'S' and resid 867 through 883 removed outlier: 4.680A pdb=" N SER S 873 " --> pdb=" O ASN S 869 " (cutoff:3.500A) Processing helix chain 'S' and resid 888 through 898 Processing helix chain 'T' and resid 35 through 49 removed outlier: 3.544A pdb=" N ASP T 39 " --> pdb=" O LYS T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 95 removed outlier: 3.518A pdb=" N PHE T 85 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE T 86 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER T 95 " --> pdb=" O LYS T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 115 Processing helix chain 'T' and resid 120 through 141 removed outlier: 3.575A pdb=" N THR T 124 " --> pdb=" O PRO T 120 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET T 132 " --> pdb=" O ARG T 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL T 133 " --> pdb=" O LEU T 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP T 141 " --> pdb=" O LEU T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 163 removed outlier: 3.555A pdb=" N ARG T 162 " --> pdb=" O ALA T 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 173 through 180 removed outlier: 4.051A pdb=" N PHE T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER T 178 " --> pdb=" O PRO T 174 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP T 179 " --> pdb=" O GLU T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 211 removed outlier: 3.531A pdb=" N ILE T 199 " --> pdb=" O ASP T 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU T 201 " --> pdb=" O SER T 197 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU T 202 " --> pdb=" O GLU T 198 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU T 203 " --> pdb=" O ILE T 199 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 229 Processing helix chain 'T' and resid 230 through 240 Processing helix chain 'T' and resid 253 through 269 removed outlier: 3.606A pdb=" N TYR T 269 " --> pdb=" O GLN T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 277 removed outlier: 3.831A pdb=" N GLU T 275 " --> pdb=" O LYS T 271 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 302 removed outlier: 3.516A pdb=" N GLN T 295 " --> pdb=" O GLU T 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 303 through 305 No H-bonds generated for 'chain 'T' and resid 303 through 305' Processing helix chain 'T' and resid 312 through 318 Processing helix chain 'T' and resid 344 through 354 Processing helix chain 'T' and resid 361 through 373 removed outlier: 3.687A pdb=" N MET T 366 " --> pdb=" O SER T 362 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR T 367 " --> pdb=" O ASP T 363 " (cutoff:3.500A) Processing helix chain 'T' and resid 375 through 395 removed outlier: 3.501A pdb=" N TYR T 387 " --> pdb=" O LEU T 383 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 425 removed outlier: 3.778A pdb=" N LEU T 417 " --> pdb=" O VAL T 413 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY T 423 " --> pdb=" O ASN T 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET T 425 " --> pdb=" O LEU T 421 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 433 removed outlier: 3.882A pdb=" N TYR T 430 " --> pdb=" O LEU T 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG T 431 " --> pdb=" O SER T 427 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA T 432 " --> pdb=" O SER T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 458 Processing helix chain 'T' and resid 462 through 466 Processing helix chain 'T' and resid 472 through 490 removed outlier: 3.552A pdb=" N ILE T 480 " --> pdb=" O ARG T 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS T 490 " --> pdb=" O VAL T 486 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 503 removed outlier: 3.526A pdb=" N GLN T 499 " --> pdb=" O SER T 495 " (cutoff:3.500A) Processing helix chain 'T' and resid 506 through 515 removed outlier: 3.554A pdb=" N ASN T 512 " --> pdb=" O VAL T 508 " (cutoff:3.500A) Processing helix chain 'T' and resid 526 through 540 removed outlier: 3.790A pdb=" N GLN T 530 " --> pdb=" O GLU T 526 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 561 removed outlier: 3.686A pdb=" N TRP T 550 " --> pdb=" O SER T 546 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER T 561 " --> pdb=" O VAL T 557 " (cutoff:3.500A) Processing helix chain 'T' and resid 563 through 567 Processing helix chain 'T' and resid 597 through 608 Processing helix chain 'T' and resid 622 through 636 removed outlier: 3.724A pdb=" N ILE T 626 " --> pdb=" O VAL T 622 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP T 631 " --> pdb=" O GLY T 627 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE T 632 " --> pdb=" O ALA T 628 " (cutoff:3.500A) Processing helix chain 'T' and resid 640 through 646 removed outlier: 4.212A pdb=" N ASN T 644 " --> pdb=" O SER T 640 " (cutoff:3.500A) Processing helix chain 'T' and resid 703 through 726 removed outlier: 3.606A pdb=" N TRP T 716 " --> pdb=" O LYS T 712 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN T 721 " --> pdb=" O LEU T 717 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU T 722 " --> pdb=" O LYS T 718 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE T 723 " --> pdb=" O ASN T 719 " (cutoff:3.500A) Processing helix chain 'T' and resid 730 through 752 removed outlier: 3.597A pdb=" N TRP T 738 " --> pdb=" O ILE T 734 " (cutoff:3.500A) Processing helix chain 'T' and resid 770 through 790 removed outlier: 3.682A pdb=" N ILE T 774 " --> pdb=" O ASN T 770 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET T 775 " --> pdb=" O ALA T 771 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE T 782 " --> pdb=" O ASN T 778 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU T 783 " --> pdb=" O VAL T 779 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL T 786 " --> pdb=" O PHE T 782 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU T 787 " --> pdb=" O LEU T 783 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL T 788 " --> pdb=" O HIS T 784 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU T 789 " --> pdb=" O ALA T 785 " (cutoff:3.500A) Processing helix chain 'T' and resid 814 through 830 Processing helix chain 'T' and resid 839 through 844 Processing helix chain 'T' and resid 851 through 856 removed outlier: 3.916A pdb=" N ILE T 855 " --> pdb=" O LEU T 851 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE T 856 " --> pdb=" O HIS T 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 851 through 856' Processing helix chain 'T' and resid 866 through 883 removed outlier: 4.156A pdb=" N LYS T 870 " --> pdb=" O LYS T 866 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER T 873 " --> pdb=" O ASN T 869 " (cutoff:3.500A) Processing helix chain 'T' and resid 888 through 898 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.804A pdb=" N ILE A 14 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS A 331 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 16 " --> pdb=" O LYS A 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.300A pdb=" N LYS A 105 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR A 219 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 609 through 611 removed outlier: 3.891A pdb=" N VAL A 611 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 149 removed outlier: 7.582A pdb=" N LEU B 148 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 353 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG B 351 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.108A pdb=" N GLN B 153 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 355 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS B 421 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 357 " --> pdb=" O HIS B 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.832A pdb=" N TYR B 252 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.868A pdb=" N TYR B 497 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 528 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 703 " --> pdb=" O CYS B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 548 through 552 Processing sheet with id=AB1, first strand: chain 'C' and resid 81 through 84 Processing sheet with id=AB2, first strand: chain 'C' and resid 148 through 154 removed outlier: 7.579A pdb=" N LEU C 148 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 353 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 150 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY C 355 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N HIS C 152 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG C 351 " --> pdb=" O GLU C 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.668A pdb=" N ILE C 245 " --> pdb=" O TYR C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 421 through 422 Processing sheet with id=AB5, first strand: chain 'C' and resid 527 through 529 removed outlier: 6.159A pdb=" N ILE C 703 " --> pdb=" O CYS C 744 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 548 through 552 removed outlier: 3.571A pdb=" N MET C 551 " --> pdb=" O VAL C 673 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB8, first strand: chain 'D' and resid 148 through 154 removed outlier: 7.510A pdb=" N LEU D 148 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 353 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 150 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 355 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS D 152 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N PHE D 357 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N HIS D 154 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 351 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 148 through 154 removed outlier: 7.510A pdb=" N LEU D 148 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 353 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 150 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 355 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS D 152 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N PHE D 357 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N HIS D 154 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL D 419 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY D 355 " --> pdb=" O VAL D 419 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS D 421 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE D 357 " --> pdb=" O HIS D 421 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 466 " --> pdb=" O THR D 496 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N HIS D 498 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA D 468 " --> pdb=" O HIS D 498 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE D 495 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLY D 529 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR D 497 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU D 528 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 703 " --> pdb=" O CYS D 744 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC2, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AC3, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'E' and resid 148 through 154 removed outlier: 7.527A pdb=" N LEU E 148 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 353 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU E 150 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY E 355 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 152 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N PHE E 357 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N HIS E 154 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG E 351 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA E 417 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 353 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 419 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY E 355 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS E 421 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 357 " --> pdb=" O HIS E 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.811A pdb=" N ILE E 245 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR E 252 " --> pdb=" O ILE E 245 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E 247 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 496 through 498 removed outlier: 3.544A pdb=" N TYR E 497 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE E 703 " --> pdb=" O CYS E 744 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 548 through 552 Processing sheet with id=AC8, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC9, first strand: chain 'F' and resid 148 through 153 removed outlier: 5.862A pdb=" N LEU F 148 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR F 352 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 354 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS F 152 " --> pdb=" O GLU F 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AD2, first strand: chain 'F' and resid 421 through 422 Processing sheet with id=AD3, first strand: chain 'F' and resid 496 through 498 removed outlier: 6.724A pdb=" N TYR F 497 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 528 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 703 " --> pdb=" O CYS F 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 548 through 552 Processing sheet with id=AD5, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AD6, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.550A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG G 351 " --> pdb=" O GLU G 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.550A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL G 419 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY G 355 " --> pdb=" O VAL G 419 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N HIS G 421 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE G 357 " --> pdb=" O HIS G 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 245 through 247 removed outlier: 4.083A pdb=" N ILE G 245 " --> pdb=" O TYR G 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 496 through 498 removed outlier: 7.055A pdb=" N TYR G 497 " --> pdb=" O GLY G 529 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU G 528 " --> pdb=" O GLU G 704 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE G 703 " --> pdb=" O CYS G 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 548 through 552 Processing sheet with id=AE2, first strand: chain 'I' and resid 81 through 84 removed outlier: 3.576A pdb=" N LYS I 89 " --> pdb=" O LYS I 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 148 through 154 removed outlier: 7.486A pdb=" N LEU I 148 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 353 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU I 150 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY I 355 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS I 152 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE I 357 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS I 154 " --> pdb=" O PHE I 357 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 148 through 154 removed outlier: 7.486A pdb=" N LEU I 148 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 353 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU I 150 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY I 355 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS I 152 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE I 357 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS I 154 " --> pdb=" O PHE I 357 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL I 419 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY I 355 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS I 421 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE I 357 " --> pdb=" O HIS I 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'I' and resid 244 through 246 removed outlier: 3.608A pdb=" N ILE I 245 " --> pdb=" O TYR I 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR I 252 " --> pdb=" O ILE I 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 527 through 529 Processing sheet with id=AE7, first strand: chain 'I' and resid 548 through 552 Processing sheet with id=AE8, first strand: chain 'J' and resid 81 through 84 Processing sheet with id=AE9, first strand: chain 'J' and resid 148 through 154 removed outlier: 7.703A pdb=" N LEU J 148 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU J 353 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU J 150 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY J 355 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS J 152 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N PHE J 357 " --> pdb=" O HIS J 152 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N HIS J 154 " --> pdb=" O PHE J 357 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG J 351 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA J 417 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU J 353 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL J 419 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY J 355 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS J 421 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE J 357 " --> pdb=" O HIS J 421 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL J 466 " --> pdb=" O THR J 496 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N HIS J 498 " --> pdb=" O VAL J 466 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA J 468 " --> pdb=" O HIS J 498 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 527 " --> pdb=" O PHE J 495 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 245 through 246 Processing sheet with id=AF2, first strand: chain 'J' and resid 548 through 552 Processing sheet with id=AF3, first strand: chain 'J' and resid 703 through 704 removed outlier: 5.970A pdb=" N ILE J 703 " --> pdb=" O CYS J 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'K' and resid 81 through 84 Processing sheet with id=AF5, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.937A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.937A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL K 419 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY K 355 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS K 421 " --> pdb=" O GLY K 355 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE K 357 " --> pdb=" O HIS K 421 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL K 466 " --> pdb=" O THR K 496 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS K 498 " --> pdb=" O VAL K 466 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA K 468 " --> pdb=" O HIS K 498 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE K 495 " --> pdb=" O ARG K 527 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY K 529 " --> pdb=" O PHE K 495 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR K 497 " --> pdb=" O GLY K 529 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE K 703 " --> pdb=" O CYS K 744 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 548 through 552 Processing sheet with id=AF8, first strand: chain 'L' and resid 81 through 84 Processing sheet with id=AF9, first strand: chain 'L' and resid 148 through 154 removed outlier: 7.697A pdb=" N LEU L 148 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU L 353 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 150 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY L 355 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N HIS L 152 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N PHE L 357 " --> pdb=" O HIS L 152 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS L 154 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG L 351 " --> pdb=" O GLU L 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 148 through 154 removed outlier: 7.697A pdb=" N LEU L 148 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU L 353 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 150 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY L 355 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N HIS L 152 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N PHE L 357 " --> pdb=" O HIS L 152 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS L 154 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL L 419 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY L 355 " --> pdb=" O VAL L 419 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS L 421 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE L 357 " --> pdb=" O HIS L 421 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 245 through 246 Processing sheet with id=AG3, first strand: chain 'L' and resid 527 through 529 Processing sheet with id=AG4, first strand: chain 'L' and resid 548 through 552 Processing sheet with id=AG5, first strand: chain 'M' and resid 81 through 84 Processing sheet with id=AG6, first strand: chain 'M' and resid 148 through 149 removed outlier: 7.637A pdb=" N LEU M 148 " --> pdb=" O ARG M 351 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU M 353 " --> pdb=" O LEU M 148 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG M 351 " --> pdb=" O GLU M 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'M' and resid 153 through 154 removed outlier: 6.107A pdb=" N GLN M 153 " --> pdb=" O ARG M 356 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY M 355 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N HIS M 421 " --> pdb=" O GLY M 355 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE M 357 " --> pdb=" O HIS M 421 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 496 through 498 removed outlier: 6.693A pdb=" N TYR M 497 " --> pdb=" O GLY M 529 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 528 " --> pdb=" O GLU M 704 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE M 703 " --> pdb=" O CYS M 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'M' and resid 548 through 552 Processing sheet with id=AH1, first strand: chain 'N' and resid 81 through 84 Processing sheet with id=AH2, first strand: chain 'N' and resid 148 through 149 removed outlier: 7.643A pdb=" N LEU N 148 " --> pdb=" O ARG N 351 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU N 353 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 153 through 154 removed outlier: 5.800A pdb=" N GLN N 153 " --> pdb=" O ARG N 356 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY N 355 " --> pdb=" O VAL N 419 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS N 421 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE N 357 " --> pdb=" O HIS N 421 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 245 through 246 Processing sheet with id=AH5, first strand: chain 'N' and resid 496 through 498 removed outlier: 3.504A pdb=" N TYR N 497 " --> pdb=" O ARG N 527 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU N 528 " --> pdb=" O GLU N 704 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE N 703 " --> pdb=" O CYS N 744 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 548 through 552 Processing sheet with id=AH7, first strand: chain 'O' and resid 14 through 17 removed outlier: 6.872A pdb=" N ILE O 14 " --> pdb=" O LYS O 329 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS O 331 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE O 16 " --> pdb=" O LYS O 331 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE O 342 " --> pdb=" O VAL O 330 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 104 through 106 removed outlier: 6.609A pdb=" N LYS O 105 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR O 219 " --> pdb=" O LYS O 105 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE O 216 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL O 249 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE O 218 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR O 251 " --> pdb=" O ILE O 218 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY O 252 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 609 through 611 removed outlier: 3.561A pdb=" N SER O 609 " --> pdb=" O PHE O 619 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 611 " --> pdb=" O MET O 617 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET O 617 " --> pdb=" O VAL O 611 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 104 through 106 removed outlier: 5.682A pdb=" N ILE P 216 " --> pdb=" O VAL P 247 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL P 249 " --> pdb=" O ILE P 216 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE P 218 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR P 251 " --> pdb=" O ILE P 218 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY P 252 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE P 308 " --> pdb=" O VAL P 71 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE P 73 " --> pdb=" O ILE P 308 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 609 through 612 removed outlier: 3.754A pdb=" N MET P 617 " --> pdb=" O VAL P 611 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 15 through 17 removed outlier: 6.978A pdb=" N ILE Q 16 " --> pdb=" O LYS Q 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'Q' and resid 104 through 106 removed outlier: 5.820A pdb=" N ILE Q 216 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL Q 249 " --> pdb=" O ILE Q 216 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE Q 218 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR Q 251 " --> pdb=" O ILE Q 218 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE Q 72 " --> pdb=" O ALA Q 250 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLY Q 252 " --> pdb=" O PHE Q 72 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL Q 74 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE Q 308 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE Q 73 " --> pdb=" O ILE Q 308 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 575 through 576 removed outlier: 4.240A pdb=" N ASP Q 618 " --> pdb=" O LEU Q 576 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET Q 617 " --> pdb=" O VAL Q 611 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL Q 611 " --> pdb=" O MET Q 617 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 14 through 17 removed outlier: 6.186A pdb=" N ILE R 14 " --> pdb=" O LYS R 329 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS R 331 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE R 16 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 330 " --> pdb=" O ILE R 342 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE R 342 " --> pdb=" O VAL R 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'R' and resid 104 through 106 removed outlier: 7.013A pdb=" N LYS R 105 " --> pdb=" O LEU R 217 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR R 219 " --> pdb=" O LYS R 105 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 569 through 570 Processing sheet with id=AI9, first strand: chain 'R' and resid 610 through 612 Processing sheet with id=AJ1, first strand: chain 'S' and resid 14 through 17 removed outlier: 6.495A pdb=" N ILE S 14 " --> pdb=" O LYS S 329 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS S 331 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE S 16 " --> pdb=" O LYS S 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'S' and resid 105 through 106 removed outlier: 7.388A pdb=" N LYS S 105 " --> pdb=" O LEU S 217 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR S 219 " --> pdb=" O LYS S 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE S 72 " --> pdb=" O ALA S 250 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE S 308 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE S 73 " --> pdb=" O ILE S 308 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 569 through 570 Processing sheet with id=AJ4, first strand: chain 'S' and resid 608 through 612 removed outlier: 3.633A pdb=" N MET S 617 " --> pdb=" O VAL S 611 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'T' and resid 14 through 17 removed outlier: 5.681A pdb=" N ILE T 14 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS T 331 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE T 16 " --> pdb=" O LYS T 331 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'T' and resid 104 through 106 removed outlier: 6.405A pdb=" N LYS T 105 " --> pdb=" O LEU T 217 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR T 219 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE T 216 " --> pdb=" O VAL T 247 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL T 249 " --> pdb=" O ILE T 216 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE T 218 " --> pdb=" O VAL T 249 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR T 251 " --> pdb=" O ILE T 218 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE T 72 " --> pdb=" O ALA T 250 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY T 252 " --> pdb=" O PHE T 72 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL T 74 " --> pdb=" O GLY T 252 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'T' and resid 609 through 610 6065 hydrogen bonds defined for protein. 17532 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: 57.99 Time building geometry restraints manager: 39.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 39382 1.34 - 1.46: 17985 1.46 - 1.58: 66041 1.58 - 1.70: 0 1.70 - 1.82: 929 Bond restraints: 124337 Sorted by residual: bond pdb=" N ILE P 656 " pdb=" CA ILE P 656 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N VAL S 569 " pdb=" CA VAL S 569 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.93e+00 bond pdb=" N ASN A 597 " pdb=" CA ASN A 597 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.87e+00 bond pdb=" N VAL T 611 " pdb=" CA VAL T 611 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.33e+00 bond pdb=" N MET T 617 " pdb=" CA MET T 617 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.11e+00 ... (remaining 124332 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.45: 2382 105.45 - 112.61: 64691 112.61 - 119.77: 41465 119.77 - 126.94: 57944 126.94 - 134.10: 1767 Bond angle restraints: 168249 Sorted by residual: angle pdb=" N VAL K 23 " pdb=" CA VAL K 23 " pdb=" C VAL K 23 " ideal model delta sigma weight residual 113.10 108.39 4.71 9.70e-01 1.06e+00 2.36e+01 angle pdb=" N GLY L 430 " pdb=" CA GLY L 430 " pdb=" C GLY L 430 " ideal model delta sigma weight residual 110.96 116.46 -5.50 1.19e+00 7.06e-01 2.14e+01 angle pdb=" N VAL P 133 " pdb=" CA VAL P 133 " pdb=" C VAL P 133 " ideal model delta sigma weight residual 113.42 108.15 5.27 1.17e+00 7.31e-01 2.03e+01 angle pdb=" N VAL P 811 " pdb=" CA VAL P 811 " pdb=" C VAL P 811 " ideal model delta sigma weight residual 111.90 108.54 3.36 8.10e-01 1.52e+00 1.72e+01 angle pdb=" N ILE R 544 " pdb=" CA ILE R 544 " pdb=" C ILE R 544 " ideal model delta sigma weight residual 106.21 110.58 -4.37 1.07e+00 8.73e-01 1.67e+01 ... (remaining 168244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 67487 18.01 - 36.02: 6536 36.02 - 54.03: 978 54.03 - 72.05: 189 72.05 - 90.06: 106 Dihedral angle restraints: 75296 sinusoidal: 30845 harmonic: 44451 Sorted by residual: dihedral pdb=" CA ASN A 647 " pdb=" C ASN A 647 " pdb=" N LYS A 648 " pdb=" CA LYS A 648 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR J 647 " pdb=" C THR J 647 " pdb=" N GLY J 648 " pdb=" CA GLY J 648 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR D 433 " pdb=" C TYR D 433 " pdb=" N PRO D 434 " pdb=" CA PRO D 434 " ideal model delta harmonic sigma weight residual 180.00 -160.61 -19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 75293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 14266 0.042 - 0.084: 3363 0.084 - 0.125: 885 0.125 - 0.167: 42 0.167 - 0.209: 12 Chirality restraints: 18568 Sorted by residual: chirality pdb=" CA GLU Q 279 " pdb=" N GLU Q 279 " pdb=" C GLU Q 279 " pdb=" CB GLU Q 279 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE P 656 " pdb=" N ILE P 656 " pdb=" C ILE P 656 " pdb=" CB ILE P 656 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU A 599 " pdb=" N LEU A 599 " pdb=" C LEU A 599 " pdb=" CB LEU A 599 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 18565 not shown) Planarity restraints: 21596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 408 " -0.091 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO B 409 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 738 " -0.025 2.00e-02 2.50e+03 1.84e-02 8.51e+00 pdb=" CG TRP Q 738 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 738 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 738 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 738 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 738 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 738 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 738 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 738 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 738 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 230 " -0.018 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP F 230 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP F 230 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 230 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 230 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 230 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 230 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 230 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 230 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 230 " -0.000 2.00e-02 2.50e+03 ... (remaining 21593 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1937 2.66 - 3.22: 121144 3.22 - 3.78: 194684 3.78 - 4.34: 265616 4.34 - 4.90: 419975 Nonbonded interactions: 1003356 Sorted by model distance: nonbonded pdb=" O ILE L 195 " pdb=" OD1 ASP L 196 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLN A 159 " pdb=" OH TYR A 189 " model vdw 2.196 2.440 nonbonded pdb=" O GLY Q 735 " pdb=" OG SER Q 739 " model vdw 2.205 2.440 nonbonded pdb=" OG SER N 548 " pdb=" OE2 GLU N 674 " model vdw 2.205 2.440 nonbonded pdb=" OE2 GLU N 269 " pdb=" OH TYR N 295 " model vdw 2.207 2.440 ... (remaining 1003351 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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = (chain 'B' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'C' and (resid 1 through 310 or resid 329 through 640 or (resid 641 and ( \ name N or name CA or name C or name O or name CB )) or resid 642 through 798)) selection = (chain 'D' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'E' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'F' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'G' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'I' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'J' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'K' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'L' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'M' and (resid 1 through 310 or (resid 329 through 330 and (name N or nam \ e CA or name C or name O or name CB )) or resid 331 through 615 or (resid 616 th \ rough 617 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 798)) selection = (chain 'N' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.110 Extract box with map and model: 22.340 Check model and map are aligned: 1.310 Set scattering table: 0.780 Process input model: 238.020 Find NCS groups from input model: 8.090 Set up NCS constraints: 0.550 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 277.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.002 0.056 124337 Z= 0.143 Angle : 0.524 10.120 168249 Z= 0.281 Chirality : 0.038 0.209 18568 Planarity : 0.003 0.137 21596 Dihedral : 14.322 90.058 46430 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.07), residues: 14986 helix: 0.51 (0.06), residues: 8206 sheet: -1.09 (0.20), residues: 701 loop : -0.89 (0.08), residues: 6079 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1001 time to evaluate : 10.622 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: 9 outliers final: 0 residues processed: 1009 average time/residue: 1.0555 time to fit residues: 1874.1312 Evaluate side-chains 687 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 10.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 14.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1271 optimal weight: 8.9990 chunk 1141 optimal weight: 9.9990 chunk 633 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 769 optimal weight: 5.9990 chunk 609 optimal weight: 9.9990 chunk 1180 optimal weight: 0.9990 chunk 456 optimal weight: 1.9990 chunk 717 optimal weight: 7.9990 chunk 878 optimal weight: 0.8980 chunk 1367 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 384 HIS D 445 GLN D 570 HIS ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 HIS ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 787 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS J 787 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN K 789 ASN ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 HIS ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 381 GLN ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 624 ASN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 GLN ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 374 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN T 614 ASN ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 124337 Z= 0.195 Angle : 0.565 10.743 168249 Z= 0.294 Chirality : 0.040 0.217 18568 Planarity : 0.004 0.087 21596 Dihedral : 4.109 20.345 16469 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.07), residues: 14986 helix: 0.86 (0.06), residues: 8487 sheet: -1.09 (0.21), residues: 636 loop : -0.87 (0.08), residues: 5863 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 805 time to evaluate : 10.788 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: 67 outliers final: 39 residues processed: 846 average time/residue: 1.0492 time to fit residues: 1573.4242 Evaluate side-chains 707 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 668 time to evaluate : 10.610 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.8515 time to fit residues: 76.3882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 760 optimal weight: 9.9990 chunk 424 optimal weight: 8.9990 chunk 1138 optimal weight: 5.9990 chunk 931 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 chunk 1370 optimal weight: 10.0000 chunk 1480 optimal weight: 7.9990 chunk 1220 optimal weight: 30.0000 chunk 1358 optimal weight: 9.9990 chunk 467 optimal weight: 10.0000 chunk 1099 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN ** B 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 589 HIS C 787 ASN ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 435 HIS ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** J 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 445 GLN J 570 HIS K 7 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN K 787 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN O 276 GLN ** O 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 552 ASN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 839 HIS P 165 HIS P 226 GLN ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 461 ASN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 369 ASN R 575 GLN R 624 ASN R 647 ASN R 747 ASN ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 315 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 907 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 124337 Z= 0.410 Angle : 0.679 11.234 168249 Z= 0.349 Chirality : 0.043 0.236 18568 Planarity : 0.005 0.074 21596 Dihedral : 4.544 23.060 16469 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.07), residues: 14986 helix: 0.60 (0.06), residues: 8543 sheet: -1.38 (0.21), residues: 650 loop : -1.08 (0.08), residues: 5793 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 705 time to evaluate : 10.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 65 residues processed: 794 average time/residue: 1.0049 time to fit residues: 1420.0154 Evaluate side-chains 707 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 642 time to evaluate : 10.663 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.8710 time to fit residues: 121.2755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1353 optimal weight: 10.0000 chunk 1030 optimal weight: 4.9990 chunk 711 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 653 optimal weight: 0.4980 chunk 919 optimal weight: 6.9990 chunk 1374 optimal weight: 5.9990 chunk 1455 optimal weight: 40.0000 chunk 718 optimal weight: 5.9990 chunk 1303 optimal weight: 5.9990 chunk 392 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 787 ASN L 7 ASN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 789 ASN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN O 186 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 469 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 165 HIS ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 647 ASN ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 778 ASN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 124337 Z= 0.254 Angle : 0.568 11.375 168249 Z= 0.292 Chirality : 0.040 0.284 18568 Planarity : 0.004 0.065 21596 Dihedral : 4.387 20.920 16469 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.07), residues: 14986 helix: 0.76 (0.06), residues: 8557 sheet: -1.35 (0.21), residues: 627 loop : -1.04 (0.08), residues: 5802 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 728 time to evaluate : 10.860 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: 147 outliers final: 56 residues processed: 842 average time/residue: 1.0299 time to fit residues: 1547.8261 Evaluate side-chains 716 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 660 time to evaluate : 10.719 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.8826 time to fit residues: 107.7567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1212 optimal weight: 3.9990 chunk 826 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 1083 optimal weight: 5.9990 chunk 600 optimal weight: 0.0870 chunk 1242 optimal weight: 20.0000 chunk 1006 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 743 optimal weight: 9.9990 chunk 1306 optimal weight: 30.0000 chunk 367 optimal weight: 3.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 GLN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 474 HIS ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS N 605 GLN N 668 GLN O 357 ASN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 GLN S 552 ASN T 194 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 530 GLN ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 124337 Z= 0.262 Angle : 0.575 12.214 168249 Z= 0.294 Chirality : 0.040 0.273 18568 Planarity : 0.004 0.060 21596 Dihedral : 4.377 20.924 16469 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.07), residues: 14986 helix: 0.81 (0.06), residues: 8556 sheet: -1.35 (0.21), residues: 617 loop : -1.06 (0.08), residues: 5813 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 705 time to evaluate : 10.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 61 residues processed: 846 average time/residue: 1.0607 time to fit residues: 1601.2247 Evaluate side-chains 724 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 663 time to evaluate : 10.691 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.8891 time to fit residues: 118.6437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 489 optimal weight: 8.9990 chunk 1310 optimal weight: 40.0000 chunk 287 optimal weight: 0.9990 chunk 854 optimal weight: 0.5980 chunk 359 optimal weight: 5.9990 chunk 1457 optimal weight: 7.9990 chunk 1209 optimal weight: 8.9990 chunk 674 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 482 optimal weight: 8.9990 chunk 764 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 7 ASN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN C 789 ASN D 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN O 155 ASN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 469 GLN ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 346 GLN P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 GLN S 552 ASN S 751 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 124337 Z= 0.199 Angle : 0.544 12.731 168249 Z= 0.277 Chirality : 0.039 0.261 18568 Planarity : 0.004 0.055 21596 Dihedral : 4.254 20.588 16469 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.07), residues: 14986 helix: 0.95 (0.06), residues: 8559 sheet: -1.27 (0.22), residues: 607 loop : -1.00 (0.08), residues: 5820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 728 time to evaluate : 10.990 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: 116 outliers final: 49 residues processed: 817 average time/residue: 1.0552 time to fit residues: 1531.6047 Evaluate side-chains 721 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 672 time to evaluate : 10.748 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.8886 time to fit residues: 97.1388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1404 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 830 optimal weight: 6.9990 chunk 1064 optimal weight: 8.9990 chunk 824 optimal weight: 20.0000 chunk 1226 optimal weight: 4.9990 chunk 813 optimal weight: 10.0000 chunk 1451 optimal weight: 5.9990 chunk 908 optimal weight: 4.9990 chunk 884 optimal weight: 0.1980 chunk 670 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN C 789 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN O 357 ASN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 124337 Z= 0.271 Angle : 0.584 15.866 168249 Z= 0.296 Chirality : 0.040 0.250 18568 Planarity : 0.004 0.055 21596 Dihedral : 4.343 20.892 16469 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.07), residues: 14986 helix: 0.91 (0.06), residues: 8565 sheet: -1.33 (0.21), residues: 613 loop : -1.06 (0.08), residues: 5808 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 694 time to evaluate : 10.705 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: 113 outliers final: 43 residues processed: 785 average time/residue: 1.0295 time to fit residues: 1440.1489 Evaluate side-chains 709 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 666 time to evaluate : 10.691 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.8947 time to fit residues: 86.8875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 898 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 866 optimal weight: 0.6980 chunk 437 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 922 optimal weight: 0.6980 chunk 988 optimal weight: 5.9990 chunk 717 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 1140 optimal weight: 30.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 213 ASN C 789 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 HIS ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 789 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** N 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 513 GLN S 751 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 124337 Z= 0.190 Angle : 0.548 13.754 168249 Z= 0.276 Chirality : 0.039 0.257 18568 Planarity : 0.004 0.057 21596 Dihedral : 4.217 20.401 16469 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.07), residues: 14986 helix: 1.06 (0.06), residues: 8526 sheet: -1.03 (0.23), residues: 547 loop : -1.01 (0.08), residues: 5913 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 732 time to evaluate : 10.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 31 residues processed: 793 average time/residue: 1.1381 time to fit residues: 1609.8327 Evaluate side-chains 712 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 681 time to evaluate : 10.730 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.0011 time to fit residues: 73.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1320 optimal weight: 20.0000 chunk 1390 optimal weight: 0.9990 chunk 1268 optimal weight: 8.9990 chunk 1352 optimal weight: 9.9990 chunk 814 optimal weight: 3.9990 chunk 589 optimal weight: 9.9990 chunk 1062 optimal weight: 40.0000 chunk 415 optimal weight: 5.9990 chunk 1222 optimal weight: 5.9990 chunk 1279 optimal weight: 6.9990 chunk 1347 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 499 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 597 ASN ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 747 ASN ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 124337 Z= 0.270 Angle : 0.595 14.208 168249 Z= 0.299 Chirality : 0.041 0.277 18568 Planarity : 0.004 0.056 21596 Dihedral : 4.322 21.678 16469 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.07), residues: 14986 helix: 0.97 (0.06), residues: 8539 sheet: -1.12 (0.23), residues: 557 loop : -1.05 (0.08), residues: 5890 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 697 time to evaluate : 10.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 22 residues processed: 738 average time/residue: 1.0852 time to fit residues: 1421.5331 Evaluate side-chains 692 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 670 time to evaluate : 9.601 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.8356 time to fit residues: 47.6489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 888 optimal weight: 8.9990 chunk 1430 optimal weight: 8.9990 chunk 873 optimal weight: 0.8980 chunk 678 optimal weight: 5.9990 chunk 994 optimal weight: 0.8980 chunk 1500 optimal weight: 20.0000 chunk 1380 optimal weight: 20.0000 chunk 1194 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 922 optimal weight: 0.0770 chunk 732 optimal weight: 10.0000 overall best weight: 2.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS J 605 GLN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 GLN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 499 GLN ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 155 ASN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 124337 Z= 0.193 Angle : 0.563 13.153 168249 Z= 0.282 Chirality : 0.040 0.393 18568 Planarity : 0.004 0.057 21596 Dihedral : 4.227 23.210 16469 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.07), residues: 14986 helix: 1.09 (0.06), residues: 8517 sheet: -1.11 (0.23), residues: 539 loop : -0.99 (0.08), residues: 5930 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 725 time to evaluate : 10.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 747 average time/residue: 1.1604 time to fit residues: 1541.9419 Evaluate side-chains 705 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 692 time to evaluate : 10.690 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.9833 time to fit residues: 39.3016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 949 optimal weight: 10.0000 chunk 1272 optimal weight: 20.0000 chunk 366 optimal weight: 0.5980 chunk 1101 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 1196 optimal weight: 2.9990 chunk 500 optimal weight: 9.9990 chunk 1228 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN C 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 248 ASN ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 GLN M 7 ASN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 912 ASN ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 552 ASN S 597 ASN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.101423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.083852 restraints weight = 430463.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082899 restraints weight = 429486.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083193 restraints weight = 360497.913| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 124337 Z= 0.314 Angle : 0.636 14.619 168249 Z= 0.319 Chirality : 0.042 0.273 18568 Planarity : 0.004 0.055 21596 Dihedral : 4.444 21.232 16469 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.07), residues: 14986 helix: 0.90 (0.06), residues: 8540 sheet: -1.28 (0.23), residues: 538 loop : -1.11 (0.08), residues: 5908 =============================================================================== Job complete usr+sys time: 23606.68 seconds wall clock time: 418 minutes 48.83 seconds (25128.83 seconds total)