Starting phenix.real_space_refine on Sun Mar 24 16:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkf_41349/03_2024/8tkf_41349_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.126 sd= 1.558 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 52 5.49 5 S 448 5.16 5 C 47332 2.51 5 N 12492 2.21 5 O 13768 1.98 5 H 72976 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 36472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 36472 Classifications: {'peptide': 2272} Link IDs: {'PCIS': 3, 'PTRANS': 61, 'TRANS': 2207} Chain breaks: 14 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 36472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 36472 Classifications: {'peptide': 2272} Link IDs: {'PCIS': 3, 'PTRANS': 61, 'TRANS': 2207} Chain breaks: 14 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 36472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 36472 Classifications: {'peptide': 2272} Link IDs: {'PCIS': 3, 'PTRANS': 61, 'TRANS': 2207} Chain breaks: 14 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 36472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 36472 Classifications: {'peptide': 2272} Link IDs: {'PCIS': 3, 'PTRANS': 61, 'TRANS': 2207} Chain breaks: 14 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 297 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 4, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 297 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 4, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 297 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 4, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 297 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 4, 'PT5': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34925 SG CYS A2538 146.293 121.357 104.890 1.00 87.33 S ATOM 34974 SG CYS A2541 144.566 120.817 102.510 1.00 62.06 S ATOM 71397 SG CYS B2538 119.794 145.778 104.868 1.00 87.33 S ATOM 71446 SG CYS B2541 120.334 144.048 102.490 1.00 62.06 S ATOM A062L SG CYS C2538 95.415 119.318 104.867 1.00 87.33 S ATOM A063Y SG CYS C2541 97.145 119.854 102.489 1.00 62.06 S ATOM A0Y7P SG CYS D2538 121.834 94.952 104.909 1.00 87.33 S ATOM A0Y92 SG CYS D2541 121.298 96.680 102.528 1.00 62.06 S Time building chain proxies: 47.32, per 1000 atoms: 0.32 Number of scatterers: 147076 At special positions: 0 Unit cell: (242.165, 241.536, 185.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 448 16.00 P 52 15.00 O 13768 8.00 N 12492 7.00 C 47332 6.00 H 72976 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 89.92 Conformation dependent library (CDL) restraints added in 9.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B2702 " pdb="ZN ZN B2702 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2702 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2702 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2702 " - pdb=" SG CYS B2538 " pdb=" ZN C2702 " pdb="ZN ZN C2702 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2702 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2702 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2702 " - pdb=" SG CYS C2538 " pdb=" ZN D2702 " pdb="ZN ZN D2702 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2702 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2702 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2702 " - pdb=" SG CYS D2538 " Number of angles added : 4 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17416 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 408 helices and 40 sheets defined 70.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.00 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.274A pdb=" N GLY A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.292A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 462 Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.826A pdb=" N ASN A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.547A pdb=" N LEU A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 542' Processing helix chain 'A' and resid 543 through 565 Proline residue: A 548 - end of helix removed outlier: 3.590A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.163A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.935A pdb=" N ILE A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 603 removed outlier: 3.597A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.984A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 removed outlier: 3.669A pdb=" N ASP A 658 " --> pdb=" O LYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 Processing helix chain 'A' and resid 744 through 756 removed outlier: 4.191A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 824 removed outlier: 5.131A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.532A pdb=" N GLU A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.505A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 961 through 1003 Proline residue: A1003 - end of helix Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.804A pdb=" N MET A1035 " --> pdb=" O GLN A1031 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.523A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.889A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.826A pdb=" N GLN A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 5.383A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.137A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 3.789A pdb=" N ALA A1237 " --> pdb=" O GLN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 3.906A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1271 through 1278 Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.643A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.991A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.700A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 3.984A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 3.770A pdb=" N GLU A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 Processing helix chain 'A' and resid 1406 through 1421 Processing helix chain 'A' and resid 1434 through 1458 removed outlier: 4.471A pdb=" N TRP A1438 " --> pdb=" O SER A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.871A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1489 removed outlier: 4.986A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1483 through 1489' Processing helix chain 'A' and resid 1491 through 1512 Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1515 through 1537 removed outlier: 3.614A pdb=" N LYS A1519 " --> pdb=" O GLN A1515 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A1520 " --> pdb=" O GLN A1516 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1557 Processing helix chain 'A' and resid 1587 through 1624 Proline residue: A1608 - end of helix removed outlier: 3.721A pdb=" N LEU A1617 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A1619 " --> pdb=" O SER A1615 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 3.504A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 removed outlier: 3.606A pdb=" N LYS A1652 " --> pdb=" O ILE A1648 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A1653 " --> pdb=" O GLN A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 5.219A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1718 through 1732 Processing helix chain 'A' and resid 1733 through 1744 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1804 Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.557A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 Processing helix chain 'A' and resid 1902 through 1916 Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 3.948A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 4.364A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A1929 " --> pdb=" O LEU A1925 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1924 through 1930' Processing helix chain 'A' and resid 1931 through 1950 removed outlier: 5.268A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A1950 " --> pdb=" O GLU A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 3.928A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1985 removed outlier: 3.813A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 removed outlier: 3.734A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A2005 " --> pdb=" O LEU A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.935A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2036 removed outlier: 5.362A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2065 removed outlier: 3.584A pdb=" N VAL A2049 " --> pdb=" O SER A2045 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A2064 " --> pdb=" O LEU A2060 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS A2065 " --> pdb=" O SER A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2072 removed outlier: 3.598A pdb=" N LYS A2072 " --> pdb=" O GLN A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 4.206A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2159 removed outlier: 3.823A pdb=" N THR A2159 " --> pdb=" O LEU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 3.558A pdb=" N SER A2175 " --> pdb=" O PHE A2171 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A2191 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Proline residue: A2192 - end of helix Processing helix chain 'A' and resid 2193 through 2202 removed outlier: 4.055A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2223 Processing helix chain 'A' and resid 2231 through 2236 removed outlier: 3.773A pdb=" N ASP A2235 " --> pdb=" O THR A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2254 removed outlier: 3.637A pdb=" N ALA A2253 " --> pdb=" O PHE A2249 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2276 Proline residue: A2263 - end of helix Processing helix chain 'A' and resid 2277 through 2305 removed outlier: 3.652A pdb=" N THR A2281 " --> pdb=" O GLY A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.858A pdb=" N MET A2314 " --> pdb=" O GLY A2310 " (cutoff:3.500A) Processing helix chain 'A' and resid 2318 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.813A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2366 removed outlier: 3.811A pdb=" N VAL A2358 " --> pdb=" O THR A2354 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A2359 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A2365 " --> pdb=" O SER A2361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A2366 " --> pdb=" O VAL A2362 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2390 Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 4.219A pdb=" N CYS A2461 " --> pdb=" O THR A2457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2476 through 2481 removed outlier: 3.747A pdb=" N LEU A2480 " --> pdb=" O VAL A2476 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2476 through 2481' Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2506 through 2537 removed outlier: 4.718A pdb=" N ASN A2510 " --> pdb=" O ILE A2506 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A2517 " --> pdb=" O PHE A2513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A2535 " --> pdb=" O GLU A2531 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.251A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2549' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2607 through 2615 removed outlier: 3.894A pdb=" N ASN A2613 " --> pdb=" O SER A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2651 removed outlier: 4.485A pdb=" N ASN A2620 " --> pdb=" O GLU A2616 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A2621 " --> pdb=" O GLY A2617 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE A2622 " --> pdb=" O GLU A2618 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG A2623 " --> pdb=" O GLN A2619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A2624 " --> pdb=" O ASN A2620 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.274A pdb=" N GLY B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 44' Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.292A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 462 Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.826A pdb=" N ASN B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.546A pdb=" N LEU B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 542' Processing helix chain 'B' and resid 543 through 565 Proline residue: B 548 - end of helix removed outlier: 3.590A pdb=" N GLN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.163A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.935A pdb=" N ILE B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 603 removed outlier: 3.597A pdb=" N THR B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.984A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 658 removed outlier: 3.669A pdb=" N ASP B 658 " --> pdb=" O LYS B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 Processing helix chain 'B' and resid 744 through 756 removed outlier: 4.191A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 766 Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 811 through 824 removed outlier: 5.131A pdb=" N ASP B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 3.531A pdb=" N GLU B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 removed outlier: 3.504A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 Processing helix chain 'B' and resid 961 through 1003 Proline residue: B1003 - end of helix Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.805A pdb=" N MET B1035 " --> pdb=" O GLN B1031 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 3.523A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.889A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 removed outlier: 3.826A pdb=" N GLN B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 5.384A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP B1127 " --> pdb=" O LYS B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.138A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1201 Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1218 through 1237 removed outlier: 3.789A pdb=" N ALA B1237 " --> pdb=" O GLN B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 3.906A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1271 through 1278 Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.643A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 3.992A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.701A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 3.983A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 3.770A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 Processing helix chain 'B' and resid 1406 through 1421 Processing helix chain 'B' and resid 1434 through 1458 removed outlier: 4.471A pdb=" N TRP B1438 " --> pdb=" O SER B1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.870A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B1482 " --> pdb=" O ALA B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1489 removed outlier: 4.986A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B1489 " --> pdb=" O SER B1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1483 through 1489' Processing helix chain 'B' and resid 1491 through 1512 Proline residue: B1512 - end of helix Processing helix chain 'B' and resid 1515 through 1537 removed outlier: 3.614A pdb=" N LYS B1519 " --> pdb=" O GLN B1515 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY B1520 " --> pdb=" O GLN B1516 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B1521 " --> pdb=" O GLN B1517 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1557 Processing helix chain 'B' and resid 1587 through 1624 Proline residue: B1608 - end of helix removed outlier: 3.720A pdb=" N LEU B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B1618 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B1619 " --> pdb=" O SER B1615 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 removed outlier: 3.504A pdb=" N GLY B1641 " --> pdb=" O ARG B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.606A pdb=" N LYS B1652 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 5.219A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1718 through 1732 Processing helix chain 'B' and resid 1733 through 1744 Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 Processing helix chain 'B' and resid 1781 through 1804 Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.556A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 Processing helix chain 'B' and resid 1902 through 1916 Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 3.947A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 4.363A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B1929 " --> pdb=" O LEU B1925 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1924 through 1930' Processing helix chain 'B' and resid 1931 through 1950 removed outlier: 5.269A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY B1950 " --> pdb=" O GLU B1946 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 3.927A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1985 removed outlier: 3.812A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 removed outlier: 3.734A pdb=" N MET B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B2005 " --> pdb=" O LEU B2001 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.936A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2036 removed outlier: 5.362A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2065 removed outlier: 3.584A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS B2065 " --> pdb=" O SER B2061 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2072 removed outlier: 3.598A pdb=" N LYS B2072 " --> pdb=" O GLN B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 4.206A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2159 removed outlier: 3.823A pdb=" N THR B2159 " --> pdb=" O LEU B2155 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 3.559A pdb=" N SER B2175 " --> pdb=" O PHE B2171 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET B2191 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Proline residue: B2192 - end of helix Processing helix chain 'B' and resid 2193 through 2202 removed outlier: 4.055A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2223 Processing helix chain 'B' and resid 2231 through 2236 removed outlier: 3.772A pdb=" N ASP B2235 " --> pdb=" O THR B2231 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2254 removed outlier: 3.637A pdb=" N ALA B2253 " --> pdb=" O PHE B2249 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU B2254 " --> pdb=" O SER B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2259 through 2276 Proline residue: B2263 - end of helix Processing helix chain 'B' and resid 2277 through 2305 removed outlier: 3.652A pdb=" N THR B2281 " --> pdb=" O GLY B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.858A pdb=" N MET B2314 " --> pdb=" O GLY B2310 " (cutoff:3.500A) Processing helix chain 'B' and resid 2318 through 2336 Processing helix chain 'B' and resid 2337 through 2353 removed outlier: 4.813A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2366 removed outlier: 3.811A pdb=" N VAL B2358 " --> pdb=" O THR B2354 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B2359 " --> pdb=" O LEU B2355 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B2365 " --> pdb=" O SER B2361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B2366 " --> pdb=" O VAL B2362 " (cutoff:3.500A) Processing helix chain 'B' and resid 2367 through 2390 Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 4.219A pdb=" N CYS B2461 " --> pdb=" O THR B2457 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) Processing helix chain 'B' and resid 2476 through 2481 removed outlier: 3.747A pdb=" N LEU B2480 " --> pdb=" O VAL B2476 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2476 through 2481' Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2506 through 2537 removed outlier: 4.718A pdb=" N ASN B2510 " --> pdb=" O ILE B2506 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B2515 " --> pdb=" O LEU B2511 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B2516 " --> pdb=" O ILE B2512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B2517 " --> pdb=" O PHE B2513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B2535 " --> pdb=" O GLU B2531 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.251A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2607 through 2615 removed outlier: 3.894A pdb=" N ASN B2613 " --> pdb=" O SER B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2651 removed outlier: 4.485A pdb=" N ASN B2620 " --> pdb=" O GLU B2616 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU B2621 " --> pdb=" O GLY B2617 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B2622 " --> pdb=" O GLU B2618 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG B2623 " --> pdb=" O GLN B2619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B2624 " --> pdb=" O ASN B2620 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.274A pdb=" N GLY C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.292A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 462 Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.826A pdb=" N ASN C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.547A pdb=" N LEU C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 542' Processing helix chain 'C' and resid 543 through 565 Proline residue: C 548 - end of helix removed outlier: 3.590A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.164A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.936A pdb=" N ILE C 585 " --> pdb=" O MET C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 603 removed outlier: 3.597A pdb=" N THR C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.984A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 658 removed outlier: 3.670A pdb=" N ASP C 658 " --> pdb=" O LYS C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 Processing helix chain 'C' and resid 744 through 756 removed outlier: 4.192A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 766 Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 824 removed outlier: 5.131A pdb=" N ASP C 824 " --> pdb=" O ASN C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 3.532A pdb=" N GLU C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 874 removed outlier: 3.505A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 Processing helix chain 'C' and resid 961 through 1003 Proline residue: C1003 - end of helix Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.804A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 3.523A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.889A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 removed outlier: 3.826A pdb=" N GLN C1094 " --> pdb=" O HIS C1090 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C1095 " --> pdb=" O THR C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 5.383A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.137A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1189 through 1201 Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 3.788A pdb=" N ALA C1237 " --> pdb=" O GLN C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 3.907A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 Processing helix chain 'C' and resid 1271 through 1278 Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.643A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.991A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.701A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 3.984A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1392 removed outlier: 3.771A pdb=" N GLU C1384 " --> pdb=" O ASN C1380 " (cutoff:3.500A) Proline residue: C1392 - end of helix Processing helix chain 'C' and resid 1393 through 1402 Processing helix chain 'C' and resid 1406 through 1421 Processing helix chain 'C' and resid 1434 through 1458 removed outlier: 4.470A pdb=" N TRP C1438 " --> pdb=" O SER C1434 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.871A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C1482 " --> pdb=" O ALA C1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 1483 through 1489 removed outlier: 4.985A pdb=" N ASN C1487 " --> pdb=" O PRO C1483 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C1489 " --> pdb=" O SER C1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1483 through 1489' Processing helix chain 'C' and resid 1491 through 1512 Proline residue: C1512 - end of helix Processing helix chain 'C' and resid 1515 through 1537 removed outlier: 3.613A pdb=" N LYS C1519 " --> pdb=" O GLN C1515 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY C1520 " --> pdb=" O GLN C1516 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1557 Processing helix chain 'C' and resid 1587 through 1624 Proline residue: C1608 - end of helix removed outlier: 3.720A pdb=" N LEU C1617 " --> pdb=" O GLU C1613 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL C1618 " --> pdb=" O LEU C1614 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C1619 " --> pdb=" O SER C1615 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 removed outlier: 3.504A pdb=" N GLY C1641 " --> pdb=" O ARG C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1655 removed outlier: 3.606A pdb=" N LYS C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C1653 " --> pdb=" O GLN C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 5.219A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1718 through 1732 Processing helix chain 'C' and resid 1733 through 1744 Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1804 Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.557A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 3.949A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 4.364A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C1929 " --> pdb=" O LEU C1925 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1924 through 1930' Processing helix chain 'C' and resid 1931 through 1950 removed outlier: 5.268A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY C1950 " --> pdb=" O GLU C1946 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 3.928A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1985 removed outlier: 3.812A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 removed outlier: 3.733A pdb=" N MET C2004 " --> pdb=" O LEU C2000 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C2005 " --> pdb=" O LEU C2001 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 3.935A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2036 removed outlier: 5.361A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2065 removed outlier: 3.583A pdb=" N VAL C2049 " --> pdb=" O SER C2045 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C2064 " --> pdb=" O LEU C2060 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS C2065 " --> pdb=" O SER C2061 " (cutoff:3.500A) Processing helix chain 'C' and resid 2066 through 2072 removed outlier: 3.598A pdb=" N LYS C2072 " --> pdb=" O GLN C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 4.206A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 removed outlier: 3.823A pdb=" N THR C2159 " --> pdb=" O LEU C2155 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 3.557A pdb=" N SER C2175 " --> pdb=" O PHE C2171 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET C2191 " --> pdb=" O LYS C2187 " (cutoff:3.500A) Proline residue: C2192 - end of helix Processing helix chain 'C' and resid 2193 through 2202 removed outlier: 4.055A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) Processing helix chain 'C' and resid 2203 through 2223 Processing helix chain 'C' and resid 2231 through 2236 removed outlier: 3.773A pdb=" N ASP C2235 " --> pdb=" O THR C2231 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2254 removed outlier: 3.638A pdb=" N ALA C2253 " --> pdb=" O PHE C2249 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU C2254 " --> pdb=" O SER C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2259 through 2276 Proline residue: C2263 - end of helix Processing helix chain 'C' and resid 2277 through 2305 removed outlier: 3.652A pdb=" N THR C2281 " --> pdb=" O GLY C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.857A pdb=" N MET C2314 " --> pdb=" O GLY C2310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2337 through 2353 removed outlier: 4.813A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2366 removed outlier: 3.811A pdb=" N VAL C2358 " --> pdb=" O THR C2354 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C2359 " --> pdb=" O LEU C2355 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C2365 " --> pdb=" O SER C2361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C2366 " --> pdb=" O VAL C2362 " (cutoff:3.500A) Processing helix chain 'C' and resid 2367 through 2390 Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 4.220A pdb=" N CYS C2461 " --> pdb=" O THR C2457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) Processing helix chain 'C' and resid 2476 through 2481 removed outlier: 3.748A pdb=" N LEU C2480 " --> pdb=" O VAL C2476 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2476 through 2481' Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2506 through 2537 removed outlier: 4.718A pdb=" N ASN C2510 " --> pdb=" O ILE C2506 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C2515 " --> pdb=" O LEU C2511 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C2516 " --> pdb=" O ILE C2512 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C2517 " --> pdb=" O PHE C2513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C2535 " --> pdb=" O GLU C2531 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.252A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2607 through 2615 removed outlier: 3.894A pdb=" N ASN C2613 " --> pdb=" O SER C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2616 through 2651 removed outlier: 4.485A pdb=" N ASN C2620 " --> pdb=" O GLU C2616 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C2621 " --> pdb=" O GLY C2617 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE C2622 " --> pdb=" O GLU C2618 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG C2623 " --> pdb=" O GLN C2619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C2624 " --> pdb=" O ASN C2620 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.273A pdb=" N GLY D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 44' Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.292A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 462 Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.825A pdb=" N ASN D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.547A pdb=" N LEU D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 537 through 542' Processing helix chain 'D' and resid 543 through 565 Proline residue: D 548 - end of helix removed outlier: 3.590A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.164A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.935A pdb=" N ILE D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 603 removed outlier: 3.598A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.984A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 removed outlier: 3.670A pdb=" N ASP D 658 " --> pdb=" O LYS D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 Processing helix chain 'D' and resid 744 through 756 removed outlier: 4.191A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 766 Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 824 removed outlier: 5.131A pdb=" N ASP D 824 " --> pdb=" O ASN D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 848 removed outlier: 3.531A pdb=" N GLU D 847 " --> pdb=" O ASN D 843 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 874 removed outlier: 3.504A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 Processing helix chain 'D' and resid 961 through 1003 Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1037 removed outlier: 3.805A pdb=" N MET D1035 " --> pdb=" O GLN D1031 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY D1037 " --> pdb=" O GLU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 3.522A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.889A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.826A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 5.383A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.138A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1189 through 1201 Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 3.789A pdb=" N ALA D1237 " --> pdb=" O GLN D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 3.907A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 Processing helix chain 'D' and resid 1271 through 1278 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.643A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 3.991A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.701A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.984A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 removed outlier: 3.771A pdb=" N GLU D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 Processing helix chain 'D' and resid 1406 through 1421 Processing helix chain 'D' and resid 1434 through 1458 removed outlier: 4.471A pdb=" N TRP D1438 " --> pdb=" O SER D1434 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.871A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D1482 " --> pdb=" O ALA D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1483 through 1489 removed outlier: 4.985A pdb=" N ASN D1487 " --> pdb=" O PRO D1483 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D1489 " --> pdb=" O SER D1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1483 through 1489' Processing helix chain 'D' and resid 1491 through 1512 Proline residue: D1512 - end of helix Processing helix chain 'D' and resid 1515 through 1537 removed outlier: 3.613A pdb=" N LYS D1519 " --> pdb=" O GLN D1515 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D1520 " --> pdb=" O GLN D1516 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1557 Processing helix chain 'D' and resid 1587 through 1624 Proline residue: D1608 - end of helix removed outlier: 3.721A pdb=" N LEU D1617 " --> pdb=" O GLU D1613 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D1618 " --> pdb=" O LEU D1614 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP D1619 " --> pdb=" O SER D1615 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 3.504A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.606A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.218A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1718 through 1732 Processing helix chain 'D' and resid 1733 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1804 Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 3.556A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1902 through 1916 Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 3.948A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 4.364A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D1929 " --> pdb=" O LEU D1925 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1924 through 1930' Processing helix chain 'D' and resid 1931 through 1950 removed outlier: 5.268A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY D1950 " --> pdb=" O GLU D1946 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 3.928A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1979 through 1985 removed outlier: 3.813A pdb=" N LYS D1983 " --> pdb=" O SER D1979 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 removed outlier: 3.734A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D2005 " --> pdb=" O LEU D2001 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.935A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2036 removed outlier: 5.362A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2065 removed outlier: 3.584A pdb=" N VAL D2049 " --> pdb=" O SER D2045 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D2064 " --> pdb=" O LEU D2060 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS D2065 " --> pdb=" O SER D2061 " (cutoff:3.500A) Processing helix chain 'D' and resid 2066 through 2072 removed outlier: 3.599A pdb=" N LYS D2072 " --> pdb=" O GLN D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 4.205A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2159 removed outlier: 3.823A pdb=" N THR D2159 " --> pdb=" O LEU D2155 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 3.558A pdb=" N SER D2175 " --> pdb=" O PHE D2171 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET D2191 " --> pdb=" O LYS D2187 " (cutoff:3.500A) Proline residue: D2192 - end of helix Processing helix chain 'D' and resid 2193 through 2202 removed outlier: 4.055A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) Processing helix chain 'D' and resid 2203 through 2223 Processing helix chain 'D' and resid 2231 through 2236 removed outlier: 3.773A pdb=" N ASP D2235 " --> pdb=" O THR D2231 " (cutoff:3.500A) Processing helix chain 'D' and resid 2237 through 2254 removed outlier: 3.636A pdb=" N ALA D2253 " --> pdb=" O PHE D2249 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU D2254 " --> pdb=" O SER D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2259 through 2276 Proline residue: D2263 - end of helix Processing helix chain 'D' and resid 2277 through 2305 removed outlier: 3.652A pdb=" N THR D2281 " --> pdb=" O GLY D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.858A pdb=" N MET D2314 " --> pdb=" O GLY D2310 " (cutoff:3.500A) Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.813A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2366 removed outlier: 3.811A pdb=" N VAL D2358 " --> pdb=" O THR D2354 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D2359 " --> pdb=" O LEU D2355 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D2365 " --> pdb=" O SER D2361 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D2366 " --> pdb=" O VAL D2362 " (cutoff:3.500A) Processing helix chain 'D' and resid 2367 through 2390 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 4.219A pdb=" N CYS D2461 " --> pdb=" O THR D2457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) Processing helix chain 'D' and resid 2476 through 2481 removed outlier: 3.748A pdb=" N LEU D2480 " --> pdb=" O VAL D2476 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2476 through 2481' Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2506 through 2537 removed outlier: 4.717A pdb=" N ASN D2510 " --> pdb=" O ILE D2506 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D2515 " --> pdb=" O LEU D2511 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE D2516 " --> pdb=" O ILE D2512 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D2517 " --> pdb=" O PHE D2513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D2535 " --> pdb=" O GLU D2531 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.252A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2549' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2607 through 2615 removed outlier: 3.895A pdb=" N ASN D2613 " --> pdb=" O SER D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2616 through 2651 removed outlier: 4.485A pdb=" N ASN D2620 " --> pdb=" O GLU D2616 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU D2621 " --> pdb=" O GLY D2617 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D2622 " --> pdb=" O GLU D2618 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG D2623 " --> pdb=" O GLN D2619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D2624 " --> pdb=" O ASN D2620 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 13 through 20 removed outlier: 6.848A pdb=" N ILE A 13 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 218 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N THR A 217 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 185 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP A 181 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 13.149A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 195 through 198 removed outlier: 3.974A pdb=" N GLU A 209 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.389A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 13.944A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 239 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 315 through 320 removed outlier: 7.301A pdb=" N LYS A 351 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 367 through 371 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'A' and resid 396 through 402 removed outlier: 4.298A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 666 through 672 removed outlier: 3.986A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.079A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.907A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= 11, first strand: chain 'B' and resid 13 through 20 removed outlier: 6.848A pdb=" N ILE B 13 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 218 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N THR B 217 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 185 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 181 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N ILE B 122 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL B 135 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 195 through 198 removed outlier: 3.974A pdb=" N GLU B 209 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.389A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 13.944A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP B 239 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 315 through 320 removed outlier: 7.301A pdb=" N LYS B 351 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 367 through 371 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'B' and resid 396 through 402 removed outlier: 4.298A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 666 through 672 removed outlier: 3.986A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.079A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 7.907A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 241 through 245 Processing sheet with id= 21, first strand: chain 'C' and resid 13 through 20 removed outlier: 6.848A pdb=" N ILE C 13 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 218 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N THR C 217 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 185 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP C 181 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N ILE C 122 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N VAL C 135 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 195 through 198 removed outlier: 3.974A pdb=" N GLU C 209 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.389A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 13.944A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP C 239 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 315 through 320 removed outlier: 7.301A pdb=" N LYS C 351 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 367 through 371 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'C' and resid 396 through 402 removed outlier: 4.298A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 666 through 672 removed outlier: 3.986A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.079A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 2395 through 2399 removed outlier: 7.907A pdb=" N PHE C2395 " --> pdb=" O ALA C2454 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER C2450 " --> pdb=" O VAL C2399 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 241 through 245 Processing sheet with id= 31, first strand: chain 'D' and resid 13 through 20 removed outlier: 6.848A pdb=" N ILE D 13 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 218 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N THR D 217 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 185 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP D 181 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 13.150A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 195 through 198 removed outlier: 3.973A pdb=" N GLU D 209 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.389A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 13.944A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP D 239 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 315 through 320 removed outlier: 7.300A pdb=" N LYS D 351 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 367 through 371 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'D' and resid 396 through 402 removed outlier: 4.298A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 666 through 672 removed outlier: 3.986A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.078A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.907A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 241 through 245 4448 hydrogen bonds defined for protein. 13308 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: 70.55 Time building geometry restraints manager: 94.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 72804 1.03 - 1.23: 205 1.23 - 1.42: 30839 1.42 - 1.62: 43800 1.62 - 1.81: 764 Bond restraints: 148412 Sorted by residual: bond pdb=" CD2 HIS C1090 " pdb=" HD2 HIS C1090 " ideal model delta sigma weight residual 0.930 1.315 -0.385 2.00e-02 2.50e+03 3.72e+02 bond pdb=" CD2 HIS B1090 " pdb=" HD2 HIS B1090 " ideal model delta sigma weight residual 0.930 1.315 -0.385 2.00e-02 2.50e+03 3.71e+02 bond pdb=" CD2 HIS A1090 " pdb=" HD2 HIS A1090 " ideal model delta sigma weight residual 0.930 1.315 -0.385 2.00e-02 2.50e+03 3.71e+02 bond pdb=" CD2 HIS D1090 " pdb=" HD2 HIS D1090 " ideal model delta sigma weight residual 0.930 1.315 -0.385 2.00e-02 2.50e+03 3.70e+02 bond pdb=" NE2 HIS B1090 " pdb=" HE2 HIS B1090 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.57e+01 ... (remaining 148407 not shown) Histogram of bond angle deviations from ideal: 20.29 - 46.51: 8 46.51 - 72.74: 8 72.74 - 98.96: 24 98.96 - 125.18: 264676 125.18 - 151.41: 3156 Bond angle restraints: 267872 Sorted by residual: angle pdb=" CG HIS C1090 " pdb=" CD2 HIS C1090 " pdb=" HD2 HIS C1090 " ideal model delta sigma weight residual 126.40 20.29 106.11 3.00e+00 1.11e-01 1.25e+03 angle pdb=" CG HIS A1090 " pdb=" CD2 HIS A1090 " pdb=" HD2 HIS A1090 " ideal model delta sigma weight residual 126.40 20.29 106.11 3.00e+00 1.11e-01 1.25e+03 angle pdb=" CG HIS B1090 " pdb=" CD2 HIS B1090 " pdb=" HD2 HIS B1090 " ideal model delta sigma weight residual 126.40 20.30 106.10 3.00e+00 1.11e-01 1.25e+03 angle pdb=" CG HIS D1090 " pdb=" CD2 HIS D1090 " pdb=" HD2 HIS D1090 " ideal model delta sigma weight residual 126.40 20.31 106.09 3.00e+00 1.11e-01 1.25e+03 angle pdb=" NE2 HIS C1090 " pdb=" CE1 HIS C1090 " pdb=" HE1 HIS C1090 " ideal model delta sigma weight residual 125.80 42.73 83.07 3.00e+00 1.11e-01 7.67e+02 ... (remaining 267867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 68592 35.70 - 71.41: 1060 71.41 - 107.11: 60 107.11 - 142.81: 28 142.81 - 178.51: 12 Dihedral angle restraints: 69752 sinusoidal: 38420 harmonic: 31332 Sorted by residual: dihedral pdb=" CG HIS A1090 " pdb=" ND1 HIS A1090 " pdb=" CE1 HIS A1090 " pdb=" HE1 HIS A1090 " ideal model delta harmonic sigma weight residual 180.00 28.97 151.03 0 5.00e+00 4.00e-02 9.12e+02 dihedral pdb=" CG HIS B1090 " pdb=" ND1 HIS B1090 " pdb=" CE1 HIS B1090 " pdb=" HE1 HIS B1090 " ideal model delta harmonic sigma weight residual 180.00 28.97 151.03 0 5.00e+00 4.00e-02 9.12e+02 dihedral pdb=" CG HIS C1090 " pdb=" ND1 HIS C1090 " pdb=" CE1 HIS C1090 " pdb=" HE1 HIS C1090 " ideal model delta harmonic sigma weight residual 180.00 28.98 151.02 0 5.00e+00 4.00e-02 9.12e+02 ... (remaining 69749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 10419 0.059 - 0.118: 1118 0.118 - 0.176: 63 0.176 - 0.235: 0 0.235 - 0.294: 12 Chirality restraints: 11612 Sorted by residual: chirality pdb=" C2' ATP A3004 " pdb=" C1' ATP A3004 " pdb=" C3' ATP A3004 " pdb=" O2' ATP A3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' ATP B2705 " pdb=" C1' ATP B2705 " pdb=" C3' ATP B2705 " pdb=" O2' ATP B2705 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' ATP D2705 " pdb=" C1' ATP D2705 " pdb=" C3' ATP D2705 " pdb=" O2' ATP D2705 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 11609 not shown) Planarity restraints: 21640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D1090 " 0.031 2.00e-02 2.50e+03 1.49e-01 4.97e+02 pdb=" CG HIS D1090 " 0.248 2.00e-02 2.50e+03 pdb=" ND1 HIS D1090 " -0.107 2.00e-02 2.50e+03 pdb=" CD2 HIS D1090 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 HIS D1090 " 0.166 2.00e-02 2.50e+03 pdb=" NE2 HIS D1090 " 0.157 2.00e-02 2.50e+03 pdb=" HD2 HIS D1090 " -0.208 2.00e-02 2.50e+03 pdb=" HE1 HIS D1090 " -0.062 2.00e-02 2.50e+03 pdb=" HE2 HIS D1090 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B1090 " -0.030 2.00e-02 2.50e+03 1.49e-01 4.96e+02 pdb=" CG HIS B1090 " -0.248 2.00e-02 2.50e+03 pdb=" ND1 HIS B1090 " 0.107 2.00e-02 2.50e+03 pdb=" CD2 HIS B1090 " 0.097 2.00e-02 2.50e+03 pdb=" CE1 HIS B1090 " -0.166 2.00e-02 2.50e+03 pdb=" NE2 HIS B1090 " -0.156 2.00e-02 2.50e+03 pdb=" HD2 HIS B1090 " 0.208 2.00e-02 2.50e+03 pdb=" HE1 HIS B1090 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 HIS B1090 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1090 " 0.031 2.00e-02 2.50e+03 1.48e-01 4.96e+02 pdb=" CG HIS A1090 " 0.248 2.00e-02 2.50e+03 pdb=" ND1 HIS A1090 " -0.107 2.00e-02 2.50e+03 pdb=" CD2 HIS A1090 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 HIS A1090 " 0.165 2.00e-02 2.50e+03 pdb=" NE2 HIS A1090 " 0.157 2.00e-02 2.50e+03 pdb=" HD2 HIS A1090 " -0.208 2.00e-02 2.50e+03 pdb=" HE1 HIS A1090 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 HIS A1090 " -0.127 2.00e-02 2.50e+03 ... (remaining 21637 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.77: 272 1.77 - 2.48: 95967 2.48 - 3.19: 449150 3.19 - 3.89: 566353 3.89 - 4.60: 909997 Nonbonded interactions: 2021739 Sorted by model distance: nonbonded pdb=" CD2 HIS B1090 " pdb=" HE1 HIS B1090 " model vdw 1.064 2.240 nonbonded pdb=" CD2 HIS D1090 " pdb=" HE1 HIS D1090 " model vdw 1.065 2.240 nonbonded pdb=" CD2 HIS A1090 " pdb=" HE1 HIS A1090 " model vdw 1.065 2.240 nonbonded pdb=" CD2 HIS C1090 " pdb=" HE1 HIS C1090 " model vdw 1.065 2.240 nonbonded pdb=" ND1 HIS D1090 " pdb=" HD2 HIS D1090 " model vdw 1.216 2.080 ... (remaining 2021734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 2651 or (resid 3006 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 3007 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or name C7 o \ r name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 \ or name O3P or name O4P or name P )) or (resid 3008 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C \ 6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 5 through 2651 or (resid 2706 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 2707 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or name C7 o \ r name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 \ or name O3P or name O4P or name P )) or (resid 2708 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C \ 6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 5 through 2651 or (resid 2706 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 2707 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or name C7 o \ r name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 \ or name O3P or name O4P or name P )) or (resid 2708 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C \ 6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 5 through 2651 or (resid 2706 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name \ O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or nam \ e O4P or name P )) or (resid 2707 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or name C7 o \ r name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 \ or name O3P or name O4P or name P )) or (resid 2708 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C \ 6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O \ 3 or name O31 or name O3P or name O4P or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.540 Extract box with map and model: 59.800 Check model and map are aligned: 2.000 Set scattering table: 0.970 Process input model: 426.330 Find NCS groups from input model: 7.410 Set up NCS constraints: 0.620 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: 0.040 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 518.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.062 75436 Z= 0.145 Angle : 0.787 65.548 101884 Z= 0.318 Chirality : 0.034 0.294 11612 Planarity : 0.003 0.133 12864 Dihedral : 11.617 178.514 28616 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.44 % Allowed : 2.57 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 3.77 (0.10), residues: 8968 helix: 3.67 (0.07), residues: 5760 sheet: 0.07 (0.21), residues: 656 loop : 0.32 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2184 HIS 0.206 0.002 HIS D1090 PHE 0.011 0.001 PHE D2209 TYR 0.012 0.001 TYR D2322 ARG 0.002 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 2093 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2057 time to evaluate : 8.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.8012 (m110) cc_final: 0.7744 (m-40) REVERT: A 239 ASP cc_start: 0.7764 (m-30) cc_final: 0.7536 (m-30) REVERT: A 286 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7662 (mt-10) REVERT: A 289 HIS cc_start: 0.7858 (m-70) cc_final: 0.7656 (m-70) REVERT: A 375 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6944 (mm-40) REVERT: A 416 MET cc_start: 0.8051 (ttm) cc_final: 0.7828 (ttm) REVERT: A 441 ASP cc_start: 0.7678 (m-30) cc_final: 0.7425 (m-30) REVERT: A 504 GLU cc_start: 0.7280 (mp0) cc_final: 0.6972 (mp0) REVERT: A 614 GLU cc_start: 0.7854 (mp0) cc_final: 0.7498 (mp0) REVERT: A 616 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 690 GLU cc_start: 0.7679 (mp0) cc_final: 0.7428 (mt-10) REVERT: A 740 CYS cc_start: 0.7899 (m) cc_final: 0.7576 (m) REVERT: A 835 GLU cc_start: 0.7843 (tt0) cc_final: 0.7590 (tt0) REVERT: A 1094 GLN cc_start: 0.8392 (mt0) cc_final: 0.8158 (mt0) REVERT: A 1108 LYS cc_start: 0.7982 (mttm) cc_final: 0.7731 (mtmt) REVERT: A 1234 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8434 (mtmt) REVERT: A 1273 GLN cc_start: 0.8258 (tp40) cc_final: 0.7908 (tp40) REVERT: A 1301 ASP cc_start: 0.7694 (m-30) cc_final: 0.7468 (m-30) REVERT: A 1347 ASP cc_start: 0.8141 (m-30) cc_final: 0.7850 (m-30) REVERT: A 1363 MET cc_start: 0.8090 (mmt) cc_final: 0.7829 (mmm) REVERT: A 1367 SER cc_start: 0.8485 (m) cc_final: 0.8255 (p) REVERT: A 1377 GLU cc_start: 0.7616 (tt0) cc_final: 0.7295 (tt0) REVERT: A 1411 MET cc_start: 0.8238 (ttt) cc_final: 0.8005 (ttp) REVERT: A 1597 ASP cc_start: 0.8365 (t0) cc_final: 0.8072 (t0) REVERT: A 1619 ASP cc_start: 0.7869 (m-30) cc_final: 0.7487 (m-30) REVERT: A 1645 SER cc_start: 0.8101 (t) cc_final: 0.7839 (m) REVERT: A 1689 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7910 (mtm) REVERT: A 1905 CYS cc_start: 0.7879 (m) cc_final: 0.7406 (m) REVERT: A 1994 ASP cc_start: 0.7935 (t70) cc_final: 0.7675 (t0) REVERT: A 2070 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8797 (mt) REVERT: A 2133 MET cc_start: 0.8609 (mtm) cc_final: 0.8228 (mtm) REVERT: A 2149 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 2316 MET cc_start: 0.7653 (tmm) cc_final: 0.7389 (tpp) REVERT: A 2341 TYR cc_start: 0.8673 (m-80) cc_final: 0.8137 (m-80) REVERT: B 370 ASP cc_start: 0.8455 (t0) cc_final: 0.8037 (t0) REVERT: B 416 MET cc_start: 0.7667 (ttm) cc_final: 0.7419 (ttm) REVERT: B 527 ARG cc_start: 0.7413 (ttm170) cc_final: 0.7103 (ttp-170) REVERT: B 653 CYS cc_start: 0.7781 (m) cc_final: 0.7460 (m) REVERT: B 669 GLU cc_start: 0.7734 (pt0) cc_final: 0.7518 (pt0) REVERT: B 835 GLU cc_start: 0.7722 (tt0) cc_final: 0.7509 (tt0) REVERT: B 1272 TYR cc_start: 0.8529 (t80) cc_final: 0.8256 (t80) REVERT: B 1344 HIS cc_start: 0.7619 (t-170) cc_final: 0.7401 (t-170) REVERT: B 1347 ASP cc_start: 0.7996 (m-30) cc_final: 0.7650 (m-30) REVERT: B 1350 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8474 (ttmm) REVERT: B 1370 ASP cc_start: 0.8139 (m-30) cc_final: 0.7798 (m-30) REVERT: B 1625 GLU cc_start: 0.8028 (pm20) cc_final: 0.7486 (pm20) REVERT: B 1689 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: B 1954 GLU cc_start: 0.7696 (mp0) cc_final: 0.7446 (mp0) REVERT: B 2070 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8838 (mt) REVERT: B 2123 GLN cc_start: 0.8138 (pt0) cc_final: 0.7933 (pt0) REVERT: B 2292 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7686 (t0) REVERT: B 2316 MET cc_start: 0.7415 (tmm) cc_final: 0.7165 (tpp) REVERT: C 47 ASN cc_start: 0.7967 (m-40) cc_final: 0.7753 (m110) REVERT: C 107 GLU cc_start: 0.7991 (tp30) cc_final: 0.7744 (tp30) REVERT: C 108 ASN cc_start: 0.7981 (m-40) cc_final: 0.7708 (m-40) REVERT: C 286 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 370 ASP cc_start: 0.8660 (t0) cc_final: 0.8436 (t0) REVERT: C 416 MET cc_start: 0.7874 (ttm) cc_final: 0.7619 (ttm) REVERT: C 424 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7464 (mm-30) REVERT: C 459 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7090 (mp) REVERT: C 504 GLU cc_start: 0.7707 (mp0) cc_final: 0.7455 (mp0) REVERT: C 563 SER cc_start: 0.8159 (m) cc_final: 0.7844 (p) REVERT: C 602 ASN cc_start: 0.8149 (t0) cc_final: 0.7879 (t0) REVERT: C 614 GLU cc_start: 0.7938 (mp0) cc_final: 0.7400 (mp0) REVERT: C 616 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 754 GLN cc_start: 0.8784 (tt0) cc_final: 0.8495 (tm-30) REVERT: C 799 PHE cc_start: 0.8063 (m-80) cc_final: 0.7745 (m-10) REVERT: C 1094 GLN cc_start: 0.8251 (mt0) cc_final: 0.7819 (mt0) REVERT: C 1115 ASP cc_start: 0.7286 (m-30) cc_final: 0.7036 (m-30) REVERT: C 1206 MET cc_start: 0.8285 (mmt) cc_final: 0.8022 (mmt) REVERT: C 1370 ASP cc_start: 0.8229 (m-30) cc_final: 0.7863 (m-30) REVERT: C 1619 ASP cc_start: 0.7896 (m-30) cc_final: 0.7555 (m-30) REVERT: C 1645 SER cc_start: 0.8291 (t) cc_final: 0.7801 (m) REVERT: C 1689 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: C 1770 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8041 (tttp) REVERT: C 1891 PHE cc_start: 0.8065 (t80) cc_final: 0.7857 (t80) REVERT: C 1897 ASN cc_start: 0.8112 (m-40) cc_final: 0.7863 (m110) REVERT: C 1954 GLU cc_start: 0.7715 (mp0) cc_final: 0.7460 (mp0) REVERT: C 2014 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7606 (mm-30) REVERT: C 2026 VAL cc_start: 0.8309 (t) cc_final: 0.8105 (m) REVERT: C 2123 GLN cc_start: 0.8194 (pt0) cc_final: 0.7979 (pt0) REVERT: C 2553 VAL cc_start: 0.8145 (m) cc_final: 0.7738 (p) REVERT: D 107 GLU cc_start: 0.7845 (tp30) cc_final: 0.7407 (mm-30) REVERT: D 370 ASP cc_start: 0.8942 (t0) cc_final: 0.8725 (t0) REVERT: D 424 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7502 (mm-30) REVERT: D 614 GLU cc_start: 0.7859 (mp0) cc_final: 0.7517 (mp0) REVERT: D 616 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7428 (mm-30) REVERT: D 739 MET cc_start: 0.7456 (mtm) cc_final: 0.7230 (mtm) REVERT: D 1177 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 1322 MET cc_start: 0.8380 (tpt) cc_final: 0.7678 (tpt) REVERT: D 1363 MET cc_start: 0.8070 (mmt) cc_final: 0.7833 (mmm) REVERT: D 1411 MET cc_start: 0.8216 (ttt) cc_final: 0.7994 (ttp) REVERT: D 1481 SER cc_start: 0.8681 (t) cc_final: 0.8390 (p) REVERT: D 1597 ASP cc_start: 0.8204 (t0) cc_final: 0.7953 (t0) REVERT: D 1619 ASP cc_start: 0.8071 (m-30) cc_final: 0.7755 (m-30) REVERT: D 1645 SER cc_start: 0.8209 (t) cc_final: 0.7900 (m) REVERT: D 1689 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7893 (mtm) REVERT: D 1727 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7744 (ttt180) REVERT: D 1784 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7653 (mmm-85) REVERT: D 1891 PHE cc_start: 0.8195 (t80) cc_final: 0.7946 (t80) REVERT: D 1905 CYS cc_start: 0.8041 (m) cc_final: 0.7627 (m) REVERT: D 1986 MET cc_start: 0.7453 (tpt) cc_final: 0.7098 (tpt) REVERT: D 1994 ASP cc_start: 0.7567 (t70) cc_final: 0.7249 (t0) REVERT: D 2070 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8800 (mt) REVERT: D 2122 SER cc_start: 0.8657 (m) cc_final: 0.8417 (p) REVERT: D 2123 GLN cc_start: 0.8358 (pt0) cc_final: 0.8085 (pt0) REVERT: D 2283 ASN cc_start: 0.8144 (m-40) cc_final: 0.7796 (m110) REVERT: D 2289 ASN cc_start: 0.7841 (t0) cc_final: 0.7572 (t0) REVERT: D 2316 MET cc_start: 0.7412 (tmm) cc_final: 0.7144 (tpp) outliers start: 36 outliers final: 5 residues processed: 2067 average time/residue: 1.7748 time to fit residues: 6172.1886 Evaluate side-chains 1701 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1687 time to evaluate : 8.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 2070 LEU Chi-restraints excluded: chain B residue 2292 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 2070 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 766 optimal weight: 1.9990 chunk 688 optimal weight: 5.9990 chunk 381 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 464 optimal weight: 0.8980 chunk 367 optimal weight: 2.9990 chunk 711 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 432 optimal weight: 1.9990 chunk 529 optimal weight: 4.9990 chunk 824 optimal weight: 3.9990 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 104 ASN A 512 GLN A 601 ASN A 642 HIS A 661 ASN A 783 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN A1487 ASN A1518 HIS A1650 HIS A2292 ASN A2528 GLN B 104 ASN B 601 ASN B 661 ASN B 703 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1298 GLN B1318 GLN B1650 HIS B1897 ASN B2066 GLN B2528 GLN C 104 ASN C 399 GLN C 512 GLN C 703 HIS C 783 HIS C1298 GLN C1318 GLN C1337 ASN D 104 ASN D 289 HIS D 375 GLN D 399 GLN D 512 GLN D 754 GLN ** D1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1180 ASN ** D1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1318 GLN D1327 ASN D1650 HIS D2161 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 75436 Z= 0.416 Angle : 0.537 8.758 101884 Z= 0.284 Chirality : 0.038 0.188 11612 Planarity : 0.004 0.055 12864 Dihedral : 10.398 128.504 10766 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.98 % Allowed : 7.14 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.93 (0.09), residues: 8968 helix: 3.00 (0.07), residues: 5832 sheet: -0.16 (0.20), residues: 680 loop : -0.10 (0.13), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B2601 HIS 0.010 0.001 HIS D 195 PHE 0.026 0.002 PHE A1235 TYR 0.023 0.002 TYR D1382 ARG 0.005 0.001 ARG A2524 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1870 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1791 time to evaluate : 8.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8020 (tp30) cc_final: 0.7757 (tp30) REVERT: A 111 VAL cc_start: 0.8254 (t) cc_final: 0.8008 (p) REVERT: A 204 ASN cc_start: 0.8279 (m110) cc_final: 0.8021 (m-40) REVERT: A 232 GLU cc_start: 0.8006 (pt0) cc_final: 0.7469 (pt0) REVERT: A 614 GLU cc_start: 0.8050 (mp0) cc_final: 0.7429 (mp0) REVERT: A 616 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 690 GLU cc_start: 0.7733 (mp0) cc_final: 0.7433 (mt-10) REVERT: A 740 CYS cc_start: 0.8073 (m) cc_final: 0.7792 (m) REVERT: A 835 GLU cc_start: 0.8016 (tt0) cc_final: 0.7804 (tt0) REVERT: A 1094 GLN cc_start: 0.8696 (mt0) cc_final: 0.8413 (mt0) REVERT: A 1108 LYS cc_start: 0.8083 (mttm) cc_final: 0.7836 (mtmt) REVERT: A 1280 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 1347 ASP cc_start: 0.8194 (m-30) cc_final: 0.7931 (m-30) REVERT: A 1363 MET cc_start: 0.8165 (mmt) cc_final: 0.7919 (mmm) REVERT: A 1411 MET cc_start: 0.8404 (ttt) cc_final: 0.8086 (ttp) REVERT: A 1674 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 1689 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: A 1905 CYS cc_start: 0.8294 (m) cc_final: 0.7757 (m) REVERT: A 1994 ASP cc_start: 0.7961 (t70) cc_final: 0.7744 (t0) REVERT: A 2149 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 2316 MET cc_start: 0.7821 (tmm) cc_final: 0.7592 (tpp) REVERT: A 2553 VAL cc_start: 0.8530 (m) cc_final: 0.8110 (p) REVERT: B 470 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.7872 (mtp-110) REVERT: B 527 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7272 (ttp-170) REVERT: B 614 GLU cc_start: 0.8096 (mp0) cc_final: 0.7483 (mp0) REVERT: B 624 LYS cc_start: 0.8244 (tttm) cc_final: 0.7995 (ttpt) REVERT: B 690 GLU cc_start: 0.7712 (mp0) cc_final: 0.7345 (mt-10) REVERT: B 835 GLU cc_start: 0.7910 (tt0) cc_final: 0.7710 (tt0) REVERT: B 984 ASP cc_start: 0.8155 (t70) cc_final: 0.7931 (t0) REVERT: B 1347 ASP cc_start: 0.8066 (m-30) cc_final: 0.7703 (m-30) REVERT: B 1363 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: B 1630 GLU cc_start: 0.8212 (tp30) cc_final: 0.7968 (mm-30) REVERT: B 1674 LEU cc_start: 0.8470 (tp) cc_final: 0.8186 (mp) REVERT: B 1689 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8045 (mtm) REVERT: B 1770 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8074 (tttp) REVERT: B 1795 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7753 (ttt90) REVERT: B 1905 CYS cc_start: 0.8268 (m) cc_final: 0.7813 (m) REVERT: B 2123 GLN cc_start: 0.8327 (pt0) cc_final: 0.7982 (pt0) REVERT: B 2292 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7898 (t0) REVERT: B 2316 MET cc_start: 0.7661 (tmm) cc_final: 0.7415 (tpp) REVERT: B 2553 VAL cc_start: 0.8434 (m) cc_final: 0.8058 (p) REVERT: C 100 GLU cc_start: 0.7357 (tt0) cc_final: 0.6868 (tt0) REVERT: C 286 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7988 (mt-10) REVERT: C 309 LEU cc_start: 0.8908 (tp) cc_final: 0.8682 (tt) REVERT: C 494 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9023 (mp) REVERT: C 504 GLU cc_start: 0.7766 (mp0) cc_final: 0.7439 (mp0) REVERT: C 616 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7692 (tp30) REVERT: C 650 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 739 MET cc_start: 0.7960 (mtm) cc_final: 0.7639 (mtm) REVERT: C 988 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8291 (m) REVERT: C 1066 ASP cc_start: 0.7635 (p0) cc_final: 0.6960 (t0) REVERT: C 1094 GLN cc_start: 0.8642 (mt0) cc_final: 0.8177 (mt0) REVERT: C 1116 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7896 (mtp85) REVERT: C 1206 MET cc_start: 0.8462 (mmt) cc_final: 0.8147 (mmt) REVERT: C 1301 ASP cc_start: 0.7738 (m-30) cc_final: 0.7497 (m-30) REVERT: C 1370 ASP cc_start: 0.8254 (m-30) cc_final: 0.7947 (m-30) REVERT: C 1689 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: C 1905 CYS cc_start: 0.8266 (m) cc_final: 0.7722 (m) REVERT: C 2014 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7590 (mm-30) REVERT: C 2024 GLU cc_start: 0.8281 (mp0) cc_final: 0.7807 (mp0) REVERT: C 2066 GLN cc_start: 0.8240 (tt0) cc_final: 0.7965 (tt0) REVERT: C 2199 ARG cc_start: 0.7971 (ttt90) cc_final: 0.7463 (ttm-80) REVERT: C 2553 VAL cc_start: 0.8339 (m) cc_final: 0.7963 (p) REVERT: D 108 ASN cc_start: 0.8023 (m-40) cc_final: 0.7729 (m-40) REVERT: D 111 VAL cc_start: 0.8393 (t) cc_final: 0.8171 (p) REVERT: D 424 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7702 (mm-30) REVERT: D 451 MET cc_start: 0.8312 (mtt) cc_final: 0.8021 (mtt) REVERT: D 494 LEU cc_start: 0.9129 (tp) cc_final: 0.8910 (mm) REVERT: D 536 VAL cc_start: 0.8976 (t) cc_final: 0.8565 (p) REVERT: D 566 ASP cc_start: 0.8136 (t70) cc_final: 0.7781 (t0) REVERT: D 614 GLU cc_start: 0.8085 (mp0) cc_final: 0.7426 (mp0) REVERT: D 616 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 690 GLU cc_start: 0.7891 (mp0) cc_final: 0.7562 (mp0) REVERT: D 740 CYS cc_start: 0.8149 (m) cc_final: 0.7915 (m) REVERT: D 1094 GLN cc_start: 0.8732 (mt0) cc_final: 0.8353 (mt0) REVERT: D 1223 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 1395 ASP cc_start: 0.7667 (m-30) cc_final: 0.7383 (t0) REVERT: D 1402 HIS cc_start: 0.8121 (t-90) cc_final: 0.7761 (t-90) REVERT: D 1411 MET cc_start: 0.8467 (ttt) cc_final: 0.8179 (ttp) REVERT: D 1531 MET cc_start: 0.8380 (ttm) cc_final: 0.7996 (mtm) REVERT: D 1597 ASP cc_start: 0.8315 (t0) cc_final: 0.8050 (t0) REVERT: D 1619 ASP cc_start: 0.8209 (m-30) cc_final: 0.7846 (m-30) REVERT: D 1636 GLN cc_start: 0.7834 (tp40) cc_final: 0.7633 (tp40) REVERT: D 1689 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7969 (mtm) REVERT: D 1737 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7671 (m) REVERT: D 1784 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7707 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8281 (m) cc_final: 0.7803 (m) REVERT: D 1994 ASP cc_start: 0.7814 (t70) cc_final: 0.7555 (t0) REVERT: D 2066 GLN cc_start: 0.8121 (tt0) cc_final: 0.7836 (tt0) REVERT: D 2133 MET cc_start: 0.8522 (mtm) cc_final: 0.8199 (mtm) REVERT: D 2316 MET cc_start: 0.7733 (tmm) cc_final: 0.7500 (tpp) REVERT: D 2528 GLN cc_start: 0.8076 (tp40) cc_final: 0.7778 (tt0) outliers start: 79 outliers final: 41 residues processed: 1819 average time/residue: 1.6983 time to fit residues: 5218.8719 Evaluate side-chains 1738 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1687 time to evaluate : 8.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 1326 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1913 ILE Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2292 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 988 SER Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1446 LEU Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1913 ILE Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 1293 HIS Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1674 LEU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 458 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 686 optimal weight: 0.8980 chunk 561 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 826 optimal weight: 1.9990 chunk 892 optimal weight: 0.9980 chunk 735 optimal weight: 4.9990 chunk 819 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 662 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 402 ASN A 661 ASN A 754 GLN A 783 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1897 ASN A2528 GLN B 289 HIS B 399 GLN B 512 GLN B 661 ASN B 754 GLN ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1650 HIS B2066 GLN B2528 GLN C 754 GLN C 783 HIS C1106 ASN C1193 GLN C1897 ASN D 375 GLN D 642 HIS D1065 HIS D1106 ASN D1193 GLN D1327 ASN D1650 HIS D1797 GLN D1897 ASN D2180 ASN D2292 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 75436 Z= 0.192 Angle : 0.414 7.294 101884 Z= 0.220 Chirality : 0.034 0.152 11612 Planarity : 0.003 0.054 12864 Dihedral : 8.673 103.001 10756 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.93 % Allowed : 8.50 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 3.12 (0.09), residues: 8968 helix: 3.18 (0.07), residues: 5824 sheet: -0.14 (0.20), residues: 676 loop : -0.12 (0.13), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2184 HIS 0.005 0.001 HIS A1518 PHE 0.020 0.001 PHE B2307 TYR 0.013 0.001 TYR A2496 ARG 0.007 0.000 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1787 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1712 time to evaluate : 8.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7984 (tp30) cc_final: 0.7729 (tp30) REVERT: A 111 VAL cc_start: 0.8210 (t) cc_final: 0.7979 (p) REVERT: A 203 ASP cc_start: 0.8045 (t0) cc_final: 0.7833 (t0) REVERT: A 204 ASN cc_start: 0.8261 (m110) cc_final: 0.7783 (m110) REVERT: A 232 GLU cc_start: 0.7949 (pt0) cc_final: 0.7719 (pt0) REVERT: A 614 GLU cc_start: 0.8040 (mp0) cc_final: 0.7455 (mp0) REVERT: A 616 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 690 GLU cc_start: 0.7758 (mp0) cc_final: 0.7457 (mt-10) REVERT: A 740 CYS cc_start: 0.8089 (m) cc_final: 0.7801 (m) REVERT: A 835 GLU cc_start: 0.7973 (tt0) cc_final: 0.7742 (tt0) REVERT: A 1094 GLN cc_start: 0.8623 (mt0) cc_final: 0.8383 (mt0) REVERT: A 1108 LYS cc_start: 0.8059 (mttm) cc_final: 0.7815 (mtmt) REVERT: A 1115 ASP cc_start: 0.7593 (m-30) cc_final: 0.7275 (m-30) REVERT: A 1280 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7064 (tm-30) REVERT: A 1347 ASP cc_start: 0.8176 (m-30) cc_final: 0.7923 (m-30) REVERT: A 1363 MET cc_start: 0.8147 (mmt) cc_final: 0.7851 (mmm) REVERT: A 1411 MET cc_start: 0.8370 (ttt) cc_final: 0.8056 (ttp) REVERT: A 1605 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8333 (ttt-90) REVERT: A 1619 ASP cc_start: 0.8110 (m-30) cc_final: 0.7698 (m-30) REVERT: A 1689 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7917 (mtm) REVERT: A 1905 CYS cc_start: 0.8260 (m) cc_final: 0.7718 (m) REVERT: A 2123 GLN cc_start: 0.8359 (pt0) cc_final: 0.8002 (pt0) REVERT: A 2149 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 2316 MET cc_start: 0.7834 (tmm) cc_final: 0.7549 (tpp) REVERT: A 2553 VAL cc_start: 0.8523 (m) cc_final: 0.8089 (p) REVERT: B 470 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.7882 (ttp80) REVERT: B 527 ARG cc_start: 0.7617 (ttm170) cc_final: 0.7295 (ttp-170) REVERT: B 614 GLU cc_start: 0.8065 (mp0) cc_final: 0.7488 (mp0) REVERT: B 624 LYS cc_start: 0.8218 (tttm) cc_final: 0.7982 (ttpt) REVERT: B 653 CYS cc_start: 0.7615 (m) cc_final: 0.7395 (m) REVERT: B 669 GLU cc_start: 0.7655 (pt0) cc_final: 0.7448 (pt0) REVERT: B 690 GLU cc_start: 0.7724 (mp0) cc_final: 0.7330 (mt-10) REVERT: B 740 CYS cc_start: 0.8154 (m) cc_final: 0.7861 (m) REVERT: B 984 ASP cc_start: 0.8199 (t70) cc_final: 0.7936 (t0) REVERT: B 1347 ASP cc_start: 0.8046 (m-30) cc_final: 0.7674 (m-30) REVERT: B 1363 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7692 (mmm) REVERT: B 1517 GLN cc_start: 0.8673 (mp10) cc_final: 0.8441 (mp10) REVERT: B 1674 LEU cc_start: 0.8328 (tp) cc_final: 0.8018 (mp) REVERT: B 1689 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: B 1770 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8062 (tttp) REVERT: B 1795 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7754 (ttt90) REVERT: B 1905 CYS cc_start: 0.8270 (m) cc_final: 0.7720 (m) REVERT: B 1954 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 2123 GLN cc_start: 0.8360 (pt0) cc_final: 0.8032 (pt0) REVERT: B 2316 MET cc_start: 0.7669 (tmm) cc_final: 0.7433 (tpp) REVERT: B 2553 VAL cc_start: 0.8358 (m) cc_final: 0.8030 (p) REVERT: C 100 GLU cc_start: 0.7384 (tt0) cc_final: 0.6908 (tt0) REVERT: C 286 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 494 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9025 (mp) REVERT: C 504 GLU cc_start: 0.7804 (mp0) cc_final: 0.7461 (mp0) REVERT: C 616 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7752 (mm-30) REVERT: C 650 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 1066 ASP cc_start: 0.7633 (p0) cc_final: 0.7000 (t0) REVERT: C 1094 GLN cc_start: 0.8595 (mt0) cc_final: 0.8151 (mt0) REVERT: C 1116 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7918 (mtp85) REVERT: C 1206 MET cc_start: 0.8435 (mmt) cc_final: 0.8101 (mmt) REVERT: C 1280 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 1301 ASP cc_start: 0.7751 (m-30) cc_final: 0.7506 (m-30) REVERT: C 1510 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7219 (mm-30) REVERT: C 1689 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: C 1891 PHE cc_start: 0.8291 (t80) cc_final: 0.7950 (t80) REVERT: C 1905 CYS cc_start: 0.8255 (m) cc_final: 0.7661 (m) REVERT: C 2014 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 2066 GLN cc_start: 0.8248 (tt0) cc_final: 0.7951 (tt0) REVERT: C 2123 GLN cc_start: 0.8411 (pt0) cc_final: 0.8012 (pt0) REVERT: C 2553 VAL cc_start: 0.8349 (m) cc_final: 0.8017 (p) REVERT: D 107 GLU cc_start: 0.8060 (tp30) cc_final: 0.7705 (tp30) REVERT: D 111 VAL cc_start: 0.8354 (t) cc_final: 0.8091 (p) REVERT: D 233 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 424 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 614 GLU cc_start: 0.8082 (mp0) cc_final: 0.7442 (mp0) REVERT: D 616 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 740 CYS cc_start: 0.8064 (m) cc_final: 0.7836 (m) REVERT: D 1094 GLN cc_start: 0.8687 (mt0) cc_final: 0.8310 (mt0) REVERT: D 1201 ASP cc_start: 0.7934 (m-30) cc_final: 0.7606 (t0) REVERT: D 1221 MET cc_start: 0.8097 (tpt) cc_final: 0.7849 (tpt) REVERT: D 1223 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 1277 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7171 (mt-10) REVERT: D 1395 ASP cc_start: 0.7532 (m-30) cc_final: 0.7219 (t0) REVERT: D 1402 HIS cc_start: 0.8111 (t-90) cc_final: 0.7726 (t-90) REVERT: D 1411 MET cc_start: 0.8396 (ttt) cc_final: 0.8071 (ttp) REVERT: D 1443 ASN cc_start: 0.7856 (t0) cc_final: 0.7505 (t0) REVERT: D 1531 MET cc_start: 0.8401 (ttm) cc_final: 0.8013 (mtm) REVERT: D 1597 ASP cc_start: 0.8343 (t0) cc_final: 0.8089 (t0) REVERT: D 1603 GLU cc_start: 0.8136 (tt0) cc_final: 0.7822 (tt0) REVERT: D 1689 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: D 1737 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (m) REVERT: D 1784 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7732 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8273 (m) cc_final: 0.7811 (m) REVERT: D 1994 ASP cc_start: 0.7792 (t70) cc_final: 0.7535 (t0) REVERT: D 2066 GLN cc_start: 0.8134 (tt0) cc_final: 0.7854 (tt0) REVERT: D 2316 MET cc_start: 0.7793 (tmm) cc_final: 0.7550 (tpp) REVERT: D 2528 GLN cc_start: 0.8041 (tp40) cc_final: 0.7764 (tt0) outliers start: 75 outliers final: 50 residues processed: 1734 average time/residue: 1.6198 time to fit residues: 4743.7735 Evaluate side-chains 1724 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1667 time to evaluate : 8.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2292 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 1106 ASN Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1446 LEU Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1913 ILE Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2018 ILE Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 1106 ASN Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1621 LEU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1913 ILE Chi-restraints excluded: chain D residue 2535 LYS Chi-restraints excluded: chain D residue 2577 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 816 optimal weight: 9.9990 chunk 621 optimal weight: 2.9990 chunk 428 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 394 optimal weight: 1.9990 chunk 554 optimal weight: 4.9990 chunk 829 optimal weight: 3.9990 chunk 877 optimal weight: 2.9990 chunk 433 optimal weight: 2.9990 chunk 785 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN A 754 GLN A 783 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1897 ASN ** A2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS B 399 GLN B 602 ASN B 661 ASN B 703 HIS B 754 GLN B 783 HIS B 791 GLN ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1298 GLN B1318 GLN B1650 HIS B2066 GLN B2528 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 783 HIS C 791 GLN C2528 GLN D 289 HIS D 375 GLN D 399 GLN D 642 HIS D 754 GLN D 783 HIS D1327 ASN D1650 HIS D1897 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 75436 Z= 0.515 Angle : 0.518 5.484 101884 Z= 0.281 Chirality : 0.039 0.151 11612 Planarity : 0.004 0.053 12864 Dihedral : 8.934 88.752 10756 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.48 % Allowed : 9.19 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.56 (0.09), residues: 8968 helix: 2.76 (0.07), residues: 5812 sheet: -0.30 (0.20), residues: 672 loop : -0.37 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A2601 HIS 0.009 0.001 HIS A 195 PHE 0.020 0.002 PHE B2307 TYR 0.021 0.002 TYR C2326 ARG 0.007 0.001 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1880 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1760 time to evaluate : 9.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8284 (m-30) cc_final: 0.7996 (m-30) REVERT: A 233 GLU cc_start: 0.8214 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 566 ASP cc_start: 0.8195 (t0) cc_final: 0.7658 (t0) REVERT: A 590 LEU cc_start: 0.8418 (mt) cc_final: 0.8154 (mp) REVERT: A 614 GLU cc_start: 0.7943 (mp0) cc_final: 0.7417 (mp0) REVERT: A 616 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 690 GLU cc_start: 0.7794 (mp0) cc_final: 0.7426 (mt-10) REVERT: A 740 CYS cc_start: 0.8106 (m) cc_final: 0.7821 (m) REVERT: A 835 GLU cc_start: 0.8021 (tt0) cc_final: 0.7797 (tt0) REVERT: A 1094 GLN cc_start: 0.8782 (mt0) cc_final: 0.8576 (mt0) REVERT: A 1108 LYS cc_start: 0.8133 (mttm) cc_final: 0.7863 (mtmt) REVERT: A 1347 ASP cc_start: 0.8181 (m-30) cc_final: 0.7969 (m-30) REVERT: A 1402 HIS cc_start: 0.8063 (t-90) cc_final: 0.7651 (t-90) REVERT: A 1411 MET cc_start: 0.8452 (ttt) cc_final: 0.8113 (ttp) REVERT: A 1605 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8395 (ttt-90) REVERT: A 1613 GLU cc_start: 0.8314 (tt0) cc_final: 0.8047 (tt0) REVERT: A 1795 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7707 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8342 (m) cc_final: 0.7815 (m) REVERT: A 2200 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8007 (mtt90) REVERT: A 2316 MET cc_start: 0.7860 (tmm) cc_final: 0.7634 (tpp) REVERT: A 2532 GLU cc_start: 0.7781 (tt0) cc_final: 0.7369 (tp30) REVERT: A 2553 VAL cc_start: 0.8571 (m) cc_final: 0.8147 (p) REVERT: B 100 GLU cc_start: 0.7318 (tt0) cc_final: 0.7077 (tt0) REVERT: B 470 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8000 (mtp-110) REVERT: B 614 GLU cc_start: 0.8046 (mp0) cc_final: 0.7472 (mp0) REVERT: B 624 LYS cc_start: 0.8264 (tttm) cc_final: 0.8056 (ttmt) REVERT: B 690 GLU cc_start: 0.7764 (mp0) cc_final: 0.7391 (mp0) REVERT: B 740 CYS cc_start: 0.8195 (m) cc_final: 0.7890 (m) REVERT: B 990 LEU cc_start: 0.7938 (mt) cc_final: 0.7723 (mt) REVERT: B 1118 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8026 (ttm-80) REVERT: B 1322 MET cc_start: 0.8424 (tpt) cc_final: 0.7969 (tpt) REVERT: B 1347 ASP cc_start: 0.8106 (m-30) cc_final: 0.7776 (m-30) REVERT: B 1363 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: B 1404 ASP cc_start: 0.7400 (m-30) cc_final: 0.6937 (m-30) REVERT: B 1619 ASP cc_start: 0.8159 (m-30) cc_final: 0.7761 (m-30) REVERT: B 1689 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8003 (mtm) REVERT: B 1795 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7779 (ttt90) REVERT: B 1905 CYS cc_start: 0.8386 (m) cc_final: 0.8140 (m) REVERT: B 1954 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8005 (mm-30) REVERT: B 2183 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 2200 ARG cc_start: 0.8443 (mtt90) cc_final: 0.7791 (mtt90) REVERT: B 2292 ASN cc_start: 0.8233 (t0) cc_final: 0.7867 (t0) REVERT: B 2316 MET cc_start: 0.7883 (tmm) cc_final: 0.7661 (tpp) REVERT: B 2532 GLU cc_start: 0.7513 (tt0) cc_final: 0.7203 (tt0) REVERT: B 2553 VAL cc_start: 0.8505 (m) cc_final: 0.8168 (p) REVERT: C 54 ASP cc_start: 0.8305 (m-30) cc_final: 0.8099 (m-30) REVERT: C 487 PRO cc_start: 0.7929 (Cg_exo) cc_final: 0.7691 (Cg_endo) REVERT: C 494 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9068 (mp) REVERT: C 504 GLU cc_start: 0.7870 (mp0) cc_final: 0.7601 (mp0) REVERT: C 616 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7572 (tp30) REVERT: C 739 MET cc_start: 0.8116 (mtm) cc_final: 0.7906 (mtm) REVERT: C 1066 ASP cc_start: 0.7837 (p0) cc_final: 0.7345 (t0) REVERT: C 1094 GLN cc_start: 0.8754 (mt0) cc_final: 0.8365 (mt0) REVERT: C 1111 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7492 (ttpt) REVERT: C 1116 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7921 (mtp85) REVERT: C 1118 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7735 (ttm-80) REVERT: C 1206 MET cc_start: 0.8482 (mmt) cc_final: 0.8194 (mmt) REVERT: C 1280 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 1301 ASP cc_start: 0.7943 (m-30) cc_final: 0.7633 (m-30) REVERT: C 1689 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: C 1905 CYS cc_start: 0.8360 (m) cc_final: 0.7721 (m) REVERT: C 2066 GLN cc_start: 0.8296 (tt0) cc_final: 0.8025 (tt0) REVERT: C 2123 GLN cc_start: 0.8442 (pt0) cc_final: 0.7915 (pt0) REVERT: C 2199 ARG cc_start: 0.8070 (ttt90) cc_final: 0.7484 (ttm-80) REVERT: C 2292 ASN cc_start: 0.8289 (t0) cc_final: 0.8066 (t0) REVERT: C 2553 VAL cc_start: 0.8448 (m) cc_final: 0.8060 (p) REVERT: D 204 ASN cc_start: 0.8228 (m110) cc_final: 0.8003 (m110) REVERT: D 451 MET cc_start: 0.8286 (mtt) cc_final: 0.8027 (mtt) REVERT: D 539 GLU cc_start: 0.8690 (mp0) cc_final: 0.8425 (mp0) REVERT: D 566 ASP cc_start: 0.8199 (t0) cc_final: 0.7661 (t0) REVERT: D 590 LEU cc_start: 0.8435 (mt) cc_final: 0.8227 (mp) REVERT: D 614 GLU cc_start: 0.8017 (mp0) cc_final: 0.7431 (mp0) REVERT: D 616 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7711 (mm-30) REVERT: D 690 GLU cc_start: 0.7908 (mp0) cc_final: 0.7534 (mp0) REVERT: D 740 CYS cc_start: 0.8150 (m) cc_final: 0.7893 (m) REVERT: D 885 THR cc_start: 0.8022 (m) cc_final: 0.7798 (m) REVERT: D 1094 GLN cc_start: 0.8870 (mt0) cc_final: 0.8523 (mt0) REVERT: D 1201 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7722 (t70) REVERT: D 1206 MET cc_start: 0.8449 (mmt) cc_final: 0.7961 (mmt) REVERT: D 1223 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7990 (mm-30) REVERT: D 1277 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 1284 GLN cc_start: 0.8220 (tp40) cc_final: 0.7921 (mm-40) REVERT: D 1367 SER cc_start: 0.8475 (m) cc_final: 0.8216 (p) REVERT: D 1402 HIS cc_start: 0.8115 (t-90) cc_final: 0.7724 (t-90) REVERT: D 1404 ASP cc_start: 0.7524 (m-30) cc_final: 0.7315 (m-30) REVERT: D 1411 MET cc_start: 0.8495 (ttt) cc_final: 0.8206 (ttp) REVERT: D 1603 GLU cc_start: 0.8225 (tt0) cc_final: 0.7901 (tt0) REVERT: D 1619 ASP cc_start: 0.8253 (m-30) cc_final: 0.7894 (m-30) REVERT: D 1689 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7996 (mtm) REVERT: D 1737 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7722 (m) REVERT: D 1784 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7771 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8310 (m) cc_final: 0.7824 (m) REVERT: D 1994 ASP cc_start: 0.7875 (t70) cc_final: 0.7654 (t0) REVERT: D 2065 LYS cc_start: 0.8124 (tppt) cc_final: 0.7919 (mmmm) REVERT: D 2066 GLN cc_start: 0.8215 (tt0) cc_final: 0.7914 (tt0) REVERT: D 2200 ARG cc_start: 0.8459 (mtt90) cc_final: 0.8256 (mtt90) REVERT: D 2316 MET cc_start: 0.7910 (tmm) cc_final: 0.7706 (tpp) REVERT: D 2528 GLN cc_start: 0.8083 (tp40) cc_final: 0.7853 (tt0) REVERT: D 2535 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7860 (mtmm) outliers start: 120 outliers final: 83 residues processed: 1816 average time/residue: 1.6523 time to fit residues: 5062.8431 Evaluate side-chains 1793 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1700 time to evaluate : 8.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1496 THR Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1674 LEU Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ARG Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 1118 ARG Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1201 ASP Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1674 LEU Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2535 LYS Chi-restraints excluded: chain D residue 2577 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 730 optimal weight: 5.9990 chunk 498 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 653 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 748 optimal weight: 1.9990 chunk 606 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 448 optimal weight: 0.9990 chunk 787 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 783 HIS A1106 ASN A1193 GLN A1251 HIS A1650 HIS A2066 GLN A2528 GLN B 467 ASN B 661 ASN B 703 HIS B 783 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1650 HIS B2528 GLN ** B2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 HIS C 754 GLN C2528 GLN D 642 HIS D 783 HIS D1327 ASN D1650 HIS D1897 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 75436 Z= 0.239 Angle : 0.435 6.952 101884 Z= 0.233 Chirality : 0.035 0.182 11612 Planarity : 0.003 0.047 12864 Dihedral : 8.407 87.665 10754 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 10.12 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.75 (0.09), residues: 8968 helix: 2.95 (0.07), residues: 5816 sheet: -0.37 (0.20), residues: 648 loop : -0.35 (0.13), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2184 HIS 0.005 0.001 HIS A1251 PHE 0.022 0.001 PHE A2307 TYR 0.014 0.001 TYR C2496 ARG 0.006 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1825 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1722 time to evaluate : 8.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.8193 (t0) cc_final: 0.7625 (t0) REVERT: A 590 LEU cc_start: 0.8416 (mt) cc_final: 0.8166 (mp) REVERT: A 614 GLU cc_start: 0.7935 (mp0) cc_final: 0.7423 (mp0) REVERT: A 616 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 690 GLU cc_start: 0.7797 (mp0) cc_final: 0.7430 (mt-10) REVERT: A 740 CYS cc_start: 0.8128 (m) cc_final: 0.7870 (m) REVERT: A 835 GLU cc_start: 0.7974 (tt0) cc_final: 0.7762 (tt0) REVERT: A 1094 GLN cc_start: 0.8675 (mt0) cc_final: 0.8459 (mt0) REVERT: A 1108 LYS cc_start: 0.8102 (mttm) cc_final: 0.7837 (mtmt) REVERT: A 1347 ASP cc_start: 0.8136 (m-30) cc_final: 0.7916 (m-30) REVERT: A 1411 MET cc_start: 0.8406 (ttt) cc_final: 0.8065 (ttp) REVERT: A 1596 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7953 (mm-40) REVERT: A 1613 GLU cc_start: 0.8287 (tt0) cc_final: 0.8024 (tt0) REVERT: A 1689 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: A 1795 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7699 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8295 (m) cc_final: 0.7764 (m) REVERT: A 2200 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7929 (mtt90) REVERT: A 2316 MET cc_start: 0.7888 (tmm) cc_final: 0.7649 (tpp) REVERT: A 2532 GLU cc_start: 0.7795 (tt0) cc_final: 0.7389 (tp30) REVERT: A 2553 VAL cc_start: 0.8532 (m) cc_final: 0.8134 (p) REVERT: B 100 GLU cc_start: 0.7287 (tt0) cc_final: 0.7020 (tt0) REVERT: B 256 GLU cc_start: 0.7889 (tt0) cc_final: 0.7687 (tt0) REVERT: B 470 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.7965 (ttp80) REVERT: B 614 GLU cc_start: 0.8004 (mp0) cc_final: 0.7439 (mp0) REVERT: B 624 LYS cc_start: 0.8244 (tttm) cc_final: 0.8037 (ttmt) REVERT: B 690 GLU cc_start: 0.7787 (mp0) cc_final: 0.7408 (mp0) REVERT: B 740 CYS cc_start: 0.8166 (m) cc_final: 0.7884 (m) REVERT: B 1248 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8302 (ttmt) REVERT: B 1322 MET cc_start: 0.8449 (tpt) cc_final: 0.7875 (tpt) REVERT: B 1347 ASP cc_start: 0.8060 (m-30) cc_final: 0.7724 (m-30) REVERT: B 1363 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: B 1404 ASP cc_start: 0.7402 (m-30) cc_final: 0.6894 (m-30) REVERT: B 1619 ASP cc_start: 0.8160 (m-30) cc_final: 0.7730 (m-30) REVERT: B 1689 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: B 1795 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7768 (ttt90) REVERT: B 1905 CYS cc_start: 0.8329 (m) cc_final: 0.8076 (m) REVERT: B 1954 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 2183 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 2292 ASN cc_start: 0.8236 (t0) cc_final: 0.7888 (t0) REVERT: B 2316 MET cc_start: 0.7888 (tmm) cc_final: 0.7657 (tpp) REVERT: B 2553 VAL cc_start: 0.8475 (m) cc_final: 0.8152 (p) REVERT: C 100 GLU cc_start: 0.7360 (tt0) cc_final: 0.7095 (tt0) REVERT: C 487 PRO cc_start: 0.7909 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: C 494 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9048 (mp) REVERT: C 504 GLU cc_start: 0.7846 (mp0) cc_final: 0.7573 (mp0) REVERT: C 616 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 740 CYS cc_start: 0.8173 (m) cc_final: 0.7911 (m) REVERT: C 1066 ASP cc_start: 0.7790 (p0) cc_final: 0.7293 (t0) REVERT: C 1094 GLN cc_start: 0.8698 (mt0) cc_final: 0.8303 (mt0) REVERT: C 1106 ASN cc_start: 0.8441 (m-40) cc_final: 0.8170 (t0) REVERT: C 1116 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7955 (mtp85) REVERT: C 1206 MET cc_start: 0.8492 (mmt) cc_final: 0.8183 (mmt) REVERT: C 1689 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: C 1891 PHE cc_start: 0.8289 (t80) cc_final: 0.8030 (t80) REVERT: C 1905 CYS cc_start: 0.8313 (m) cc_final: 0.7683 (m) REVERT: C 2066 GLN cc_start: 0.8284 (tt0) cc_final: 0.7978 (tt0) REVERT: C 2123 GLN cc_start: 0.8427 (pt0) cc_final: 0.7914 (pt0) REVERT: C 2199 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7547 (ttm-80) REVERT: C 2553 VAL cc_start: 0.8434 (m) cc_final: 0.8067 (p) REVERT: D 539 GLU cc_start: 0.8685 (mp0) cc_final: 0.8433 (mp0) REVERT: D 566 ASP cc_start: 0.8192 (t0) cc_final: 0.7650 (t0) REVERT: D 590 LEU cc_start: 0.8433 (mt) cc_final: 0.8220 (mp) REVERT: D 616 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7728 (mm-30) REVERT: D 690 GLU cc_start: 0.7909 (mp0) cc_final: 0.7645 (mp0) REVERT: D 740 CYS cc_start: 0.8101 (m) cc_final: 0.7859 (m) REVERT: D 1094 GLN cc_start: 0.8818 (mt0) cc_final: 0.8455 (mt0) REVERT: D 1201 ASP cc_start: 0.7980 (m-30) cc_final: 0.7698 (t0) REVERT: D 1206 MET cc_start: 0.8458 (mmt) cc_final: 0.7939 (mmt) REVERT: D 1223 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7967 (mm-30) REVERT: D 1277 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7259 (mt-10) REVERT: D 1284 GLN cc_start: 0.8111 (tp40) cc_final: 0.7833 (mm-40) REVERT: D 1367 SER cc_start: 0.8462 (m) cc_final: 0.8194 (p) REVERT: D 1395 ASP cc_start: 0.7524 (m-30) cc_final: 0.7194 (t0) REVERT: D 1411 MET cc_start: 0.8460 (ttt) cc_final: 0.8161 (ttp) REVERT: D 1603 GLU cc_start: 0.8210 (tt0) cc_final: 0.7879 (tt0) REVERT: D 1689 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: D 1737 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7660 (m) REVERT: D 1784 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7755 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8293 (m) cc_final: 0.7827 (m) REVERT: D 1994 ASP cc_start: 0.7856 (t70) cc_final: 0.7622 (t0) REVERT: D 2065 LYS cc_start: 0.8142 (tppt) cc_final: 0.7934 (mmmm) REVERT: D 2066 GLN cc_start: 0.8200 (tt0) cc_final: 0.7932 (tt0) REVERT: D 2123 GLN cc_start: 0.8404 (pt0) cc_final: 0.7895 (pt0) REVERT: D 2316 MET cc_start: 0.7919 (tmm) cc_final: 0.7711 (tpp) REVERT: D 2531 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 2535 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7764 (mtmm) outliers start: 103 outliers final: 77 residues processed: 1771 average time/residue: 1.6795 time to fit residues: 5042.2513 Evaluate side-chains 1782 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1697 time to evaluate : 8.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1182 MET Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1692 GLN Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2018 ILE Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1446 LEU Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2535 LYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 295 optimal weight: 0.7980 chunk 790 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 515 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 878 optimal weight: 6.9990 chunk 729 optimal weight: 1.9990 chunk 406 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 461 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN A 754 GLN A 783 HIS A1168 ASN A1251 HIS A1337 ASN A1402 HIS A1650 HIS A2066 GLN A2528 GLN B 467 ASN B 754 GLN B 783 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1650 HIS B2528 GLN C1168 ASN C2528 GLN D 642 HIS D 783 HIS D1327 ASN D1650 HIS D2528 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 75436 Z= 0.293 Angle : 0.442 5.746 101884 Z= 0.237 Chirality : 0.035 0.169 11612 Planarity : 0.003 0.056 12864 Dihedral : 8.225 88.068 10751 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.31 % Allowed : 10.55 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.74 (0.09), residues: 8968 helix: 2.95 (0.07), residues: 5808 sheet: -0.37 (0.20), residues: 644 loop : -0.39 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2184 HIS 0.005 0.001 HIS A 868 PHE 0.024 0.001 PHE A2307 TYR 0.016 0.001 TYR A1107 ARG 0.007 0.000 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1827 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1721 time to evaluate : 8.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7999 (tp30) cc_final: 0.7725 (tp30) REVERT: A 614 GLU cc_start: 0.7911 (mp0) cc_final: 0.7383 (mp0) REVERT: A 616 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 690 GLU cc_start: 0.7813 (mp0) cc_final: 0.7426 (mt-10) REVERT: A 740 CYS cc_start: 0.8148 (m) cc_final: 0.7883 (m) REVERT: A 835 GLU cc_start: 0.7981 (tt0) cc_final: 0.7767 (tt0) REVERT: A 1094 GLN cc_start: 0.8698 (mt0) cc_final: 0.8479 (mt0) REVERT: A 1347 ASP cc_start: 0.8133 (m-30) cc_final: 0.7921 (m-30) REVERT: A 1411 MET cc_start: 0.8412 (ttt) cc_final: 0.8074 (ttp) REVERT: A 1596 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7959 (mm-40) REVERT: A 1613 GLU cc_start: 0.8287 (tt0) cc_final: 0.8035 (tt0) REVERT: A 1689 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: A 1795 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7699 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8310 (m) cc_final: 0.7767 (m) REVERT: A 2200 ARG cc_start: 0.8495 (mtt90) cc_final: 0.7962 (mtt90) REVERT: A 2316 MET cc_start: 0.7924 (tmm) cc_final: 0.7623 (tpp) REVERT: A 2532 GLU cc_start: 0.7799 (tt0) cc_final: 0.7404 (tp30) REVERT: A 2553 VAL cc_start: 0.8515 (m) cc_final: 0.8136 (p) REVERT: A 2581 THR cc_start: 0.8749 (m) cc_final: 0.8447 (p) REVERT: B 100 GLU cc_start: 0.7313 (tt0) cc_final: 0.7060 (tt0) REVERT: B 470 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.7941 (mtp-110) REVERT: B 614 GLU cc_start: 0.7988 (mp0) cc_final: 0.7415 (mp0) REVERT: B 624 LYS cc_start: 0.8254 (tttm) cc_final: 0.7992 (ttmt) REVERT: B 690 GLU cc_start: 0.7790 (mp0) cc_final: 0.7413 (mp0) REVERT: B 740 CYS cc_start: 0.8156 (m) cc_final: 0.7883 (m) REVERT: B 1053 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7333 (ttm110) REVERT: B 1248 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8299 (ttmt) REVERT: B 1322 MET cc_start: 0.8474 (tpt) cc_final: 0.7915 (tpt) REVERT: B 1347 ASP cc_start: 0.8090 (m-30) cc_final: 0.7772 (m-30) REVERT: B 1350 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8586 (ttmm) REVERT: B 1363 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7855 (mmm) REVERT: B 1404 ASP cc_start: 0.7458 (m-30) cc_final: 0.6948 (m-30) REVERT: B 1619 ASP cc_start: 0.8158 (m-30) cc_final: 0.7740 (m-30) REVERT: B 1689 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: B 1795 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7781 (ttt90) REVERT: B 1905 CYS cc_start: 0.8334 (m) cc_final: 0.8067 (m) REVERT: B 1954 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7982 (mm-30) REVERT: B 2200 ARG cc_start: 0.8475 (mtt90) cc_final: 0.7755 (mtt90) REVERT: B 2292 ASN cc_start: 0.8242 (t0) cc_final: 0.7886 (t0) REVERT: B 2316 MET cc_start: 0.7895 (tmm) cc_final: 0.7678 (tpp) REVERT: B 2553 VAL cc_start: 0.8489 (m) cc_final: 0.8161 (p) REVERT: C 100 GLU cc_start: 0.7385 (tt0) cc_final: 0.7136 (tt0) REVERT: C 487 PRO cc_start: 0.7906 (Cg_exo) cc_final: 0.7660 (Cg_endo) REVERT: C 504 GLU cc_start: 0.7858 (mp0) cc_final: 0.7645 (mp0) REVERT: C 616 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7808 (mm-30) REVERT: C 740 CYS cc_start: 0.8183 (m) cc_final: 0.7913 (m) REVERT: C 1066 ASP cc_start: 0.7793 (p0) cc_final: 0.7326 (t0) REVERT: C 1094 GLN cc_start: 0.8706 (mt0) cc_final: 0.8336 (mt0) REVERT: C 1116 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7954 (mtp85) REVERT: C 1206 MET cc_start: 0.8490 (mmt) cc_final: 0.8181 (mmt) REVERT: C 1402 HIS cc_start: 0.8193 (t-90) cc_final: 0.7909 (t-90) REVERT: C 1689 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7997 (mtm) REVERT: C 1891 PHE cc_start: 0.8270 (t80) cc_final: 0.8038 (t80) REVERT: C 1905 CYS cc_start: 0.8315 (m) cc_final: 0.7667 (m) REVERT: C 2066 GLN cc_start: 0.8277 (tt0) cc_final: 0.7982 (tt0) REVERT: C 2123 GLN cc_start: 0.8427 (pt0) cc_final: 0.7918 (pt0) REVERT: C 2553 VAL cc_start: 0.8459 (m) cc_final: 0.8088 (p) REVERT: D 539 GLU cc_start: 0.8686 (mp0) cc_final: 0.8437 (mp0) REVERT: D 566 ASP cc_start: 0.8211 (t0) cc_final: 0.7671 (t0) REVERT: D 590 LEU cc_start: 0.8449 (mt) cc_final: 0.8228 (mp) REVERT: D 614 GLU cc_start: 0.8017 (mp0) cc_final: 0.7396 (mp0) REVERT: D 616 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7684 (mm-30) REVERT: D 690 GLU cc_start: 0.7910 (mp0) cc_final: 0.7643 (mp0) REVERT: D 740 CYS cc_start: 0.8125 (m) cc_final: 0.7888 (m) REVERT: D 1094 GLN cc_start: 0.8801 (mt0) cc_final: 0.8435 (mt0) REVERT: D 1201 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7713 (t0) REVERT: D 1206 MET cc_start: 0.8460 (mmt) cc_final: 0.7932 (mmt) REVERT: D 1223 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7949 (mm-30) REVERT: D 1277 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7291 (mt-10) REVERT: D 1367 SER cc_start: 0.8463 (m) cc_final: 0.8206 (p) REVERT: D 1395 ASP cc_start: 0.7530 (m-30) cc_final: 0.7182 (t0) REVERT: D 1411 MET cc_start: 0.8470 (ttt) cc_final: 0.8176 (ttp) REVERT: D 1603 GLU cc_start: 0.8230 (tt0) cc_final: 0.7904 (tt0) REVERT: D 1689 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: D 1737 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7675 (m) REVERT: D 1784 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7765 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8308 (m) cc_final: 0.7796 (m) REVERT: D 1994 ASP cc_start: 0.7862 (t70) cc_final: 0.7637 (t0) REVERT: D 2065 LYS cc_start: 0.8160 (tppt) cc_final: 0.7945 (mmmm) REVERT: D 2066 GLN cc_start: 0.8219 (tt0) cc_final: 0.7926 (tt0) REVERT: D 2123 GLN cc_start: 0.8402 (pt0) cc_final: 0.7917 (pt0) outliers start: 106 outliers final: 92 residues processed: 1776 average time/residue: 1.7100 time to fit residues: 5198.9285 Evaluate side-chains 1807 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1708 time to evaluate : 8.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1482 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1446 LEU Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1201 ASP Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 847 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 500 optimal weight: 1.9990 chunk 641 optimal weight: 2.9990 chunk 497 optimal weight: 2.9990 chunk 739 optimal weight: 3.9990 chunk 490 optimal weight: 3.9990 chunk 875 optimal weight: 0.2980 chunk 547 optimal weight: 2.9990 chunk 533 optimal weight: 2.9990 chunk 404 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN A1251 HIS A1650 HIS A2066 GLN A2528 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1650 HIS B2528 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2528 GLN D 642 HIS D1327 ASN D1650 HIS D2528 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 75436 Z= 0.432 Angle : 0.490 5.324 101884 Z= 0.264 Chirality : 0.037 0.163 11612 Planarity : 0.003 0.060 12864 Dihedral : 8.254 88.315 10751 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.63 % Allowed : 10.65 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.51 (0.09), residues: 8968 helix: 2.78 (0.07), residues: 5812 sheet: -0.45 (0.20), residues: 644 loop : -0.50 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2601 HIS 0.006 0.001 HIS B 195 PHE 0.025 0.002 PHE B2307 TYR 0.019 0.001 TYR D2326 ARG 0.006 0.000 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1875 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1743 time to evaluate : 8.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8013 (tp30) cc_final: 0.7751 (tp30) REVERT: A 566 ASP cc_start: 0.8255 (t0) cc_final: 0.7784 (t0) REVERT: A 614 GLU cc_start: 0.7896 (mp0) cc_final: 0.7357 (mp0) REVERT: A 616 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 690 GLU cc_start: 0.7820 (mp0) cc_final: 0.7395 (mt-10) REVERT: A 740 CYS cc_start: 0.8152 (m) cc_final: 0.7881 (m) REVERT: A 835 GLU cc_start: 0.7994 (tt0) cc_final: 0.7782 (tt0) REVERT: A 990 LEU cc_start: 0.7941 (mp) cc_final: 0.7726 (mt) REVERT: A 1108 LYS cc_start: 0.8098 (mttm) cc_final: 0.7819 (mtmt) REVERT: A 1177 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 1347 ASP cc_start: 0.8136 (m-30) cc_final: 0.7932 (m-30) REVERT: A 1370 ASP cc_start: 0.8184 (m-30) cc_final: 0.7890 (m-30) REVERT: A 1404 ASP cc_start: 0.7441 (m-30) cc_final: 0.7056 (m-30) REVERT: A 1411 MET cc_start: 0.8447 (ttt) cc_final: 0.8122 (ttp) REVERT: A 1486 GLU cc_start: 0.8335 (pt0) cc_final: 0.8129 (pt0) REVERT: A 1596 GLN cc_start: 0.8237 (mm-40) cc_final: 0.8001 (mm-40) REVERT: A 1613 GLU cc_start: 0.8312 (tt0) cc_final: 0.8057 (tt0) REVERT: A 1689 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: A 1795 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7738 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8307 (m) cc_final: 0.7757 (m) REVERT: A 2183 GLU cc_start: 0.8045 (tp30) cc_final: 0.7727 (mm-30) REVERT: A 2316 MET cc_start: 0.7928 (tmm) cc_final: 0.7647 (tpp) REVERT: A 2532 GLU cc_start: 0.7810 (tt0) cc_final: 0.7373 (tp30) REVERT: A 2553 VAL cc_start: 0.8534 (m) cc_final: 0.8141 (p) REVERT: A 2581 THR cc_start: 0.8745 (m) cc_final: 0.8448 (p) REVERT: B 100 GLU cc_start: 0.7307 (tt0) cc_final: 0.7045 (tt0) REVERT: B 470 ARG cc_start: 0.8434 (mtp-110) cc_final: 0.7998 (ttp80) REVERT: B 614 GLU cc_start: 0.7946 (mp0) cc_final: 0.7403 (mp0) REVERT: B 624 LYS cc_start: 0.8264 (tttm) cc_final: 0.8020 (ttpt) REVERT: B 690 GLU cc_start: 0.7790 (mp0) cc_final: 0.7394 (mp0) REVERT: B 740 CYS cc_start: 0.8153 (m) cc_final: 0.7872 (m) REVERT: B 1118 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8029 (ttm-80) REVERT: B 1248 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8308 (ttmt) REVERT: B 1322 MET cc_start: 0.8486 (tpt) cc_final: 0.7815 (tpt) REVERT: B 1347 ASP cc_start: 0.8093 (m-30) cc_final: 0.7812 (m-30) REVERT: B 1363 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: B 1404 ASP cc_start: 0.7530 (m-30) cc_final: 0.6987 (m-30) REVERT: B 1619 ASP cc_start: 0.8192 (m-30) cc_final: 0.7827 (m-30) REVERT: B 1625 GLU cc_start: 0.8228 (pm20) cc_final: 0.7612 (pm20) REVERT: B 1689 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: B 1795 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7800 (ttt90) REVERT: B 1905 CYS cc_start: 0.8377 (m) cc_final: 0.8117 (m) REVERT: B 1954 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 2183 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 2292 ASN cc_start: 0.8249 (t0) cc_final: 0.7868 (t0) REVERT: B 2532 GLU cc_start: 0.7495 (tt0) cc_final: 0.7159 (tt0) REVERT: B 2553 VAL cc_start: 0.8540 (m) cc_final: 0.8196 (p) REVERT: C 100 GLU cc_start: 0.7414 (tt0) cc_final: 0.7138 (tt0) REVERT: C 487 PRO cc_start: 0.7946 (Cg_exo) cc_final: 0.7714 (Cg_endo) REVERT: C 504 GLU cc_start: 0.7883 (mp0) cc_final: 0.7608 (mp0) REVERT: C 616 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 740 CYS cc_start: 0.8150 (m) cc_final: 0.7902 (m) REVERT: C 988 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (m) REVERT: C 1066 ASP cc_start: 0.7872 (p0) cc_final: 0.7522 (t0) REVERT: C 1094 GLN cc_start: 0.8760 (mt0) cc_final: 0.8414 (mt0) REVERT: C 1116 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7961 (mtp85) REVERT: C 1206 MET cc_start: 0.8510 (mmt) cc_final: 0.8203 (mmt) REVERT: C 1301 ASP cc_start: 0.7965 (m-30) cc_final: 0.7656 (m-30) REVERT: C 1402 HIS cc_start: 0.8194 (t-90) cc_final: 0.7903 (t-90) REVERT: C 1619 ASP cc_start: 0.8194 (m-30) cc_final: 0.7960 (m-30) REVERT: C 1689 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: C 1905 CYS cc_start: 0.8340 (m) cc_final: 0.7713 (m) REVERT: C 2066 GLN cc_start: 0.8298 (tt0) cc_final: 0.8003 (tt0) REVERT: C 2181 GLU cc_start: 0.7590 (tt0) cc_final: 0.7280 (tt0) REVERT: C 2553 VAL cc_start: 0.8500 (m) cc_final: 0.8107 (p) REVERT: D 54 ASP cc_start: 0.8359 (m-30) cc_final: 0.8095 (m-30) REVERT: D 566 ASP cc_start: 0.8266 (t0) cc_final: 0.7729 (t0) REVERT: D 590 LEU cc_start: 0.8461 (mt) cc_final: 0.8227 (mp) REVERT: D 614 GLU cc_start: 0.7993 (mp0) cc_final: 0.7378 (mp0) REVERT: D 616 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 690 GLU cc_start: 0.7931 (mp0) cc_final: 0.7645 (mp0) REVERT: D 740 CYS cc_start: 0.8148 (m) cc_final: 0.7894 (m) REVERT: D 1094 GLN cc_start: 0.8844 (mt0) cc_final: 0.8508 (mt0) REVERT: D 1108 LYS cc_start: 0.8122 (mttm) cc_final: 0.7840 (mtmt) REVERT: D 1201 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7745 (t0) REVERT: D 1206 MET cc_start: 0.8458 (mmt) cc_final: 0.7957 (mmt) REVERT: D 1223 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 1277 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 1284 GLN cc_start: 0.8290 (tp40) cc_final: 0.7455 (mp10) REVERT: D 1367 SER cc_start: 0.8459 (m) cc_final: 0.8231 (p) REVERT: D 1395 ASP cc_start: 0.7577 (m-30) cc_final: 0.7204 (t0) REVERT: D 1402 HIS cc_start: 0.8135 (t-90) cc_final: 0.7791 (t-90) REVERT: D 1411 MET cc_start: 0.8494 (ttt) cc_final: 0.8210 (ttp) REVERT: D 1603 GLU cc_start: 0.8270 (tt0) cc_final: 0.7966 (tt0) REVERT: D 1619 ASP cc_start: 0.8236 (m-30) cc_final: 0.7911 (m-30) REVERT: D 1689 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: D 1737 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7745 (m) REVERT: D 1784 ARG cc_start: 0.7984 (mmm160) cc_final: 0.7772 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8328 (m) cc_final: 0.7849 (m) REVERT: D 1994 ASP cc_start: 0.7909 (t70) cc_final: 0.7705 (t0) REVERT: D 2065 LYS cc_start: 0.8213 (tppt) cc_final: 0.7983 (mmmm) REVERT: D 2066 GLN cc_start: 0.8253 (tt0) cc_final: 0.7960 (tt0) REVERT: D 2531 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7994 (mm-30) REVERT: D 2535 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7825 (mtmm) REVERT: D 2581 THR cc_start: 0.8683 (m) cc_final: 0.8419 (p) outliers start: 132 outliers final: 108 residues processed: 1810 average time/residue: 1.6762 time to fit residues: 5160.7876 Evaluate side-chains 1831 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1713 time to evaluate : 8.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1906 GLU Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1118 ARG Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1464 LEU Chi-restraints excluded: chain B residue 1482 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 988 SER Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1182 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1675 LYS Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2370 LEU Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1201 ASP Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1919 THR Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2535 LYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 541 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 522 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 556 optimal weight: 3.9990 chunk 596 optimal weight: 3.9990 chunk 432 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 687 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A2066 GLN A2528 GLN B 467 ASN B 512 GLN B 754 GLN B 783 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1337 ASN B1650 HIS B2528 GLN C1106 ASN C1193 GLN C1288 HIS C1751 GLN C2528 GLN D 642 HIS D 783 HIS D1168 ASN D1327 ASN D1650 HIS D2528 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 75436 Z= 0.389 Angle : 0.479 5.883 101884 Z= 0.258 Chirality : 0.037 0.162 11612 Planarity : 0.003 0.064 12864 Dihedral : 8.124 88.764 10751 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.53 % Allowed : 11.10 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.46 (0.09), residues: 8968 helix: 2.78 (0.07), residues: 5800 sheet: -0.55 (0.20), residues: 652 loop : -0.57 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2601 HIS 0.009 0.001 HIS C1288 PHE 0.026 0.001 PHE A2307 TYR 0.017 0.001 TYR B2326 ARG 0.009 0.000 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1860 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1736 time to evaluate : 8.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8012 (tp30) cc_final: 0.7750 (tp30) REVERT: A 566 ASP cc_start: 0.8280 (t0) cc_final: 0.7913 (t0) REVERT: A 614 GLU cc_start: 0.7882 (mp0) cc_final: 0.7317 (mp0) REVERT: A 616 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 690 GLU cc_start: 0.7812 (mp0) cc_final: 0.7373 (mt-10) REVERT: A 740 CYS cc_start: 0.8168 (m) cc_final: 0.7892 (m) REVERT: A 835 GLU cc_start: 0.7991 (tt0) cc_final: 0.7785 (tt0) REVERT: A 990 LEU cc_start: 0.7953 (mp) cc_final: 0.7735 (mt) REVERT: A 1108 LYS cc_start: 0.8131 (mttm) cc_final: 0.7842 (mtmt) REVERT: A 1370 ASP cc_start: 0.8190 (m-30) cc_final: 0.7888 (m-30) REVERT: A 1404 ASP cc_start: 0.7455 (m-30) cc_final: 0.7052 (m-30) REVERT: A 1411 MET cc_start: 0.8438 (ttt) cc_final: 0.8115 (ttp) REVERT: A 1486 GLU cc_start: 0.8334 (pt0) cc_final: 0.8129 (pt0) REVERT: A 1596 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7979 (mm-40) REVERT: A 1613 GLU cc_start: 0.8307 (tt0) cc_final: 0.8047 (tt0) REVERT: A 1619 ASP cc_start: 0.8182 (m-30) cc_final: 0.7910 (m-30) REVERT: A 1689 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7913 (mtm) REVERT: A 1795 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7744 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8303 (m) cc_final: 0.7799 (m) REVERT: A 2316 MET cc_start: 0.7954 (tmm) cc_final: 0.7734 (tpp) REVERT: A 2532 GLU cc_start: 0.7820 (tt0) cc_final: 0.7387 (tp30) REVERT: A 2581 THR cc_start: 0.8738 (m) cc_final: 0.8447 (p) REVERT: B 100 GLU cc_start: 0.7291 (tt0) cc_final: 0.7010 (tt0) REVERT: B 470 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.7921 (mtp-110) REVERT: B 614 GLU cc_start: 0.7954 (mp0) cc_final: 0.7447 (mp0) REVERT: B 624 LYS cc_start: 0.8254 (tttm) cc_final: 0.7991 (ttmt) REVERT: B 690 GLU cc_start: 0.7772 (mp0) cc_final: 0.7361 (mp0) REVERT: B 740 CYS cc_start: 0.8161 (m) cc_final: 0.7886 (m) REVERT: B 1248 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8307 (ttmt) REVERT: B 1347 ASP cc_start: 0.8109 (m-30) cc_final: 0.7861 (m-30) REVERT: B 1350 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8603 (ttmm) REVERT: B 1363 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: B 1404 ASP cc_start: 0.7561 (m-30) cc_final: 0.7083 (m-30) REVERT: B 1619 ASP cc_start: 0.8217 (m-30) cc_final: 0.7855 (m-30) REVERT: B 1689 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: B 1795 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7798 (ttt90) REVERT: B 1905 CYS cc_start: 0.8373 (m) cc_final: 0.8116 (m) REVERT: B 1954 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8003 (mm-30) REVERT: B 2183 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 2200 ARG cc_start: 0.8574 (mtt90) cc_final: 0.7987 (mtt90) REVERT: B 2292 ASN cc_start: 0.8247 (t0) cc_final: 0.7867 (t0) REVERT: B 2532 GLU cc_start: 0.7498 (tt0) cc_final: 0.7164 (tt0) REVERT: B 2553 VAL cc_start: 0.8557 (m) cc_final: 0.8205 (p) REVERT: C 100 GLU cc_start: 0.7410 (tt0) cc_final: 0.7123 (tt0) REVERT: C 447 ASP cc_start: 0.8039 (m-30) cc_final: 0.7745 (m-30) REVERT: C 487 PRO cc_start: 0.7941 (Cg_exo) cc_final: 0.7705 (Cg_endo) REVERT: C 504 GLU cc_start: 0.7890 (mp0) cc_final: 0.7608 (mp0) REVERT: C 614 GLU cc_start: 0.7961 (mp0) cc_final: 0.7340 (mp0) REVERT: C 616 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 740 CYS cc_start: 0.8142 (m) cc_final: 0.7891 (m) REVERT: C 988 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8230 (m) REVERT: C 1066 ASP cc_start: 0.7870 (p0) cc_final: 0.7613 (t0) REVERT: C 1094 GLN cc_start: 0.8750 (mt0) cc_final: 0.8398 (mt0) REVERT: C 1116 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7970 (mtp85) REVERT: C 1118 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: C 1206 MET cc_start: 0.8515 (mmt) cc_final: 0.8211 (mmt) REVERT: C 1402 HIS cc_start: 0.8198 (t-90) cc_final: 0.7900 (t-90) REVERT: C 1619 ASP cc_start: 0.8191 (m-30) cc_final: 0.7969 (m-30) REVERT: C 1689 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: C 1905 CYS cc_start: 0.8335 (m) cc_final: 0.7702 (m) REVERT: C 2066 GLN cc_start: 0.8293 (tt0) cc_final: 0.8001 (tt0) REVERT: C 2181 GLU cc_start: 0.7582 (tt0) cc_final: 0.7258 (tt0) REVERT: C 2553 VAL cc_start: 0.8520 (m) cc_final: 0.8095 (p) REVERT: D 54 ASP cc_start: 0.8328 (m-30) cc_final: 0.8092 (m-30) REVERT: D 566 ASP cc_start: 0.8276 (t0) cc_final: 0.7736 (t0) REVERT: D 614 GLU cc_start: 0.7990 (mp0) cc_final: 0.7369 (mp0) REVERT: D 616 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 690 GLU cc_start: 0.7922 (mp0) cc_final: 0.7627 (mp0) REVERT: D 740 CYS cc_start: 0.8148 (m) cc_final: 0.7906 (m) REVERT: D 1094 GLN cc_start: 0.8851 (mt0) cc_final: 0.8530 (mt0) REVERT: D 1108 LYS cc_start: 0.8119 (mttm) cc_final: 0.7830 (mtmt) REVERT: D 1201 ASP cc_start: 0.7993 (m-30) cc_final: 0.7739 (t0) REVERT: D 1206 MET cc_start: 0.8460 (mmt) cc_final: 0.7957 (mmt) REVERT: D 1223 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 1248 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8276 (ttmt) REVERT: D 1277 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7326 (mt-10) REVERT: D 1284 GLN cc_start: 0.8255 (tp40) cc_final: 0.7475 (mp10) REVERT: D 1367 SER cc_start: 0.8455 (m) cc_final: 0.8242 (p) REVERT: D 1395 ASP cc_start: 0.7572 (m-30) cc_final: 0.7230 (t0) REVERT: D 1404 ASP cc_start: 0.7390 (m-30) cc_final: 0.7108 (m-30) REVERT: D 1411 MET cc_start: 0.8500 (ttt) cc_final: 0.8220 (ttp) REVERT: D 1603 GLU cc_start: 0.8267 (tt0) cc_final: 0.7971 (tt0) REVERT: D 1619 ASP cc_start: 0.8216 (m-30) cc_final: 0.7889 (m-30) REVERT: D 1689 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: D 1737 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7726 (m) REVERT: D 1784 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7771 (mmm-85) REVERT: D 1905 CYS cc_start: 0.8318 (m) cc_final: 0.7842 (m) REVERT: D 1994 ASP cc_start: 0.7893 (t70) cc_final: 0.7631 (t0) REVERT: D 2065 LYS cc_start: 0.8270 (tppt) cc_final: 0.8037 (mmmm) REVERT: D 2066 GLN cc_start: 0.8274 (tt0) cc_final: 0.7988 (tt0) REVERT: D 2123 GLN cc_start: 0.8410 (pt0) cc_final: 0.7926 (pt0) REVERT: D 2200 ARG cc_start: 0.8575 (mtt90) cc_final: 0.7986 (mtt90) REVERT: D 2581 THR cc_start: 0.8681 (m) cc_final: 0.8412 (p) outliers start: 124 outliers final: 109 residues processed: 1801 average time/residue: 1.6221 time to fit residues: 4933.8191 Evaluate side-chains 1835 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1718 time to evaluate : 8.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1332 VAL Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1464 LEU Chi-restraints excluded: chain B residue 1482 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 988 SER Chi-restraints excluded: chain C residue 1106 ASN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1118 ARG Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1675 LYS Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1332 VAL Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1464 LEU Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1919 THR Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2331 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 796 optimal weight: 2.9990 chunk 838 optimal weight: 1.9990 chunk 764 optimal weight: 2.9990 chunk 815 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 640 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 736 optimal weight: 2.9990 chunk 771 optimal weight: 1.9990 chunk 812 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A1090 HIS A1251 HIS A1650 HIS A2066 GLN A2528 GLN B 512 GLN B 783 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS B2528 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C1327 ASN C2528 GLN D 642 HIS D 783 HIS D1650 HIS D2528 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 75436 Z= 0.412 Angle : 0.489 5.217 101884 Z= 0.263 Chirality : 0.037 0.159 11612 Planarity : 0.003 0.060 12864 Dihedral : 8.136 88.597 10749 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.58 % Allowed : 11.23 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.40 (0.09), residues: 8968 helix: 2.73 (0.07), residues: 5804 sheet: -0.58 (0.20), residues: 652 loop : -0.60 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2601 HIS 0.008 0.001 HIS A1288 PHE 0.028 0.002 PHE C2307 TYR 0.018 0.001 TYR B2326 ARG 0.008 0.000 ARG D2131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1848 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1720 time to evaluate : 8.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8018 (tp30) cc_final: 0.7758 (tp30) REVERT: A 566 ASP cc_start: 0.8299 (t0) cc_final: 0.7926 (t0) REVERT: A 614 GLU cc_start: 0.7901 (mp0) cc_final: 0.7362 (mp0) REVERT: A 616 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 690 GLU cc_start: 0.7838 (mp0) cc_final: 0.7366 (mt-10) REVERT: A 740 CYS cc_start: 0.8171 (m) cc_final: 0.7888 (m) REVERT: A 835 GLU cc_start: 0.7997 (tt0) cc_final: 0.7791 (tt0) REVERT: A 990 LEU cc_start: 0.7957 (mp) cc_final: 0.7755 (mt) REVERT: A 1108 LYS cc_start: 0.8140 (mttm) cc_final: 0.7852 (mtmt) REVERT: A 1370 ASP cc_start: 0.8193 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1404 ASP cc_start: 0.7459 (m-30) cc_final: 0.7062 (m-30) REVERT: A 1411 MET cc_start: 0.8440 (ttt) cc_final: 0.8118 (ttp) REVERT: A 1596 GLN cc_start: 0.8232 (mm-40) cc_final: 0.8006 (mm-40) REVERT: A 1613 GLU cc_start: 0.8308 (tt0) cc_final: 0.8049 (tt0) REVERT: A 1619 ASP cc_start: 0.8192 (m-30) cc_final: 0.7921 (m-30) REVERT: A 1689 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: A 1795 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7734 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8297 (m) cc_final: 0.7792 (m) REVERT: A 2200 ARG cc_start: 0.8522 (mtt90) cc_final: 0.7972 (mtt90) REVERT: A 2316 MET cc_start: 0.7929 (tmm) cc_final: 0.7717 (tpp) REVERT: A 2532 GLU cc_start: 0.7817 (tt0) cc_final: 0.7390 (tp30) REVERT: A 2581 THR cc_start: 0.8796 (m) cc_final: 0.8506 (p) REVERT: B 100 GLU cc_start: 0.7304 (tt0) cc_final: 0.7013 (tt0) REVERT: B 470 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.7940 (mtp-110) REVERT: B 614 GLU cc_start: 0.7949 (mp0) cc_final: 0.7439 (mp0) REVERT: B 624 LYS cc_start: 0.8254 (tttm) cc_final: 0.7990 (ttmt) REVERT: B 690 GLU cc_start: 0.7786 (mp0) cc_final: 0.7353 (mp0) REVERT: B 740 CYS cc_start: 0.8148 (m) cc_final: 0.7870 (m) REVERT: B 1248 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8309 (ttmt) REVERT: B 1347 ASP cc_start: 0.8104 (m-30) cc_final: 0.7845 (m-30) REVERT: B 1350 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8603 (ttmm) REVERT: B 1363 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (mmm) REVERT: B 1404 ASP cc_start: 0.7581 (m-30) cc_final: 0.7081 (m-30) REVERT: B 1605 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8315 (ttt-90) REVERT: B 1619 ASP cc_start: 0.8209 (m-30) cc_final: 0.7872 (m-30) REVERT: B 1625 GLU cc_start: 0.8211 (pm20) cc_final: 0.7571 (pm20) REVERT: B 1689 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: B 1795 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7815 (ttt90) REVERT: B 1905 CYS cc_start: 0.8376 (m) cc_final: 0.8128 (m) REVERT: B 1954 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 2183 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 2200 ARG cc_start: 0.8585 (mtt90) cc_final: 0.7962 (mtt90) REVERT: B 2292 ASN cc_start: 0.8249 (t0) cc_final: 0.7868 (t0) REVERT: B 2532 GLU cc_start: 0.7499 (tt0) cc_final: 0.7168 (tt0) REVERT: B 2553 VAL cc_start: 0.8582 (m) cc_final: 0.8226 (p) REVERT: C 100 GLU cc_start: 0.7414 (tt0) cc_final: 0.7121 (tt0) REVERT: C 447 ASP cc_start: 0.8040 (m-30) cc_final: 0.7749 (m-30) REVERT: C 487 PRO cc_start: 0.7937 (Cg_exo) cc_final: 0.7702 (Cg_endo) REVERT: C 614 GLU cc_start: 0.7943 (mp0) cc_final: 0.7347 (mp0) REVERT: C 616 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 740 CYS cc_start: 0.8126 (m) cc_final: 0.7881 (m) REVERT: C 988 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8234 (m) REVERT: C 1066 ASP cc_start: 0.7883 (p0) cc_final: 0.7658 (t0) REVERT: C 1094 GLN cc_start: 0.8782 (mt0) cc_final: 0.8440 (mt0) REVERT: C 1116 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7992 (mtp85) REVERT: C 1118 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7786 (ttm-80) REVERT: C 1206 MET cc_start: 0.8518 (mmt) cc_final: 0.8194 (mmt) REVERT: C 1402 HIS cc_start: 0.8201 (t-90) cc_final: 0.7815 (t-90) REVERT: C 1404 ASP cc_start: 0.7485 (m-30) cc_final: 0.7062 (m-30) REVERT: C 1619 ASP cc_start: 0.8190 (m-30) cc_final: 0.7967 (m-30) REVERT: C 1689 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8152 (mtp) REVERT: C 1905 CYS cc_start: 0.8351 (m) cc_final: 0.7707 (m) REVERT: C 2066 GLN cc_start: 0.8299 (tt0) cc_final: 0.8013 (tt0) REVERT: C 2181 GLU cc_start: 0.7583 (tt0) cc_final: 0.7265 (tt0) REVERT: D 54 ASP cc_start: 0.8343 (m-30) cc_final: 0.8099 (m-30) REVERT: D 566 ASP cc_start: 0.8287 (t0) cc_final: 0.7755 (t0) REVERT: D 614 GLU cc_start: 0.7982 (mp0) cc_final: 0.7363 (mp0) REVERT: D 616 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7715 (mm-30) REVERT: D 690 GLU cc_start: 0.7925 (mp0) cc_final: 0.7627 (mp0) REVERT: D 740 CYS cc_start: 0.8129 (m) cc_final: 0.7896 (m) REVERT: D 1094 GLN cc_start: 0.8855 (mt0) cc_final: 0.8542 (mt0) REVERT: D 1108 LYS cc_start: 0.8138 (mttm) cc_final: 0.7850 (mtmt) REVERT: D 1201 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7742 (t0) REVERT: D 1223 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 1248 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8273 (ttmt) REVERT: D 1277 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 1284 GLN cc_start: 0.8363 (tp40) cc_final: 0.7566 (mp10) REVERT: D 1367 SER cc_start: 0.8467 (m) cc_final: 0.8259 (p) REVERT: D 1395 ASP cc_start: 0.7577 (m-30) cc_final: 0.7271 (t0) REVERT: D 1404 ASP cc_start: 0.7411 (m-30) cc_final: 0.7130 (m-30) REVERT: D 1411 MET cc_start: 0.8512 (ttt) cc_final: 0.8234 (ttp) REVERT: D 1603 GLU cc_start: 0.8274 (tt0) cc_final: 0.7983 (tt0) REVERT: D 1619 ASP cc_start: 0.8241 (m-30) cc_final: 0.7945 (m-30) REVERT: D 1689 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: D 1737 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7730 (m) REVERT: D 1905 CYS cc_start: 0.8310 (m) cc_final: 0.7836 (m) REVERT: D 1994 ASP cc_start: 0.7904 (t70) cc_final: 0.7697 (t0) REVERT: D 2065 LYS cc_start: 0.8284 (tppt) cc_final: 0.8051 (mmmm) REVERT: D 2066 GLN cc_start: 0.8290 (tt0) cc_final: 0.7996 (tt0) REVERT: D 2123 GLN cc_start: 0.8404 (pt0) cc_final: 0.7922 (pt0) REVERT: D 2200 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8039 (mtt90) REVERT: D 2581 THR cc_start: 0.8685 (m) cc_final: 0.8411 (p) outliers start: 128 outliers final: 113 residues processed: 1789 average time/residue: 1.5783 time to fit residues: 4748.7324 Evaluate side-chains 1830 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1708 time to evaluate : 8.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1332 VAL Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1906 GLU Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1464 LEU Chi-restraints excluded: chain B residue 1482 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 988 SER Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1110 ILE Chi-restraints excluded: chain C residue 1118 ARG Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1675 LYS Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 997 GLU Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1201 ASP Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1332 VAL Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1919 THR Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2331 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 535 optimal weight: 1.9990 chunk 862 optimal weight: 2.9990 chunk 526 optimal weight: 0.9990 chunk 409 optimal weight: 1.9990 chunk 599 optimal weight: 1.9990 chunk 904 optimal weight: 4.9990 chunk 832 optimal weight: 2.9990 chunk 720 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 556 optimal weight: 0.1980 chunk 441 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A1419 HIS A1650 HIS A2066 GLN A2528 GLN B 512 GLN ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS B2528 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1327 ASN C2528 GLN ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 HIS D1650 HIS D2528 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 75436 Z= 0.277 Angle : 0.455 5.546 101884 Z= 0.243 Chirality : 0.035 0.152 11612 Planarity : 0.003 0.061 12864 Dihedral : 7.833 88.893 10747 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.33 % Allowed : 11.63 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.56 (0.09), residues: 8968 helix: 2.85 (0.07), residues: 5804 sheet: -0.55 (0.20), residues: 652 loop : -0.52 (0.13), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2184 HIS 0.007 0.001 HIS C1288 PHE 0.026 0.001 PHE A2307 TYR 0.014 0.001 TYR C2496 ARG 0.009 0.000 ARG D2131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17936 Ramachandran restraints generated. 8968 Oldfield, 0 Emsley, 8968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue LYS 2257 is missing expected H atoms. Skipping. Residue LEU 2448 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Evaluate side-chains 1831 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1723 time to evaluate : 8.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8009 (tp30) cc_final: 0.7579 (mm-30) REVERT: A 566 ASP cc_start: 0.8272 (t0) cc_final: 0.7882 (t0) REVERT: A 614 GLU cc_start: 0.7893 (mp0) cc_final: 0.7327 (mp0) REVERT: A 616 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 690 GLU cc_start: 0.7815 (mp0) cc_final: 0.7349 (mt-10) REVERT: A 740 CYS cc_start: 0.8161 (m) cc_final: 0.7891 (m) REVERT: A 835 GLU cc_start: 0.7970 (tt0) cc_final: 0.7765 (tt0) REVERT: A 1108 LYS cc_start: 0.8135 (mttm) cc_final: 0.7848 (mtmt) REVERT: A 1404 ASP cc_start: 0.7458 (m-30) cc_final: 0.7061 (m-30) REVERT: A 1411 MET cc_start: 0.8417 (ttt) cc_final: 0.8094 (ttp) REVERT: A 1596 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7982 (mm-40) REVERT: A 1689 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: A 1795 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7738 (ttt-90) REVERT: A 1905 CYS cc_start: 0.8282 (m) cc_final: 0.7772 (m) REVERT: A 2200 ARG cc_start: 0.8505 (mtt90) cc_final: 0.7923 (mtt90) REVERT: A 2316 MET cc_start: 0.7939 (tmm) cc_final: 0.7730 (tpp) REVERT: A 2532 GLU cc_start: 0.7823 (tt0) cc_final: 0.7432 (tp30) REVERT: A 2581 THR cc_start: 0.8803 (m) cc_final: 0.8521 (p) REVERT: B 100 GLU cc_start: 0.7290 (tt0) cc_final: 0.6999 (tt0) REVERT: B 470 ARG cc_start: 0.8432 (mtp-110) cc_final: 0.7930 (mtp-110) REVERT: B 614 GLU cc_start: 0.7936 (mp0) cc_final: 0.7419 (mp0) REVERT: B 624 LYS cc_start: 0.8219 (tttm) cc_final: 0.7956 (ttmt) REVERT: B 690 GLU cc_start: 0.7748 (mp0) cc_final: 0.7330 (mp0) REVERT: B 740 CYS cc_start: 0.8153 (m) cc_final: 0.7898 (m) REVERT: B 1248 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8304 (ttmt) REVERT: B 1347 ASP cc_start: 0.8086 (m-30) cc_final: 0.7830 (m-30) REVERT: B 1350 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8599 (ttmm) REVERT: B 1363 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7967 (mmm) REVERT: B 1404 ASP cc_start: 0.7582 (m-30) cc_final: 0.7100 (m-30) REVERT: B 1605 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8322 (ttt-90) REVERT: B 1619 ASP cc_start: 0.8201 (m-30) cc_final: 0.7830 (m-30) REVERT: B 1625 GLU cc_start: 0.8211 (pm20) cc_final: 0.7557 (pm20) REVERT: B 1689 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: B 1795 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7811 (ttt90) REVERT: B 1905 CYS cc_start: 0.8340 (m) cc_final: 0.8093 (m) REVERT: B 1954 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 2183 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 2200 ARG cc_start: 0.8569 (mtt90) cc_final: 0.7972 (mtt90) REVERT: B 2292 ASN cc_start: 0.8250 (t0) cc_final: 0.7892 (t0) REVERT: B 2553 VAL cc_start: 0.8567 (m) cc_final: 0.8220 (p) REVERT: C 100 GLU cc_start: 0.7415 (tt0) cc_final: 0.7121 (tt0) REVERT: C 487 PRO cc_start: 0.7924 (Cg_exo) cc_final: 0.7679 (Cg_endo) REVERT: C 504 GLU cc_start: 0.7980 (mp0) cc_final: 0.7557 (mp0) REVERT: C 616 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7783 (mm-30) REVERT: C 740 CYS cc_start: 0.8113 (m) cc_final: 0.7903 (m) REVERT: C 988 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (m) REVERT: C 1066 ASP cc_start: 0.7869 (p0) cc_final: 0.7661 (t0) REVERT: C 1094 GLN cc_start: 0.8738 (mt0) cc_final: 0.8385 (mt0) REVERT: C 1116 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8024 (mtp85) REVERT: C 1206 MET cc_start: 0.8506 (mmt) cc_final: 0.8215 (mmt) REVERT: C 1404 ASP cc_start: 0.7467 (m-30) cc_final: 0.7112 (m-30) REVERT: C 1619 ASP cc_start: 0.8204 (m-30) cc_final: 0.7987 (m-30) REVERT: C 1689 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: C 1795 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7932 (ttt90) REVERT: C 1891 PHE cc_start: 0.8283 (t80) cc_final: 0.8045 (t80) REVERT: C 1905 CYS cc_start: 0.8319 (m) cc_final: 0.7668 (m) REVERT: C 2066 GLN cc_start: 0.8294 (tt0) cc_final: 0.8007 (tt0) REVERT: C 2123 GLN cc_start: 0.8421 (pt0) cc_final: 0.7894 (pt0) REVERT: C 2181 GLU cc_start: 0.7584 (tt0) cc_final: 0.7264 (tt0) REVERT: D 566 ASP cc_start: 0.8261 (t0) cc_final: 0.7616 (t0) REVERT: D 614 GLU cc_start: 0.7973 (mp0) cc_final: 0.7350 (mp0) REVERT: D 616 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7714 (mm-30) REVERT: D 690 GLU cc_start: 0.7922 (mp0) cc_final: 0.7620 (mp0) REVERT: D 740 CYS cc_start: 0.8134 (m) cc_final: 0.7908 (m) REVERT: D 1094 GLN cc_start: 0.8829 (mt0) cc_final: 0.8490 (mt0) REVERT: D 1108 LYS cc_start: 0.8109 (mttm) cc_final: 0.7825 (mtmt) REVERT: D 1201 ASP cc_start: 0.8004 (m-30) cc_final: 0.7733 (t0) REVERT: D 1206 MET cc_start: 0.8450 (mmt) cc_final: 0.7953 (mmt) REVERT: D 1223 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7961 (mm-30) REVERT: D 1248 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8265 (ttmt) REVERT: D 1277 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7308 (mt-10) REVERT: D 1284 GLN cc_start: 0.8320 (tp40) cc_final: 0.7558 (mp10) REVERT: D 1367 SER cc_start: 0.8447 (m) cc_final: 0.8233 (p) REVERT: D 1395 ASP cc_start: 0.7536 (m-30) cc_final: 0.7166 (t0) REVERT: D 1404 ASP cc_start: 0.7358 (m-30) cc_final: 0.7053 (m-30) REVERT: D 1411 MET cc_start: 0.8480 (ttt) cc_final: 0.8197 (ttp) REVERT: D 1603 GLU cc_start: 0.8257 (tt0) cc_final: 0.7969 (tt0) REVERT: D 1605 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.8290 (ttt-90) REVERT: D 1619 ASP cc_start: 0.8207 (m-30) cc_final: 0.7900 (m-30) REVERT: D 1689 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8109 (mtp) REVERT: D 1737 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7726 (m) REVERT: D 1905 CYS cc_start: 0.8301 (m) cc_final: 0.7833 (m) REVERT: D 1994 ASP cc_start: 0.7877 (t70) cc_final: 0.7615 (t0) REVERT: D 2065 LYS cc_start: 0.8261 (tppt) cc_final: 0.8031 (mmmm) REVERT: D 2066 GLN cc_start: 0.8275 (tt0) cc_final: 0.7987 (tt0) REVERT: D 2123 GLN cc_start: 0.8402 (pt0) cc_final: 0.7910 (pt0) REVERT: D 2200 ARG cc_start: 0.8565 (mtt90) cc_final: 0.7990 (mtt90) REVERT: D 2581 THR cc_start: 0.8661 (m) cc_final: 0.8381 (p) outliers start: 108 outliers final: 98 residues processed: 1783 average time/residue: 1.6353 time to fit residues: 4945.7615 Evaluate side-chains 1814 residues out of total 8256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1709 time to evaluate : 7.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain A residue 1900 ASN Chi-restraints excluded: chain A residue 1925 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2611 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 846 SER Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1464 LEU Chi-restraints excluded: chain B residue 1482 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1689 MET Chi-restraints excluded: chain B residue 1900 ASN Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1958 CYS Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2611 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 988 SER Chi-restraints excluded: chain C residue 1124 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1675 LYS Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2611 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 697 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 795 THR Chi-restraints excluded: chain D residue 845 VAL Chi-restraints excluded: chain D residue 1124 SER Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1307 ILE Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1389 SER Chi-restraints excluded: chain D residue 1482 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1614 LEU Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1900 ASN Chi-restraints excluded: chain D residue 1919 THR Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 2331 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 572 optimal weight: 2.9990 chunk 767 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 664 optimal weight: 2.9990 chunk 106 optimal weight: 0.0170 chunk 200 optimal weight: 0.0670 chunk 721 optimal weight: 2.9990 chunk 301 optimal weight: 0.0980 chunk 740 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A 783 HIS A1650 HIS A2528 GLN B 783 HIS ** B1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1650 HIS B2528 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C1327 ASN C2528 GLN ** C2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 HIS D 783 HIS D1650 HIS D2528 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112253 restraints weight = 296200.600| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.08 r_work: 0.2973 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 75436 Z= 0.179 Angle : 0.428 6.094 101884 Z= 0.227 Chirality : 0.034 0.156 11612 Planarity : 0.003 0.062 12864 Dihedral : 7.380 87.404 10747 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.19 % Allowed : 11.90 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.79 (0.09), residues: 8968 helix: 3.03 (0.07), residues: 5788 sheet: -0.48 (0.20), residues: 652 loop : -0.41 (0.13), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2184 HIS 0.007 0.001 HIS D1288 PHE 0.025 0.001 PHE A2307 TYR 0.012 0.001 TYR B1107 ARG 0.009 0.000 ARG D2131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 64714.47 seconds wall clock time: 1103 minutes 51.07 seconds (66231.07 seconds total)