Starting phenix.real_space_refine on Mon Mar 25 02:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tk8_41323/03_2024/8tk8_41323_trim_updated.pdb" } resolution = 2.7 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= 0.159 sd= 1.900 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 48 5.49 5 S 460 5.16 5 C 47336 2.51 5 N 12508 2.21 5 O 13724 1.98 5 H 72830 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 2223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 2223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 2500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 2223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146910 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 36394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36394 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 36395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36395 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 36394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36394 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 36395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36395 Classifications: {'peptide': 2268} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 2203} Chain breaks: 14 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 379 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 287 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 379 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 287 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 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 34868 SG CYS A2538 153.240 137.337 108.074 1.00 32.16 S ATOM 34917 SG CYS A2541 151.063 138.080 105.875 1.00 37.19 S ATOM 71263 SG CYS B2538 129.715 153.303 108.049 1.00 32.16 S ATOM 71312 SG CYS B2541 128.974 151.124 105.851 1.00 37.19 S ATOM A05WP SG CYS C2538 113.582 129.593 108.029 1.00 32.16 S ATOM A05Y2 SG CYS C2541 115.763 128.850 105.834 1.00 37.19 S ATOM A0XZO SG CYS D2538 137.293 113.651 108.053 1.00 32.16 S ATOM A0Y11 SG CYS D2541 138.039 115.830 105.857 1.00 37.19 S Time building chain proxies: 50.29, per 1000 atoms: 0.34 Number of scatterers: 146910 At special positions: 0 Unit cell: (267.954, 267.954, 191.845, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 460 16.00 P 48 15.00 O 13724 8.00 N 12508 7.00 C 47336 6.00 H 72830 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 99.64 Conformation dependent library (CDL) restraints added in 11.2 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 D2703 " pdb="ZN ZN D2703 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2703 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2703 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2703 " - pdb=" SG CYS D2538 " Number of angles added : 4 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17392 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: 420 helices and 44 sheets defined 70.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 38.88 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.200A pdb=" N GLY A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 5.191A 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 51 through 56 removed outlier: 4.492A pdb=" N CYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.782A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.837A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' 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 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: 4.739A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 565 removed outlier: 3.510A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 3.535A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 590 through 600 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 4.221A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 661 through 666 removed outlier: 4.644A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 661 through 666' 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 755 removed outlier: 4.305A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 820 removed outlier: 4.091A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 4.167A pdb=" N ASN A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.549A pdb=" N GLU A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.581A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 4.058A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1003 Proline residue: A1003 - end of helix Processing helix chain 'A' and resid 1024 through 1036 removed outlier: 3.760A pdb=" N MET A1035 " --> pdb=" O GLN A1031 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1044 removed outlier: 4.241A pdb=" N SER A1043 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N MET A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1039 through 1044' Processing helix chain 'A' and resid 1052 through 1065 removed outlier: 3.614A pdb=" N MET A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.783A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 Processing helix chain 'A' and resid 1100 through 1124 Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.411A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A1172 " --> pdb=" O ASN A1168 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 removed outlier: 4.518A pdb=" N ARG A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1212 removed outlier: 3.586A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 6.233A pdb=" N MET A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU A1223 " --> pdb=" O ALA A1219 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1237 " --> pdb=" O GLN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 3.965A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 removed outlier: 4.033A pdb=" N ALA A1261 " --> pdb=" O GLY A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.895A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 4.042A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 4.028A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.900A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 3.940A pdb=" N ALA A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A1352 " --> pdb=" O MET A1348 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A1353 " --> pdb=" O MET A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 3.590A pdb=" N ALA A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 4.323A pdb=" N GLU A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A1389 " --> pdb=" O ILE A1385 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1391 " --> pdb=" O CYS A1387 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 removed outlier: 3.501A pdb=" N HIS A1402 " --> pdb=" O SER A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1428 through 1433 removed outlier: 3.998A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 removed outlier: 5.074A pdb=" N THR A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A1458 " --> pdb=" O LYS A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.633A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1488 removed outlier: 4.502A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1483 through 1488' Processing helix chain 'A' and resid 1490 through 1512 removed outlier: 4.205A pdb=" N HIS A1494 " --> pdb=" O SER A1490 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN A1495 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A1496 " --> pdb=" O GLN A1492 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL A1498 " --> pdb=" O HIS A1494 " (cutoff:3.500A) Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1515 through 1537 removed outlier: 4.071A pdb=" N GLY A1520 " --> pdb=" O GLN A1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1522 " --> pdb=" O HIS A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 3.779A pdb=" N MET A1551 " --> pdb=" O HIS A1547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1624 removed outlier: 3.769A pdb=" N LYS A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Proline residue: A1608 - end of helix Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 Processing helix chain 'A' and resid 1642 through 1655 removed outlier: 3.651A 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: 5.096A 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 1717 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: 4.406A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.502A 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 removed outlier: 3.654A pdb=" N ARG A1893 " --> pdb=" O GLN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1916 removed outlier: 3.854A pdb=" N GLU A1906 " --> pdb=" O ASN A1902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 4.200A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 4.131A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A1929 " --> pdb=" O LEU A1925 " (cutoff:3.500A) removed outlier: 4.880A 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 1949 removed outlier: 5.204A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 3.833A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1985 removed outlier: 3.749A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.981A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 removed outlier: 4.181A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A2039 " --> pdb=" O GLN A2035 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU A2040 " --> pdb=" O GLU A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2065 removed outlier: 3.851A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A2064 " --> pdb=" O LEU A2060 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS A2065 " --> pdb=" O SER A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2072 removed outlier: 3.635A 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: 4.112A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.544A 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 Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 4.567A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) removed outlier: 4.177A 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 2222 removed outlier: 3.883A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2276 removed outlier: 4.705A pdb=" N LEU A2264 " --> pdb=" O SER A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.357A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2318 removed outlier: 5.500A pdb=" N MET A2318 " --> pdb=" O MET A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2319 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.777A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.698A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2391 Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 3.956A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.691A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A2480 " --> pdb=" O VAL A2476 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2475 through 2481' Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.906A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.702A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 4.576A 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 2611 through 2648 Processing helix chain 'A' and resid 2598 through 2603 removed outlier: 4.730A pdb=" N TRP A2601 " --> pdb=" O ASN A2598 " (cutoff:3.500A) Proline residue: A2603 - end of helix Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.200A pdb=" N GLY B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 5.191A 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 51 through 56 removed outlier: 4.492A pdb=" N CYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.782A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.838A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' 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 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: 4.739A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 565 removed outlier: 3.510A pdb=" N GLN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 3.536A pdb=" N LYS B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 590 through 600 Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 640 removed outlier: 4.220A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 661 through 666 removed outlier: 4.645A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 666' 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 755 removed outlier: 4.305A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 811 through 820 removed outlier: 4.091A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 828 removed outlier: 4.168A pdb=" N ASN B 828 " --> pdb=" O ASP B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 3.549A pdb=" N GLU B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 removed outlier: 3.581A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 4.058A pdb=" N ARG B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1003 Proline residue: B1003 - end of helix Processing helix chain 'B' and resid 1024 through 1036 removed outlier: 3.760A pdb=" N MET B1035 " --> pdb=" O GLN B1031 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1044 removed outlier: 4.240A pdb=" N SER B1043 " --> pdb=" O GLY B1039 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1044' Processing helix chain 'B' and resid 1052 through 1065 removed outlier: 3.614A pdb=" N MET B1064 " --> pdb=" O ILE B1060 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.783A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 Processing helix chain 'B' and resid 1100 through 1124 Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.410A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B1171 " --> pdb=" O GLU B1167 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B1172 " --> pdb=" O ASN B1168 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 removed outlier: 4.519A pdb=" N ARG B1190 " --> pdb=" O GLY B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1212 removed outlier: 3.586A pdb=" N ILE B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1237 removed outlier: 6.233A pdb=" N MET B1222 " --> pdb=" O ASP B1218 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU B1223 " --> pdb=" O ALA B1219 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B1224 " --> pdb=" O LYS B1220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B1237 " --> pdb=" O GLN B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 3.965A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 removed outlier: 4.032A pdb=" N ALA B1261 " --> pdb=" O GLY B1257 " (cutoff:3.500A) Processing helix chain 'B' and resid 1271 through 1278 removed outlier: 3.895A pdb=" N GLU B1277 " --> pdb=" O GLN B1273 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1292 removed outlier: 4.043A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 4.028A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.900A pdb=" N ALA B1328 " --> pdb=" O GLU B1324 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 removed outlier: 3.940A pdb=" N ALA B1351 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B1352 " --> pdb=" O MET B1348 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B1353 " --> pdb=" O MET B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 3.590A pdb=" N ALA B1376 " --> pdb=" O LEU B1372 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 4.323A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER B1389 " --> pdb=" O ILE B1385 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B1390 " --> pdb=" O LYS B1386 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B1391 " --> pdb=" O CYS B1387 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 removed outlier: 3.500A pdb=" N HIS B1402 " --> pdb=" O SER B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1406 through 1420 Processing helix chain 'B' and resid 1428 through 1433 removed outlier: 3.997A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 removed outlier: 5.074A pdb=" N THR B1439 " --> pdb=" O ASN B1435 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B1458 " --> pdb=" O LYS B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.633A pdb=" N VAL B1471 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B1482 " --> pdb=" O ALA B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1488 removed outlier: 4.502A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1483 through 1488' Processing helix chain 'B' and resid 1490 through 1512 removed outlier: 4.206A pdb=" N HIS B1494 " --> pdb=" O SER B1490 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B1495 " --> pdb=" O LEU B1491 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B1496 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) Proline residue: B1512 - end of helix Processing helix chain 'B' and resid 1515 through 1537 removed outlier: 4.071A pdb=" N GLY B1520 " --> pdb=" O GLN B1516 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER B1521 " --> pdb=" O GLN B1517 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B1522 " --> pdb=" O HIS B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 removed outlier: 3.778A pdb=" N MET B1551 " --> pdb=" O HIS B1547 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B1553 " --> pdb=" O SER B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1587 through 1624 removed outlier: 3.768A pdb=" N LYS B1607 " --> pdb=" O GLU B1603 " (cutoff:3.500A) Proline residue: B1608 - end of helix Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.652A 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: 5.095A 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 1717 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: 4.406A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.501A 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 removed outlier: 3.653A pdb=" N ARG B1893 " --> pdb=" O GLN B1889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1916 removed outlier: 3.853A pdb=" N GLU B1906 " --> pdb=" O ASN B1902 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 4.200A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 4.131A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B1929 " --> pdb=" O LEU B1925 " (cutoff:3.500A) removed outlier: 4.880A 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 1949 removed outlier: 5.204A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 3.832A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1985 removed outlier: 3.749A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.980A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2040 removed outlier: 4.181A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU B2037 " --> pdb=" O TYR B2033 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B2039 " --> pdb=" O GLN B2035 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU B2040 " --> pdb=" O GLU B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2065 removed outlier: 3.851A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS B2065 " --> pdb=" O SER B2061 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2072 removed outlier: 3.635A 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: 4.112A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.854A 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 Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 4.566A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) removed outlier: 4.177A 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 2222 removed outlier: 3.884A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2260 through 2276 removed outlier: 4.705A pdb=" N LEU B2264 " --> pdb=" O SER B2260 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.357A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2318 removed outlier: 5.500A pdb=" N MET B2318 " --> pdb=" O MET B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2336 Processing helix chain 'B' and resid 2337 through 2353 removed outlier: 4.777A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 3.699A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2391 Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 3.956A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.690A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B2480 " --> pdb=" O VAL B2476 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2475 through 2481' Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.905A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.701A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 4.576A 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 2611 through 2648 Processing helix chain 'B' and resid 2598 through 2603 removed outlier: 4.730A pdb=" N TRP B2601 " --> pdb=" O ASN B2598 " (cutoff:3.500A) Proline residue: B2603 - end of helix Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.200A pdb=" N GLY C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.191A 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 51 through 56 removed outlier: 4.492A pdb=" N CYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.783A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.838A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 277' 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 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: 4.740A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 565 removed outlier: 3.510A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 3.536A pdb=" N LYS C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 590 through 600 Processing helix chain 'C' and resid 602 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 4.220A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 661 through 666 removed outlier: 4.644A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 661 through 666' 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 755 removed outlier: 4.305A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 820 removed outlier: 4.090A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 828 removed outlier: 4.167A pdb=" N ASN C 828 " --> pdb=" O ASP C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 3.550A pdb=" N GLU C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 874 removed outlier: 3.582A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 4.058A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1003 Proline residue: C1003 - end of helix Processing helix chain 'C' and resid 1024 through 1036 removed outlier: 3.759A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1044 removed outlier: 4.241A pdb=" N SER C1043 " --> pdb=" O GLY C1039 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET C1044 " --> pdb=" O LYS C1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1039 through 1044' Processing helix chain 'C' and resid 1052 through 1065 removed outlier: 3.615A pdb=" N MET C1064 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.782A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 Processing helix chain 'C' and resid 1100 through 1124 Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.410A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 removed outlier: 4.519A pdb=" N ARG C1190 " --> pdb=" O GLY C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1212 removed outlier: 3.587A pdb=" N ILE C1212 " --> pdb=" O ASP C1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 6.233A pdb=" N MET C1222 " --> pdb=" O ASP C1218 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU C1223 " --> pdb=" O ALA C1219 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C1224 " --> pdb=" O LYS C1220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C1237 " --> pdb=" O GLN C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 3.965A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 removed outlier: 4.032A pdb=" N ALA C1261 " --> pdb=" O GLY C1257 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1278 removed outlier: 3.895A pdb=" N GLU C1277 " --> pdb=" O GLN C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1292 removed outlier: 4.044A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 4.028A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.900A pdb=" N ALA C1328 " --> pdb=" O GLU C1324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 removed outlier: 3.941A pdb=" N ALA C1351 " --> pdb=" O ASP C1347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C1352 " --> pdb=" O MET C1348 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C1353 " --> pdb=" O MET C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 3.590A pdb=" N ALA C1376 " --> pdb=" O LEU C1372 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1392 removed outlier: 4.323A pdb=" N GLU C1384 " --> pdb=" O ASN C1380 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C1385 " --> pdb=" O VAL C1381 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER C1389 " --> pdb=" O ILE C1385 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU C1390 " --> pdb=" O LYS C1386 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C1391 " --> pdb=" O CYS C1387 " (cutoff:3.500A) Proline residue: C1392 - end of helix Processing helix chain 'C' and resid 1393 through 1402 removed outlier: 3.501A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1428 through 1433 removed outlier: 3.997A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 removed outlier: 5.074A pdb=" N THR C1439 " --> pdb=" O ASN C1435 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C1458 " --> pdb=" O LYS C1454 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.633A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER C1482 " --> pdb=" O ALA C1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 1483 through 1488 removed outlier: 4.502A pdb=" N ASN C1487 " --> pdb=" O PRO C1483 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1483 through 1488' Processing helix chain 'C' and resid 1490 through 1512 removed outlier: 4.205A pdb=" N HIS C1494 " --> pdb=" O SER C1490 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN C1495 " --> pdb=" O LEU C1491 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL C1498 " --> pdb=" O HIS C1494 " (cutoff:3.500A) Proline residue: C1512 - end of helix Processing helix chain 'C' and resid 1515 through 1537 removed outlier: 4.071A pdb=" N GLY C1520 " --> pdb=" O GLN C1516 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C1522 " --> pdb=" O HIS C1518 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1553 removed outlier: 3.778A pdb=" N MET C1551 " --> pdb=" O HIS C1547 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER C1553 " --> pdb=" O SER C1549 " (cutoff:3.500A) Processing helix chain 'C' and resid 1587 through 1624 removed outlier: 3.768A pdb=" N LYS C1607 " --> pdb=" O GLU C1603 " (cutoff:3.500A) Proline residue: C1608 - end of helix Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 Processing helix chain 'C' and resid 1642 through 1655 removed outlier: 3.651A 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: 5.096A 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 1717 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: 4.407A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.502A 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 removed outlier: 3.653A pdb=" N ARG C1893 " --> pdb=" O GLN C1889 " (cutoff:3.500A) Processing helix chain 'C' and resid 1902 through 1916 removed outlier: 3.854A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 4.199A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 4.131A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C1929 " --> pdb=" O LEU C1925 " (cutoff:3.500A) removed outlier: 4.880A 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 1949 removed outlier: 5.203A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 3.833A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1985 removed outlier: 3.749A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 3.981A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2040 removed outlier: 4.181A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG C2039 " --> pdb=" O GLN C2035 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU C2040 " --> pdb=" O GLU C2036 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2065 removed outlier: 3.851A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C2064 " --> pdb=" O LEU C2060 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS C2065 " --> pdb=" O SER C2061 " (cutoff:3.500A) Processing helix chain 'C' and resid 2066 through 2072 removed outlier: 3.635A 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: 4.113A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.854A 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 Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 4.566A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) removed outlier: 4.176A 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 2222 removed outlier: 3.882A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) Processing helix chain 'C' and resid 2260 through 2276 removed outlier: 4.706A pdb=" N LEU C2264 " --> pdb=" O SER C2260 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.356A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2318 removed outlier: 5.500A pdb=" N MET C2318 " --> pdb=" O MET C2314 " (cutoff:3.500A) Processing helix chain 'C' and resid 2319 through 2336 Processing helix chain 'C' and resid 2337 through 2353 removed outlier: 4.776A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 3.699A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2391 Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 3.957A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.690A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C2480 " --> pdb=" O VAL C2476 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2475 through 2481' Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.905A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.701A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 4.576A 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 2611 through 2648 Processing helix chain 'C' and resid 2598 through 2603 removed outlier: 4.730A pdb=" N TRP C2601 " --> pdb=" O ASN C2598 " (cutoff:3.500A) Proline residue: C2603 - end of helix Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.200A pdb=" N GLY D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.191A 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 51 through 56 removed outlier: 4.492A pdb=" N CYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.783A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.838A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 277' 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 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: 4.739A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 565 removed outlier: 3.510A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 3.536A pdb=" N LYS D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 590 through 600 Processing helix chain 'D' and resid 602 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 640 removed outlier: 4.220A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 Processing helix chain 'D' and resid 661 through 666 removed outlier: 4.643A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 661 through 666' 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 755 removed outlier: 4.305A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 820 removed outlier: 4.091A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 828 removed outlier: 4.166A pdb=" N ASN D 828 " --> pdb=" O ASP D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 848 removed outlier: 3.549A pdb=" N GLU D 847 " --> pdb=" O ASN D 843 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 874 removed outlier: 3.582A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 4.058A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1003 Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1036 removed outlier: 3.759A pdb=" N MET D1035 " --> pdb=" O GLN D1031 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 removed outlier: 4.241A pdb=" N SER D1043 " --> pdb=" O GLY D1039 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N MET D1044 " --> pdb=" O LYS D1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1039 through 1044' Processing helix chain 'D' and resid 1052 through 1065 removed outlier: 3.614A pdb=" N MET D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.782A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 Processing helix chain 'D' and resid 1100 through 1124 Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.410A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE D1171 " --> pdb=" O GLU D1167 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL D1172 " --> pdb=" O ASN D1168 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 removed outlier: 4.519A pdb=" N ARG D1190 " --> pdb=" O GLY D1186 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 removed outlier: 3.586A pdb=" N ILE D1212 " --> pdb=" O ASP D1208 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 6.233A pdb=" N MET D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N GLU D1223 " --> pdb=" O ALA D1219 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D1224 " --> pdb=" O LYS D1220 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D1237 " --> pdb=" O GLN D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 3.965A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 removed outlier: 4.033A pdb=" N ALA D1261 " --> pdb=" O GLY D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1271 through 1278 removed outlier: 3.895A pdb=" N GLU D1277 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1292 removed outlier: 4.043A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 4.029A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.899A pdb=" N ALA D1328 " --> pdb=" O GLU D1324 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 removed outlier: 3.940A pdb=" N ALA D1351 " --> pdb=" O ASP D1347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D1352 " --> pdb=" O MET D1348 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D1353 " --> pdb=" O MET D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.590A pdb=" N ALA D1376 " --> pdb=" O LEU D1372 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 removed outlier: 4.323A pdb=" N GLU D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D1385 " --> pdb=" O VAL D1381 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER D1389 " --> pdb=" O ILE D1385 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D1390 " --> pdb=" O LYS D1386 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D1391 " --> pdb=" O CYS D1387 " (cutoff:3.500A) Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 3.501A pdb=" N HIS D1402 " --> pdb=" O SER D1398 " (cutoff:3.500A) Processing helix chain 'D' and resid 1406 through 1420 Processing helix chain 'D' and resid 1428 through 1433 removed outlier: 3.997A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 5.073A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D1458 " --> pdb=" O LYS D1454 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.633A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D1482 " --> pdb=" O ALA D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1483 through 1488 removed outlier: 4.503A pdb=" N ASN D1487 " --> pdb=" O PRO D1483 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1483 through 1488' Processing helix chain 'D' and resid 1490 through 1512 removed outlier: 4.206A pdb=" N HIS D1494 " --> pdb=" O SER D1490 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN D1495 " --> pdb=" O LEU D1491 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL D1498 " --> pdb=" O HIS D1494 " (cutoff:3.500A) Proline residue: D1512 - end of helix Processing helix chain 'D' and resid 1515 through 1537 removed outlier: 4.071A pdb=" N GLY D1520 " --> pdb=" O GLN D1516 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D1522 " --> pdb=" O HIS D1518 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1553 removed outlier: 3.778A pdb=" N MET D1551 " --> pdb=" O HIS D1547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D1553 " --> pdb=" O SER D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1587 through 1624 removed outlier: 3.769A pdb=" N LYS D1607 " --> pdb=" O GLU D1603 " (cutoff:3.500A) Proline residue: D1608 - end of helix Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.651A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.096A 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 1717 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: 4.407A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.502A 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 removed outlier: 3.653A pdb=" N ARG D1893 " --> pdb=" O GLN D1889 " (cutoff:3.500A) Processing helix chain 'D' and resid 1902 through 1916 removed outlier: 3.854A pdb=" N GLU D1906 " --> pdb=" O ASN D1902 " (cutoff:3.500A) Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 4.200A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 4.132A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D1929 " --> pdb=" O LEU D1925 " (cutoff:3.500A) removed outlier: 4.880A 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 1949 removed outlier: 5.204A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 3.832A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1979 through 1985 removed outlier: 3.749A pdb=" N LYS D1983 " --> pdb=" O SER D1979 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.980A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2040 removed outlier: 4.180A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG D2039 " --> pdb=" O GLN D2035 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU D2040 " --> pdb=" O GLU D2036 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2065 removed outlier: 3.851A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D2064 " --> pdb=" O LEU D2060 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS D2065 " --> pdb=" O SER D2061 " (cutoff:3.500A) Processing helix chain 'D' and resid 2066 through 2072 removed outlier: 3.635A 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: 4.113A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.854A 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 Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 4.566A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) removed outlier: 4.177A 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 2222 removed outlier: 3.882A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) Processing helix chain 'D' and resid 2260 through 2276 removed outlier: 4.706A pdb=" N LEU D2264 " --> pdb=" O SER D2260 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.356A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2318 removed outlier: 5.500A pdb=" N MET D2318 " --> pdb=" O MET D2314 " (cutoff:3.500A) Processing helix chain 'D' and resid 2319 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.777A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 3.699A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2391 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 3.956A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.691A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D2480 " --> pdb=" O VAL D2476 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2475 through 2481' Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.905A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.701A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 4.576A 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 2611 through 2648 Processing helix chain 'D' and resid 2598 through 2603 removed outlier: 4.731A pdb=" N TRP D2601 " --> pdb=" O ASN D2598 " (cutoff:3.500A) Proline residue: D2603 - end of helix Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 20 removed outlier: 9.047A pdb=" N THR A 217 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 185 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 181 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 57 through 62 removed outlier: 3.934A pdb=" N MET A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL A 121 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 13.361A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 194 through 198 removed outlier: 4.093A pdb=" N GLU A 209 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.263A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 13.626A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 239 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 14.886A pdb=" N TYR A 304 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N ALA A 317 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.922A pdb=" N SER A 385 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 396 through 401 removed outlier: 3.998A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 667 through 672 removed outlier: 4.048A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 800 through 803 Processing sheet with id= 9, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.120A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.148A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 240 through 245 removed outlier: 5.419A pdb=" N VAL A 240 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 14 through 20 removed outlier: 9.046A pdb=" N THR B 217 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 185 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 181 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.934A pdb=" N MET B 62 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL B 121 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 13.362A pdb=" N ILE B 122 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N VAL B 135 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 194 through 198 removed outlier: 4.093A pdb=" N GLU B 209 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.264A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 13.626A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP B 239 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 14.886A pdb=" N TYR B 304 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N ALA B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 385 through 388 removed outlier: 3.921A pdb=" N SER B 385 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 396 through 401 removed outlier: 3.998A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 667 through 672 removed outlier: 4.048A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 800 through 803 Processing sheet with id= 20, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.120A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 7.149A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 240 through 245 removed outlier: 5.419A pdb=" N VAL B 240 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 14 through 20 removed outlier: 9.046A pdb=" N THR C 217 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU C 185 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 181 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 57 through 62 removed outlier: 3.935A pdb=" N MET C 62 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL C 121 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 13.362A pdb=" N ILE C 122 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 9.809A pdb=" N VAL C 135 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 194 through 198 removed outlier: 4.093A pdb=" N GLU C 209 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.263A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 13.626A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 239 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 14.885A pdb=" N TYR C 304 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N ALA C 317 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 385 through 388 removed outlier: 3.921A pdb=" N SER C 385 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 396 through 401 removed outlier: 3.999A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 667 through 672 removed outlier: 4.048A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 800 through 803 Processing sheet with id= 31, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.121A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 2395 through 2399 removed outlier: 7.148A pdb=" N PHE C2395 " --> pdb=" O ALA C2454 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER C2450 " --> pdb=" O VAL C2399 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 240 through 245 removed outlier: 5.420A pdb=" N VAL C 240 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 14 through 20 removed outlier: 9.046A pdb=" N THR D 217 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU D 185 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 181 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.934A pdb=" N MET D 62 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N VAL D 121 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 13.362A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 194 through 198 removed outlier: 4.093A pdb=" N GLU D 209 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.263A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 13.626A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP D 239 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 14.886A pdb=" N TYR D 304 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N ALA D 317 " --> pdb=" O TYR D 304 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 385 through 388 removed outlier: 3.922A pdb=" N SER D 385 " --> pdb=" O ILE D 431 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 396 through 401 removed outlier: 3.998A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 667 through 672 removed outlier: 4.048A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 800 through 803 Processing sheet with id= 42, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.120A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.149A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 240 through 245 removed outlier: 5.420A pdb=" N VAL D 240 " --> pdb=" O VAL D 434 " (cutoff:3.500A) 4336 hydrogen bonds defined for protein. 12972 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: 74.43 Time building geometry restraints manager: 104.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 72653 0.99 - 1.20: 17 1.20 - 1.40: 30231 1.40 - 1.61: 44528 1.61 - 1.81: 797 Bond restraints: 148226 Sorted by residual: bond pdb=" ND1 HIS A1962 " pdb=" HD1 HIS A1962 " ideal model delta sigma weight residual 0.860 1.714 -0.854 2.00e-02 2.50e+03 1.82e+03 bond pdb=" CD2 HIS A1962 " pdb=" HD2 HIS A1962 " ideal model delta sigma weight residual 0.930 1.238 -0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" CE1 HIS A1962 " pdb=" NE2 HIS A1962 " ideal model delta sigma weight residual 1.321 1.265 0.056 1.00e-02 1.00e+04 3.18e+01 bond pdb=" CE1 HIS B1962 " pdb=" NE2 HIS B1962 " ideal model delta sigma weight residual 1.321 1.265 0.056 1.00e-02 1.00e+04 3.18e+01 bond pdb=" CE1 HIS D1962 " pdb=" NE2 HIS D1962 " ideal model delta sigma weight residual 1.321 1.265 0.056 1.00e-02 1.00e+04 3.17e+01 ... (remaining 148221 not shown) Histogram of bond angle deviations from ideal: 16.25 - 44.52: 5 44.52 - 72.78: 7 72.78 - 101.04: 183 101.04 - 129.31: 266746 129.31 - 157.57: 476 Bond angle restraints: 267417 Sorted by residual: angle pdb=" CG HIS A1962 " pdb=" ND1 HIS A1962 " pdb=" HD1 HIS A1962 " ideal model delta sigma weight residual 125.35 16.25 109.10 3.00e+00 1.11e-01 1.32e+03 angle pdb=" CG HIS D1962 " pdb=" CD2 HIS D1962 " pdb=" HD2 HIS D1962 " ideal model delta sigma weight residual 126.40 23.97 102.43 3.00e+00 1.11e-01 1.17e+03 angle pdb=" CG HIS B1962 " pdb=" CD2 HIS B1962 " pdb=" HD2 HIS B1962 " ideal model delta sigma weight residual 126.40 24.04 102.36 3.00e+00 1.11e-01 1.16e+03 angle pdb=" CG HIS C1962 " pdb=" CD2 HIS C1962 " pdb=" HD2 HIS C1962 " ideal model delta sigma weight residual 126.40 24.05 102.35 3.00e+00 1.11e-01 1.16e+03 angle pdb=" NE2 HIS A1962 " pdb=" CD2 HIS A1962 " pdb=" HD2 HIS A1962 " ideal model delta sigma weight residual 126.40 39.75 86.65 3.00e+00 1.11e-01 8.34e+02 ... (remaining 267412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 68432 34.73 - 69.45: 1193 69.45 - 104.18: 116 104.18 - 138.91: 17 138.91 - 173.64: 12 Dihedral angle restraints: 69770 sinusoidal: 38562 harmonic: 31208 Sorted by residual: dihedral pdb=" ND1 HIS A1962 " pdb=" CG HIS A1962 " pdb=" CD2 HIS A1962 " pdb=" HD2 HIS A1962 " ideal model delta harmonic sigma weight residual 180.00 6.36 173.64 0 5.00e+00 4.00e-02 1.21e+03 dihedral pdb=" CG HIS C1962 " pdb=" ND1 HIS C1962 " pdb=" CE1 HIS C1962 " pdb=" HE1 HIS C1962 " ideal model delta harmonic sigma weight residual 180.00 33.44 146.56 0 5.00e+00 4.00e-02 8.59e+02 dihedral pdb=" CG HIS D1962 " pdb=" ND1 HIS D1962 " pdb=" CE1 HIS D1962 " pdb=" HE1 HIS D1962 " ideal model delta harmonic sigma weight residual 180.00 33.49 146.51 0 5.00e+00 4.00e-02 8.59e+02 ... (remaining 69767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 10401 0.058 - 0.116: 1095 0.116 - 0.175: 60 0.175 - 0.233: 4 0.233 - 0.291: 12 Chirality restraints: 11572 Sorted by residual: 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 2.12e+00 chirality pdb=" C3' ATP D2705 " pdb=" C2' ATP D2705 " pdb=" C4' ATP D2705 " pdb=" O3' ATP D2705 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C2704 " pdb=" C1' ATP C2704 " pdb=" C3' ATP C2704 " pdb=" O2' ATP C2704 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 11569 not shown) Planarity restraints: 21604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B1962 " -0.016 2.00e-02 2.50e+03 1.11e-01 2.80e+02 pdb=" CG HIS B1962 " -0.197 2.00e-02 2.50e+03 pdb=" ND1 HIS B1962 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 HIS B1962 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B1962 " -0.138 2.00e-02 2.50e+03 pdb=" NE2 HIS B1962 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS B1962 " 0.112 2.00e-02 2.50e+03 pdb=" HE1 HIS B1962 " 0.145 2.00e-02 2.50e+03 pdb=" HE2 HIS B1962 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D1962 " -0.016 2.00e-02 2.50e+03 1.11e-01 2.79e+02 pdb=" CG HIS D1962 " -0.196 2.00e-02 2.50e+03 pdb=" ND1 HIS D1962 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 HIS D1962 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D1962 " -0.138 2.00e-02 2.50e+03 pdb=" NE2 HIS D1962 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS D1962 " 0.112 2.00e-02 2.50e+03 pdb=" HE1 HIS D1962 " 0.145 2.00e-02 2.50e+03 pdb=" HE2 HIS D1962 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1962 " -0.016 2.00e-02 2.50e+03 1.11e-01 2.79e+02 pdb=" CG HIS A1962 " -0.196 2.00e-02 2.50e+03 pdb=" ND1 HIS A1962 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 HIS A1962 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A1962 " -0.137 2.00e-02 2.50e+03 pdb=" NE2 HIS A1962 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 HIS A1962 " 0.113 2.00e-02 2.50e+03 pdb=" HD2 HIS A1962 " 0.145 2.00e-02 2.50e+03 pdb=" HE2 HIS A1962 " 0.026 2.00e-02 2.50e+03 ... (remaining 21601 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.66: 67 1.66 - 2.39: 59666 2.39 - 3.13: 452493 3.13 - 3.86: 590122 3.86 - 4.60: 961795 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2064143 Sorted by model distance: nonbonded pdb=" CE1 HIS A1962 " pdb=" HD2 HIS A1962 " model vdw 0.920 2.240 nonbonded pdb=" CD2 HIS A1962 " pdb=" HD1 HIS A1962 " model vdw 1.028 2.240 nonbonded pdb=" ND1 HIS A1962 " pdb=" HD2 HIS A1962 " model vdw 1.231 2.080 nonbonded pdb=" CD2 HIS C1962 " pdb=" HE1 HIS C1962 " model vdw 1.238 2.240 nonbonded pdb=" CD2 HIS D1962 " pdb=" HE1 HIS D1962 " model vdw 1.238 2.240 ... (remaining 2064138 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 2523 or (resid 2524 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 2525 \ through 2648 or (resid 3006 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C5 or name C6 or name C7 or name C8 or na \ me 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 3007 through 3008 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or na \ me C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C4 \ 3 or name C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C \ 8 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 )))) selection = (chain 'B' and (resid 5 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH21)) or resid 139 through 2523 or \ (resid 2524 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or na \ me HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or \ name HH21 or name HH22)) or resid 2525 through 2648 or (resid 2706 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2 \ P or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 2707 thr \ ough 2708 and (name N or name C1 or name 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 C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 or nam \ e C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name C46 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 name O4P or name P )))) selection = (chain 'C' and (resid 5 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH21)) or resid 139 through 2648 or \ (resid 2706 and (name N or name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C5 or name C6 or name C7 or name C8 or name O11 or name O \ 1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name \ P )) or (resid 2707 through 2708 and (name N or name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C46 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 name O4P \ or name P )))) selection = (chain 'D' and (resid 5 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH21)) or resid 139 through 2523 or \ (resid 2524 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or na \ me HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or \ name HH21 or name HH22)) or resid 2525 through 2648 or (resid 2706 and (name N \ or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C \ 5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or name O2 \ P or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 2707 thr \ ough 2708 and (name N or name C1 or name 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 C \ 34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 or nam \ e C40 or name C41 or name C42 or name C43 or name C44 or name C45 or name C46 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 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: 21.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.670 Extract box with map and model: 61.100 Check model and map are aligned: 1.700 Set scattering table: 1.020 Process input model: 445.620 Find NCS groups from input model: 8.230 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 554.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.076 75396 Z= 0.124 Angle : 0.407 6.213 101764 Z= 0.231 Chirality : 0.035 0.291 11572 Planarity : 0.003 0.101 12844 Dihedral : 12.273 154.807 28760 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.69 % Allowed : 3.04 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 3.26 (0.09), residues: 8952 helix: 3.10 (0.07), residues: 5648 sheet: 0.08 (0.20), residues: 664 loop : 0.67 (0.13), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C2566 HIS 0.154 0.002 HIS B1962 PHE 0.014 0.001 PHE B2502 TYR 0.008 0.001 TYR B2496 ARG 0.002 0.000 ARG B2545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1965 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1909 time to evaluate : 9.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 109 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8299 (ttmt) REVERT: A 320 ASN cc_start: 0.7438 (t0) cc_final: 0.7075 (t0) REVERT: A 603 ARG cc_start: 0.8199 (ttt90) cc_final: 0.7839 (ttt180) REVERT: A 713 GLN cc_start: 0.8211 (tt0) cc_final: 0.8005 (mt0) REVERT: A 1204 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7251 (tppp) REVERT: A 1208 ASP cc_start: 0.7444 (m-30) cc_final: 0.6855 (m-30) REVERT: A 1305 THR cc_start: 0.7782 (t) cc_final: 0.6099 (m) REVERT: A 1319 ASP cc_start: 0.8115 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1430 GLU cc_start: 0.7492 (pm20) cc_final: 0.6922 (pm20) REVERT: A 1470 SER cc_start: 0.7936 (t) cc_final: 0.7547 (p) REVERT: A 1646 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7717 (mmmt) REVERT: A 1664 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8032 (mtmp) REVERT: A 1745 LYS cc_start: 0.8973 (tppp) cc_final: 0.8706 (mmtm) REVERT: A 1900 ASN cc_start: 0.8074 (m110) cc_final: 0.7836 (m110) REVERT: A 1956 GLN cc_start: 0.8118 (mt0) cc_final: 0.7900 (mt0) REVERT: A 2027 ASP cc_start: 0.7838 (m-30) cc_final: 0.7631 (m-30) REVERT: A 2314 MET cc_start: 0.7690 (ttp) cc_final: 0.7488 (ttp) REVERT: B 109 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8451 (mtmm) REVERT: B 394 THR cc_start: 0.7831 (p) cc_final: 0.7558 (p) REVERT: B 511 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7696 (mm-30) REVERT: B 653 CYS cc_start: 0.7627 (m) cc_final: 0.7227 (m) REVERT: B 1206 MET cc_start: 0.8349 (tpp) cc_final: 0.6735 (mpp) REVERT: B 1208 ASP cc_start: 0.7543 (m-30) cc_final: 0.6961 (m-30) REVERT: B 1305 THR cc_start: 0.7475 (t) cc_final: 0.6008 (m) REVERT: B 1319 ASP cc_start: 0.8208 (m-30) cc_final: 0.7967 (m-30) REVERT: B 1645 SER cc_start: 0.8182 (t) cc_final: 0.7938 (p) REVERT: B 1688 LYS cc_start: 0.8328 (tttm) cc_final: 0.8031 (ttpt) REVERT: B 1692 GLN cc_start: 0.8292 (tt0) cc_final: 0.7982 (mt0) REVERT: B 2027 ASP cc_start: 0.7834 (m-30) cc_final: 0.7556 (m-30) REVERT: B 2299 SER cc_start: 0.7984 (m) cc_final: 0.7651 (t) REVERT: B 2531 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 504 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 653 CYS cc_start: 0.7417 (m) cc_final: 0.7044 (m) REVERT: C 705 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 1033 GLU cc_start: 0.7718 (tt0) cc_final: 0.7485 (tt0) REVERT: C 1208 ASP cc_start: 0.7605 (m-30) cc_final: 0.7115 (m-30) REVERT: C 1288 HIS cc_start: 0.7390 (m170) cc_final: 0.7108 (t-170) REVERT: C 1377 GLU cc_start: 0.6897 (tt0) cc_final: 0.6691 (tt0) REVERT: C 1381 VAL cc_start: 0.8828 (p) cc_final: 0.8476 (p) REVERT: C 1463 THR cc_start: 0.8065 (p) cc_final: 0.7773 (t) REVERT: C 1516 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 1645 SER cc_start: 0.8125 (t) cc_final: 0.7759 (p) REVERT: C 1684 ASN cc_start: 0.8030 (m110) cc_final: 0.7737 (m110) REVERT: C 1692 GLN cc_start: 0.8228 (tt0) cc_final: 0.7989 (mt0) REVERT: C 1767 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7861 (mm-30) REVERT: C 2027 ASP cc_start: 0.8019 (m-30) cc_final: 0.7739 (m-30) REVERT: C 2529 LYS cc_start: 0.8139 (tttp) cc_final: 0.7881 (ttmm) REVERT: C 2531 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7326 (mm-30) REVERT: C 2544 GLU cc_start: 0.8083 (mp0) cc_final: 0.7866 (mp0) REVERT: D 33 ASP cc_start: 0.8270 (t0) cc_final: 0.8054 (t0) REVERT: D 71 TYR cc_start: 0.7637 (t80) cc_final: 0.6974 (t80) REVERT: D 94 GLN cc_start: 0.8089 (tt0) cc_final: 0.7709 (tt0) REVERT: D 320 ASN cc_start: 0.7615 (t0) cc_final: 0.7332 (t0) REVERT: D 582 GLN cc_start: 0.8088 (mt0) cc_final: 0.7783 (mt0) REVERT: D 862 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7833 (mm-30) REVERT: D 1208 ASP cc_start: 0.7604 (m-30) cc_final: 0.6982 (m-30) REVERT: D 1305 THR cc_start: 0.8214 (t) cc_final: 0.6976 (m) REVERT: D 1381 VAL cc_start: 0.8817 (p) cc_final: 0.8520 (p) REVERT: D 1430 GLU cc_start: 0.7611 (pm20) cc_final: 0.6960 (pm20) REVERT: D 1646 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7833 (mmmt) REVERT: D 1664 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7970 (mttp) REVERT: D 1684 ASN cc_start: 0.8061 (m110) cc_final: 0.7675 (m110) REVERT: D 1767 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7950 (mm-30) REVERT: D 1956 GLN cc_start: 0.8424 (mt0) cc_final: 0.7862 (mt0) REVERT: D 2027 ASP cc_start: 0.7912 (m-30) cc_final: 0.7672 (m-30) REVERT: D 2400 ASP cc_start: 0.8421 (m-30) cc_final: 0.8185 (m-30) REVERT: D 2529 LYS cc_start: 0.8025 (tttp) cc_final: 0.7773 (ttmm) outliers start: 56 outliers final: 17 residues processed: 1937 average time/residue: 3.0861 time to fit residues: 8052.2387 Evaluate side-chains 1504 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1487 time to evaluate : 8.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 1689 MET Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 1284 GLN Chi-restraints excluded: chain B residue 1531 MET Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2461 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 6.9990 chunk 685 optimal weight: 6.9990 chunk 380 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 708 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 527 optimal weight: 1.9990 chunk 820 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1415 ASN A1477 ASN A1693 ASN A1897 ASN ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 299 HIS B 446 ASN B 512 GLN ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1900 ASN B2052 ASN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2550 ASN C 289 HIS C 446 ASN C 492 ASN C 512 GLN C 513 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN C 976 GLN C1180 ASN C1477 ASN C1693 ASN C1897 ASN C1900 ASN C2052 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2550 ASN D 446 ASN D 492 ASN D 512 GLN D 513 ASN ** D 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 GLN D1477 ASN D1897 ASN D2035 GLN D2145 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 75396 Z= 0.484 Angle : 0.586 7.006 101764 Z= 0.317 Chirality : 0.041 0.177 11572 Planarity : 0.005 0.110 12844 Dihedral : 10.276 178.463 10929 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.16 % Allowed : 9.93 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.28 (0.09), residues: 8952 helix: 2.29 (0.07), residues: 5696 sheet: -0.26 (0.19), residues: 664 loop : 0.32 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 72 HIS 0.014 0.002 HIS D 551 PHE 0.025 0.002 PHE B1444 TYR 0.020 0.002 TYR D2496 ARG 0.009 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1758 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1583 time to evaluate : 9.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8359 (tppp) cc_final: 0.8106 (ttmm) REVERT: A 109 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8396 (mtmm) REVERT: A 249 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: A 351 LYS cc_start: 0.6078 (tppt) cc_final: 0.5847 (tppt) REVERT: A 451 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7761 (ttt) REVERT: A 511 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 588 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7030 (p0) REVERT: A 709 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.7911 (mtt-85) REVERT: A 1182 MET cc_start: 0.7874 (tmm) cc_final: 0.7130 (tmm) REVERT: A 1193 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7380 (mm-40) REVERT: A 1208 ASP cc_start: 0.7532 (m-30) cc_final: 0.6946 (m-30) REVERT: A 1305 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 1425 GLU cc_start: 0.7247 (pt0) cc_final: 0.7023 (pt0) REVERT: A 1448 MET cc_start: 0.8058 (mtt) cc_final: 0.7793 (mtt) REVERT: A 1528 THR cc_start: 0.8112 (t) cc_final: 0.7853 (p) REVERT: A 1646 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7803 (mmmt) REVERT: A 1684 ASN cc_start: 0.8169 (m110) cc_final: 0.7862 (m110) REVERT: A 1745 LYS cc_start: 0.8977 (tppp) cc_final: 0.8757 (mmtp) REVERT: A 1900 ASN cc_start: 0.8338 (m110) cc_final: 0.8037 (m110) REVERT: A 2014 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 2027 ASP cc_start: 0.7993 (m-30) cc_final: 0.7688 (m-30) REVERT: A 2316 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6833 (tpt) REVERT: A 2353 GLU cc_start: 0.7617 (tt0) cc_final: 0.7355 (tt0) REVERT: A 2544 GLU cc_start: 0.8113 (mp0) cc_final: 0.7883 (mp0) REVERT: B 98 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7883 (mt0) REVERT: B 109 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8479 (mtmm) REVERT: B 465 SER cc_start: 0.8263 (t) cc_final: 0.7842 (p) REVERT: B 466 GLN cc_start: 0.6989 (tt0) cc_final: 0.6727 (tp-100) REVERT: B 511 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7738 (mm-30) REVERT: B 561 ARG cc_start: 0.8277 (tmt90) cc_final: 0.7849 (tmm-80) REVERT: B 588 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: B 653 CYS cc_start: 0.7536 (m) cc_final: 0.7209 (m) REVERT: B 1103 ASP cc_start: 0.8002 (m-30) cc_final: 0.7779 (m-30) REVERT: B 1193 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7524 (mm-40) REVERT: B 1196 LEU cc_start: 0.8465 (tp) cc_final: 0.8247 (tp) REVERT: B 1208 ASP cc_start: 0.7610 (m-30) cc_final: 0.7055 (m-30) REVERT: B 1305 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8403 (p) REVERT: B 1319 ASP cc_start: 0.8341 (m-30) cc_final: 0.8080 (m-30) REVERT: B 1425 GLU cc_start: 0.7164 (pt0) cc_final: 0.6962 (pt0) REVERT: B 1507 ARG cc_start: 0.8046 (ptm-80) cc_final: 0.7840 (ptm-80) REVERT: B 1646 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7894 (mmmt) REVERT: B 1684 ASN cc_start: 0.8160 (m-40) cc_final: 0.7924 (m110) REVERT: B 1692 GLN cc_start: 0.8350 (tt0) cc_final: 0.7998 (mt0) REVERT: B 2027 ASP cc_start: 0.8034 (m-30) cc_final: 0.7698 (m-30) REVERT: B 2314 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7637 (ptm) REVERT: B 2531 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 109 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8437 (mtmm) REVERT: C 465 SER cc_start: 0.8396 (t) cc_final: 0.8110 (p) REVERT: C 511 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 793 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (mp) REVERT: C 1033 GLU cc_start: 0.7934 (tt0) cc_final: 0.7732 (tt0) REVERT: C 1208 ASP cc_start: 0.7644 (m-30) cc_final: 0.7184 (m-30) REVERT: C 1305 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8421 (p) REVERT: C 1395 ASP cc_start: 0.7514 (m-30) cc_final: 0.7304 (m-30) REVERT: C 1463 THR cc_start: 0.8120 (p) cc_final: 0.7902 (t) REVERT: C 1528 THR cc_start: 0.8129 (t) cc_final: 0.7789 (p) REVERT: C 1531 MET cc_start: 0.6850 (mpt) cc_final: 0.6561 (mpt) REVERT: C 1532 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7951 (m) REVERT: C 1646 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7844 (mmmt) REVERT: C 1684 ASN cc_start: 0.8151 (m110) cc_final: 0.7830 (m110) REVERT: C 1692 GLN cc_start: 0.8283 (tt0) cc_final: 0.8032 (mt0) REVERT: C 1783 GLU cc_start: 0.8007 (tt0) cc_final: 0.7793 (tt0) REVERT: C 2027 ASP cc_start: 0.8063 (m-30) cc_final: 0.7756 (m-30) REVERT: C 2183 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: C 2460 MET cc_start: 0.8947 (mmm) cc_final: 0.8672 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8164 (tttp) cc_final: 0.7868 (ttmm) REVERT: C 2531 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 2610 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8403 (tp) REVERT: D 109 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8336 (mtmm) REVERT: D 249 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: D 667 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7618 (mmt180) REVERT: D 709 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7809 (mtt-85) REVERT: D 1033 GLU cc_start: 0.7993 (tt0) cc_final: 0.7683 (mt-10) REVERT: D 1208 ASP cc_start: 0.7622 (m-30) cc_final: 0.7020 (m-30) REVERT: D 1305 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8362 (p) REVERT: D 1353 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8216 (mtm180) REVERT: D 1395 ASP cc_start: 0.7635 (m-30) cc_final: 0.7415 (m-30) REVERT: D 1425 GLU cc_start: 0.7421 (pt0) cc_final: 0.7212 (pt0) REVERT: D 1528 THR cc_start: 0.8183 (t) cc_final: 0.7959 (p) REVERT: D 1532 VAL cc_start: 0.8232 (p) cc_final: 0.7930 (m) REVERT: D 1646 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7811 (mmmt) REVERT: D 1684 ASN cc_start: 0.8135 (m110) cc_final: 0.7757 (m110) REVERT: D 2027 ASP cc_start: 0.8047 (m-30) cc_final: 0.7781 (m-30) REVERT: D 2353 GLU cc_start: 0.7528 (tt0) cc_final: 0.7303 (tt0) REVERT: D 2529 LYS cc_start: 0.8173 (tttp) cc_final: 0.7918 (ttmm) REVERT: D 2544 GLU cc_start: 0.8087 (mp0) cc_final: 0.7877 (mp0) outliers start: 175 outliers final: 63 residues processed: 1666 average time/residue: 3.2264 time to fit residues: 7259.3105 Evaluate side-chains 1511 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1433 time to evaluate : 8.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1963 GLU Chi-restraints excluded: chain A residue 2122 SER Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1226 ARG Chi-restraints excluded: chain B residue 1270 ASN Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 1981 LEU Chi-restraints excluded: chain B residue 2314 MET Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2537 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1054 MET Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 GLU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1353 ARG Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2122 SER Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2537 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 683 optimal weight: 0.5980 chunk 559 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 822 optimal weight: 2.9990 chunk 888 optimal weight: 2.9990 chunk 732 optimal weight: 3.9990 chunk 815 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 659 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 299 HIS A 492 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 713 GLN A 832 ASN A1284 GLN ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2164 GLN ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN B 226 GLN B 299 HIS B 976 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1693 ASN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN C1693 ASN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2528 GLN D 299 HIS D 546 ASN D 609 HIS D 832 ASN D1284 GLN D1693 ASN D1897 ASN D2145 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 75396 Z= 0.274 Angle : 0.463 5.342 101764 Z= 0.249 Chirality : 0.036 0.140 11572 Planarity : 0.004 0.076 12844 Dihedral : 9.176 177.557 10906 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.84 % Allowed : 11.99 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.42 (0.09), residues: 8952 helix: 2.46 (0.07), residues: 5676 sheet: -0.31 (0.19), residues: 664 loop : 0.25 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2601 HIS 0.009 0.001 HIS C 551 PHE 0.013 0.001 PHE B1002 TYR 0.015 0.001 TYR C2496 ARG 0.010 0.000 ARG A1507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1629 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1480 time to evaluate : 8.083 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: A 102 LYS cc_start: 0.8347 (tppp) cc_final: 0.8127 (ttmm) REVERT: A 109 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8397 (mtmm) REVERT: A 403 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 451 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7696 (ttt) REVERT: A 511 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 1182 MET cc_start: 0.7880 (tmm) cc_final: 0.7090 (tmm) REVERT: A 1193 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 1208 ASP cc_start: 0.7566 (m-30) cc_final: 0.7089 (m-30) REVERT: A 1305 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 1425 GLU cc_start: 0.7244 (pt0) cc_final: 0.7011 (pt0) REVERT: A 1448 MET cc_start: 0.8063 (mtt) cc_final: 0.7858 (mtt) REVERT: A 1469 LEU cc_start: 0.8969 (mm) cc_final: 0.8767 (mt) REVERT: A 1528 THR cc_start: 0.8226 (t) cc_final: 0.7925 (p) REVERT: A 1603 GLU cc_start: 0.7830 (tt0) cc_final: 0.7593 (tt0) REVERT: A 1646 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7792 (mmmt) REVERT: A 1684 ASN cc_start: 0.8158 (m110) cc_final: 0.7838 (m110) REVERT: A 1900 ASN cc_start: 0.8348 (m110) cc_final: 0.8079 (m110) REVERT: A 2014 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 2027 ASP cc_start: 0.8013 (m-30) cc_final: 0.7697 (m-30) REVERT: A 2353 GLU cc_start: 0.7520 (tt0) cc_final: 0.7316 (tt0) REVERT: B 98 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7886 (mt0) REVERT: B 109 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8481 (mtmm) REVERT: B 465 SER cc_start: 0.8238 (t) cc_final: 0.7932 (p) REVERT: B 511 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 561 ARG cc_start: 0.8276 (tmt90) cc_final: 0.8067 (tmt90) REVERT: B 588 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7043 (m-30) REVERT: B 608 LYS cc_start: 0.8162 (tptm) cc_final: 0.7937 (tppp) REVERT: B 653 CYS cc_start: 0.7469 (m) cc_final: 0.7155 (m) REVERT: B 1103 ASP cc_start: 0.7979 (m-30) cc_final: 0.7755 (m-30) REVERT: B 1193 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7464 (mm-40) REVERT: B 1208 ASP cc_start: 0.7604 (m-30) cc_final: 0.7067 (m-30) REVERT: B 1305 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8350 (p) REVERT: B 1319 ASP cc_start: 0.8312 (m-30) cc_final: 0.8055 (m-30) REVERT: B 1463 THR cc_start: 0.8326 (p) cc_final: 0.8071 (t) REVERT: B 1500 GLN cc_start: 0.8404 (mt0) cc_final: 0.7870 (mt0) REVERT: B 1507 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7768 (ptm-80) REVERT: B 1528 THR cc_start: 0.8076 (m) cc_final: 0.7873 (m) REVERT: B 1684 ASN cc_start: 0.8171 (m-40) cc_final: 0.7935 (m110) REVERT: B 2014 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 2027 ASP cc_start: 0.8053 (m-30) cc_final: 0.7734 (m-30) REVERT: B 2282 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 2314 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7630 (ptm) REVERT: B 2531 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 94 GLN cc_start: 0.8302 (tt0) cc_final: 0.7518 (tt0) REVERT: C 109 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8468 (mtmm) REVERT: C 351 LYS cc_start: 0.6312 (tppt) cc_final: 0.6049 (tppt) REVERT: C 468 ASP cc_start: 0.7951 (m-30) cc_final: 0.7749 (m-30) REVERT: C 511 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7777 (mm-30) REVERT: C 588 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6453 (p0) REVERT: C 604 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7832 (mttm) REVERT: C 1208 ASP cc_start: 0.7603 (m-30) cc_final: 0.7133 (m-30) REVERT: C 1280 GLU cc_start: 0.7662 (mp0) cc_final: 0.7141 (mp0) REVERT: C 1284 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: C 1305 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8415 (p) REVERT: C 1395 ASP cc_start: 0.7440 (m-30) cc_final: 0.7211 (m-30) REVERT: C 1528 THR cc_start: 0.8186 (t) cc_final: 0.7905 (p) REVERT: C 1531 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6714 (mpt) REVERT: C 1532 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7915 (m) REVERT: C 1646 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7829 (mmmt) REVERT: C 1684 ASN cc_start: 0.8164 (m110) cc_final: 0.7854 (m110) REVERT: C 1783 GLU cc_start: 0.7973 (tt0) cc_final: 0.7735 (tt0) REVERT: C 2027 ASP cc_start: 0.8076 (m-30) cc_final: 0.7751 (m-30) REVERT: C 2460 MET cc_start: 0.8957 (mmm) cc_final: 0.8672 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8171 (tttp) cc_final: 0.7883 (ttmm) REVERT: C 2531 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7335 (mm-30) REVERT: C 2610 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8372 (tp) REVERT: D 109 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8359 (mtmm) REVERT: D 746 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8487 (tt) REVERT: D 1182 MET cc_start: 0.7837 (tmm) cc_final: 0.7246 (tmm) REVERT: D 1193 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7605 (mm-40) REVERT: D 1206 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7550 (mpp) REVERT: D 1208 ASP cc_start: 0.7604 (m-30) cc_final: 0.7021 (m-30) REVERT: D 1305 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8355 (p) REVERT: D 1377 GLU cc_start: 0.7171 (tt0) cc_final: 0.6965 (tt0) REVERT: D 1395 ASP cc_start: 0.7610 (m-30) cc_final: 0.7367 (m-30) REVERT: D 1484 PHE cc_start: 0.8464 (m-80) cc_final: 0.7743 (m-10) REVERT: D 1528 THR cc_start: 0.8237 (t) cc_final: 0.7968 (p) REVERT: D 1532 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7900 (m) REVERT: D 1646 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7791 (mmmt) REVERT: D 1684 ASN cc_start: 0.8130 (m110) cc_final: 0.7738 (m110) REVERT: D 2027 ASP cc_start: 0.8053 (m-30) cc_final: 0.7769 (m-30) REVERT: D 2353 GLU cc_start: 0.7502 (tt0) cc_final: 0.7251 (tt0) REVERT: D 2529 LYS cc_start: 0.8221 (tttp) cc_final: 0.7972 (ttmm) REVERT: D 2544 GLU cc_start: 0.8070 (mp0) cc_final: 0.7857 (mp0) outliers start: 149 outliers final: 61 residues processed: 1552 average time/residue: 3.1444 time to fit residues: 6580.7844 Evaluate side-chains 1473 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1396 time to evaluate : 8.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 2006 SER Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2314 MET Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2609 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1331 ASP Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1502 LEU Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1097 LEU Chi-restraints excluded: chain D residue 1206 MET Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 5.9990 chunk 618 optimal weight: 3.9990 chunk 426 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 392 optimal weight: 0.8980 chunk 552 optimal weight: 10.0000 chunk 825 optimal weight: 2.9990 chunk 873 optimal weight: 2.9990 chunk 431 optimal weight: 2.9990 chunk 782 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 467 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 713 GLN A1284 GLN ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2164 GLN ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B1900 ASN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2528 GLN C 299 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 609 HIS D1284 GLN D1897 ASN D2145 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 75396 Z= 0.369 Angle : 0.501 6.289 101764 Z= 0.271 Chirality : 0.038 0.148 11572 Planarity : 0.004 0.086 12844 Dihedral : 8.702 161.272 10906 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 12.47 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.19 (0.09), residues: 8952 helix: 2.31 (0.07), residues: 5672 sheet: -0.29 (0.19), residues: 680 loop : 0.05 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2601 HIS 0.012 0.001 HIS C 551 PHE 0.017 0.002 PHE B1444 TYR 0.017 0.001 TYR B2496 ARG 0.008 0.000 ARG A1507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1646 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1465 time to evaluate : 9.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8366 (tppp) cc_final: 0.8164 (ttmm) REVERT: A 109 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8427 (mtmm) REVERT: A 403 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 511 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 1208 ASP cc_start: 0.7582 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1305 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8391 (p) REVERT: A 1528 THR cc_start: 0.8353 (t) cc_final: 0.8073 (p) REVERT: A 1603 GLU cc_start: 0.7852 (tt0) cc_final: 0.7643 (tt0) REVERT: A 1646 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7804 (mmmt) REVERT: A 1684 ASN cc_start: 0.8151 (m110) cc_final: 0.7842 (m110) REVERT: A 1784 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7790 (mpp80) REVERT: A 1900 ASN cc_start: 0.8351 (m110) cc_final: 0.8070 (m-40) REVERT: A 2014 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7930 (mm-30) REVERT: A 2024 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 2027 ASP cc_start: 0.8031 (m-30) cc_final: 0.7699 (m-30) REVERT: A 2353 GLU cc_start: 0.7602 (tt0) cc_final: 0.7395 (tt0) REVERT: B 98 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7908 (mt0) REVERT: B 109 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8487 (mtmm) REVERT: B 399 GLN cc_start: 0.7966 (mt0) cc_final: 0.7747 (mt0) REVERT: B 511 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 588 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: B 608 LYS cc_start: 0.8207 (tptm) cc_final: 0.7982 (tppp) REVERT: B 653 CYS cc_start: 0.7432 (m) cc_final: 0.7138 (m) REVERT: B 705 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 1103 ASP cc_start: 0.8017 (m-30) cc_final: 0.7782 (m-30) REVERT: B 1193 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7592 (mm-40) REVERT: B 1208 ASP cc_start: 0.7585 (m-30) cc_final: 0.7058 (m-30) REVERT: B 1305 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8404 (p) REVERT: B 1319 ASP cc_start: 0.8345 (m-30) cc_final: 0.8073 (m-30) REVERT: B 1448 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7878 (mtt) REVERT: B 1463 THR cc_start: 0.8335 (p) cc_final: 0.8083 (t) REVERT: B 1507 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7802 (ptm-80) REVERT: B 1528 THR cc_start: 0.8273 (m) cc_final: 0.7991 (m) REVERT: B 1646 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7878 (mmmt) REVERT: B 1684 ASN cc_start: 0.8162 (m-40) cc_final: 0.7925 (m110) REVERT: B 1783 GLU cc_start: 0.7979 (tt0) cc_final: 0.7711 (tt0) REVERT: B 2014 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 2024 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7231 (mp0) REVERT: B 2027 ASP cc_start: 0.8059 (m-30) cc_final: 0.7733 (m-30) REVERT: B 2282 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7594 (mp) REVERT: B 2531 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7355 (mm-30) REVERT: C 109 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8473 (mtmm) REVERT: C 403 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8478 (p) REVERT: C 511 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 604 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7857 (mttm) REVERT: C 754 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: C 1208 ASP cc_start: 0.7594 (m-30) cc_final: 0.7110 (m-30) REVERT: C 1280 GLU cc_start: 0.7663 (mp0) cc_final: 0.7050 (mp0) REVERT: C 1284 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: C 1305 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8408 (p) REVERT: C 1395 ASP cc_start: 0.7442 (m-30) cc_final: 0.7232 (m-30) REVERT: C 1427 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6596 (OUTLIER) REVERT: C 1484 PHE cc_start: 0.8654 (m-10) cc_final: 0.8201 (m-80) REVERT: C 1528 THR cc_start: 0.8338 (t) cc_final: 0.8066 (p) REVERT: C 1531 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6780 (mpt) REVERT: C 1532 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8003 (m) REVERT: C 1646 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7859 (mmmt) REVERT: C 1684 ASN cc_start: 0.8160 (m110) cc_final: 0.7834 (m110) REVERT: C 1783 GLU cc_start: 0.8035 (tt0) cc_final: 0.7801 (tt0) REVERT: C 2027 ASP cc_start: 0.8081 (m-30) cc_final: 0.7758 (m-30) REVERT: C 2183 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: C 2460 MET cc_start: 0.8949 (mmm) cc_final: 0.8666 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8169 (tttp) cc_final: 0.7887 (ttmm) REVERT: C 2531 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 109 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8374 (mtmm) REVERT: D 399 GLN cc_start: 0.7865 (mt0) cc_final: 0.7568 (mt0) REVERT: D 468 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7783 (t0) REVERT: D 746 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8588 (tt) REVERT: D 793 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 1182 MET cc_start: 0.7824 (tmm) cc_final: 0.6977 (tmm) REVERT: D 1193 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7474 (mm-40) REVERT: D 1305 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8404 (p) REVERT: D 1377 GLU cc_start: 0.7181 (tt0) cc_final: 0.6907 (tt0) REVERT: D 1395 ASP cc_start: 0.7622 (m-30) cc_final: 0.7400 (m-30) REVERT: D 1528 THR cc_start: 0.8351 (t) cc_final: 0.8064 (p) REVERT: D 1532 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7965 (m) REVERT: D 1646 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7798 (mmmt) REVERT: D 1684 ASN cc_start: 0.8155 (m110) cc_final: 0.7738 (m110) REVERT: D 2024 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7454 (mp0) REVERT: D 2027 ASP cc_start: 0.8066 (m-30) cc_final: 0.7807 (m-30) REVERT: D 2353 GLU cc_start: 0.7636 (tt0) cc_final: 0.7433 (tt0) REVERT: D 2529 LYS cc_start: 0.8198 (tttp) cc_final: 0.7946 (ttmm) REVERT: D 2544 GLU cc_start: 0.8043 (mp0) cc_final: 0.7842 (mp0) REVERT: D 2610 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8530 (tp) outliers start: 181 outliers final: 88 residues processed: 1547 average time/residue: 3.0610 time to fit residues: 6441.2782 Evaluate side-chains 1510 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1405 time to evaluate : 8.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1284 GLN Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1319 ASP Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2580 LYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1427 GLU Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 1981 LEU Chi-restraints excluded: chain B residue 2006 SER Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2537 THR Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1463 THR Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 2183 GLU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain D residue 353 CYS Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 468 ASP Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1431 ILE Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2537 THR Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 3.9990 chunk 496 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 650 optimal weight: 6.9990 chunk 360 optimal weight: 3.9990 chunk 745 optimal weight: 0.9980 chunk 604 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 784 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 299 HIS A 460 ASN A 467 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS ** A1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 467 ASN B 601 ASN B 754 GLN B 976 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B1900 ASN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2528 GLN C 299 HIS ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D 609 HIS D1284 GLN D1685 GLN D1897 ASN D2145 GLN D2164 GLN D2528 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 75396 Z= 0.326 Angle : 0.481 5.796 101764 Z= 0.259 Chirality : 0.037 0.159 11572 Planarity : 0.004 0.086 12844 Dihedral : 8.414 150.759 10903 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.94 % Allowed : 13.51 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.17 (0.09), residues: 8952 helix: 2.32 (0.07), residues: 5676 sheet: -0.40 (0.19), residues: 676 loop : -0.00 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2601 HIS 0.008 0.001 HIS B 551 PHE 0.016 0.001 PHE A1286 TYR 0.015 0.001 TYR B2496 ARG 0.010 0.000 ARG D1507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1596 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1439 time to evaluate : 9.031 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 109 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8429 (mtmm) REVERT: A 403 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 511 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7760 (mm-30) REVERT: A 636 ASP cc_start: 0.8189 (m-30) cc_final: 0.7893 (m-30) REVERT: A 1193 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7232 (mm-40) REVERT: A 1284 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7927 (mm110) REVERT: A 1305 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 1324 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 1427 GLU cc_start: 0.6710 (mp0) cc_final: 0.6421 (mp0) REVERT: A 1528 THR cc_start: 0.8395 (t) cc_final: 0.8101 (p) REVERT: A 1646 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7809 (mmmt) REVERT: A 1684 ASN cc_start: 0.8148 (m110) cc_final: 0.7833 (m110) REVERT: A 1727 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7731 (ttt-90) REVERT: A 1735 LYS cc_start: 0.8474 (tttm) cc_final: 0.8228 (tttt) REVERT: A 1900 ASN cc_start: 0.8349 (m110) cc_final: 0.8066 (m-40) REVERT: A 2014 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 2027 ASP cc_start: 0.8037 (m-30) cc_final: 0.7696 (m-30) REVERT: B 98 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7910 (mt0) REVERT: B 109 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8469 (mtmm) REVERT: B 399 GLN cc_start: 0.7947 (mt0) cc_final: 0.7707 (mt0) REVERT: B 474 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7788 (mm-40) REVERT: B 511 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 588 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: B 608 LYS cc_start: 0.8254 (tptm) cc_final: 0.8037 (tppp) REVERT: B 653 CYS cc_start: 0.7422 (m) cc_final: 0.7126 (m) REVERT: B 705 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 1103 ASP cc_start: 0.7995 (m-30) cc_final: 0.7766 (m-30) REVERT: B 1193 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7663 (mm-40) REVERT: B 1208 ASP cc_start: 0.7585 (m-30) cc_final: 0.7064 (m-30) REVERT: B 1305 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8370 (p) REVERT: B 1319 ASP cc_start: 0.8343 (m-30) cc_final: 0.8073 (m-30) REVERT: B 1377 GLU cc_start: 0.7189 (tt0) cc_final: 0.6919 (tt0) REVERT: B 1448 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: B 1463 THR cc_start: 0.8357 (p) cc_final: 0.8128 (t) REVERT: B 1507 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7760 (ptm-80) REVERT: B 1684 ASN cc_start: 0.8157 (m-40) cc_final: 0.7920 (m110) REVERT: B 1783 GLU cc_start: 0.7972 (tt0) cc_final: 0.7716 (tt0) REVERT: B 2014 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 2021 ARG cc_start: 0.7493 (mpp-170) cc_final: 0.7021 (mtm-85) REVERT: B 2027 ASP cc_start: 0.8053 (m-30) cc_final: 0.7730 (m-30) REVERT: B 2282 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 2531 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 109 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8471 (mtmm) REVERT: C 403 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8462 (p) REVERT: C 511 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 604 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7856 (mttm) REVERT: C 768 MET cc_start: 0.8054 (mtp) cc_final: 0.7840 (mtm) REVERT: C 802 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (tt) REVERT: C 1208 ASP cc_start: 0.7589 (m-30) cc_final: 0.7030 (m-30) REVERT: C 1280 GLU cc_start: 0.7708 (mp0) cc_final: 0.7129 (mp0) REVERT: C 1284 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: C 1305 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8412 (p) REVERT: C 1395 ASP cc_start: 0.7443 (m-30) cc_final: 0.7241 (m-30) REVERT: C 1528 THR cc_start: 0.8326 (t) cc_final: 0.8057 (p) REVERT: C 1532 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8014 (m) REVERT: C 1646 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7860 (mmmt) REVERT: C 1684 ASN cc_start: 0.8162 (m110) cc_final: 0.7832 (m110) REVERT: C 1783 GLU cc_start: 0.8030 (tt0) cc_final: 0.7789 (tt0) REVERT: C 2027 ASP cc_start: 0.8083 (m-30) cc_final: 0.7768 (m-30) REVERT: C 2460 MET cc_start: 0.8950 (mmm) cc_final: 0.8668 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8171 (tttp) cc_final: 0.7887 (ttmm) REVERT: C 2531 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 109 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8392 (mtmm) REVERT: D 399 GLN cc_start: 0.7888 (mt0) cc_final: 0.7589 (mt0) REVERT: D 746 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8604 (tt) REVERT: D 793 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8637 (mp) REVERT: D 1182 MET cc_start: 0.7838 (tmm) cc_final: 0.7007 (tmm) REVERT: D 1193 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7554 (mm-40) REVERT: D 1305 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8401 (p) REVERT: D 1377 GLU cc_start: 0.7145 (tt0) cc_final: 0.6938 (tt0) REVERT: D 1395 ASP cc_start: 0.7624 (m-30) cc_final: 0.7366 (m-30) REVERT: D 1528 THR cc_start: 0.8361 (t) cc_final: 0.8036 (p) REVERT: D 1532 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7953 (m) REVERT: D 1646 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7789 (mmmt) REVERT: D 1684 ASN cc_start: 0.8147 (m110) cc_final: 0.7730 (m110) REVERT: D 2027 ASP cc_start: 0.8065 (m-30) cc_final: 0.7817 (m-30) REVERT: D 2529 LYS cc_start: 0.8203 (tttp) cc_final: 0.7948 (ttmm) REVERT: D 2610 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8517 (tp) outliers start: 157 outliers final: 92 residues processed: 1518 average time/residue: 3.2572 time to fit residues: 6746.1548 Evaluate side-chains 1518 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1408 time to evaluate : 8.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1284 GLN Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1465 GLU Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1727 ARG Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2580 LYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1427 GLU Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1507 ARG Chi-restraints excluded: chain B residue 1630 GLU Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 2006 SER Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2537 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 2183 GLU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2600 ASP Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1431 ILE Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 0.9980 chunk 786 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 513 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 874 optimal weight: 3.9990 chunk 726 optimal weight: 2.9990 chunk 404 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 459 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 299 HIS A 460 ASN A 467 ASN A 609 HIS A1284 GLN ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2528 GLN C 195 HIS C 299 HIS C 460 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D1284 GLN D1685 GLN D2145 GLN D2528 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 75396 Z= 0.253 Angle : 0.459 6.124 101764 Z= 0.246 Chirality : 0.036 0.158 11572 Planarity : 0.004 0.091 12844 Dihedral : 8.015 143.124 10903 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.84 % Allowed : 13.83 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.31 (0.09), residues: 8952 helix: 2.43 (0.07), residues: 5676 sheet: -0.38 (0.19), residues: 668 loop : 0.08 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D2601 HIS 0.007 0.001 HIS B 551 PHE 0.015 0.001 PHE B1484 TYR 0.014 0.001 TYR C2496 ARG 0.013 0.000 ARG C2021 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1596 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1447 time to evaluate : 8.977 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 109 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8420 (mtmm) REVERT: A 403 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 511 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 608 LYS cc_start: 0.8133 (tppp) cc_final: 0.7861 (tppt) REVERT: A 636 ASP cc_start: 0.8172 (m-30) cc_final: 0.7925 (m-30) REVERT: A 1193 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7177 (mm-40) REVERT: A 1305 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 1471 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8048 (m) REVERT: A 1528 THR cc_start: 0.8432 (t) cc_final: 0.8117 (p) REVERT: A 1646 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7800 (mmmt) REVERT: A 1684 ASN cc_start: 0.8144 (m110) cc_final: 0.7811 (m110) REVERT: A 1735 LYS cc_start: 0.8477 (tttm) cc_final: 0.8236 (tttt) REVERT: A 1784 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7781 (mpp80) REVERT: A 1900 ASN cc_start: 0.8327 (m110) cc_final: 0.8046 (m-40) REVERT: A 2014 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 2027 ASP cc_start: 0.8035 (m-30) cc_final: 0.7700 (m-30) REVERT: B 98 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7913 (mt0) REVERT: B 109 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8445 (mtmm) REVERT: B 399 GLN cc_start: 0.7934 (mt0) cc_final: 0.7698 (mt0) REVERT: B 474 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7786 (mm-40) REVERT: B 511 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 588 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: B 608 LYS cc_start: 0.8243 (tptm) cc_final: 0.7985 (tppt) REVERT: B 653 CYS cc_start: 0.7412 (m) cc_final: 0.7114 (m) REVERT: B 1103 ASP cc_start: 0.7986 (m-30) cc_final: 0.7764 (m-30) REVERT: B 1193 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7686 (mm-40) REVERT: B 1208 ASP cc_start: 0.7589 (m-30) cc_final: 0.7069 (m-30) REVERT: B 1305 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8411 (p) REVERT: B 1319 ASP cc_start: 0.8335 (m-30) cc_final: 0.8070 (m-30) REVERT: B 1377 GLU cc_start: 0.7154 (tt0) cc_final: 0.6942 (tt0) REVERT: B 1448 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7880 (mtt) REVERT: B 1463 THR cc_start: 0.8359 (p) cc_final: 0.8149 (t) REVERT: B 1507 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7556 (ttt-90) REVERT: B 1684 ASN cc_start: 0.8158 (m-40) cc_final: 0.7891 (m110) REVERT: B 1783 GLU cc_start: 0.7971 (tt0) cc_final: 0.7729 (tt0) REVERT: B 2014 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 2021 ARG cc_start: 0.7471 (mpp-170) cc_final: 0.7011 (mtm-85) REVERT: B 2024 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 2027 ASP cc_start: 0.8065 (m-30) cc_final: 0.7740 (m-30) REVERT: B 2282 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 2531 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7363 (mm-30) REVERT: C 109 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8466 (mtmm) REVERT: C 511 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 604 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7857 (mttm) REVERT: C 768 MET cc_start: 0.8069 (mtp) cc_final: 0.7833 (mtm) REVERT: C 802 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8148 (tt) REVERT: C 843 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 1208 ASP cc_start: 0.7604 (m-30) cc_final: 0.7050 (m-30) REVERT: C 1280 GLU cc_start: 0.7637 (mp0) cc_final: 0.6990 (mp0) REVERT: C 1284 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: C 1305 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8414 (p) REVERT: C 1330 ASP cc_start: 0.7408 (t0) cc_final: 0.7206 (t70) REVERT: C 1395 ASP cc_start: 0.7431 (m-30) cc_final: 0.7228 (m-30) REVERT: C 1484 PHE cc_start: 0.8532 (m-10) cc_final: 0.8228 (m-80) REVERT: C 1528 THR cc_start: 0.8392 (t) cc_final: 0.8130 (p) REVERT: C 1532 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8013 (m) REVERT: C 1646 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7847 (mmmt) REVERT: C 1684 ASN cc_start: 0.8166 (m110) cc_final: 0.7833 (m110) REVERT: C 1783 GLU cc_start: 0.8009 (tt0) cc_final: 0.7776 (tt0) REVERT: C 2021 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: C 2027 ASP cc_start: 0.8080 (m-30) cc_final: 0.7780 (m-30) REVERT: C 2460 MET cc_start: 0.8940 (mmm) cc_final: 0.8657 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8165 (tttp) cc_final: 0.7879 (ttmm) REVERT: C 2531 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7318 (mm-30) REVERT: D 109 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8419 (mtmm) REVERT: D 399 GLN cc_start: 0.7860 (mt0) cc_final: 0.7540 (mt0) REVERT: D 746 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8614 (tt) REVERT: D 793 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8664 (mp) REVERT: D 1048 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: D 1182 MET cc_start: 0.7841 (tmm) cc_final: 0.7037 (tmm) REVERT: D 1193 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7586 (mm-40) REVERT: D 1208 ASP cc_start: 0.7557 (m-30) cc_final: 0.7013 (m-30) REVERT: D 1305 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8413 (p) REVERT: D 1395 ASP cc_start: 0.7594 (m-30) cc_final: 0.7348 (m-30) REVERT: D 1425 GLU cc_start: 0.7596 (pt0) cc_final: 0.7377 (pt0) REVERT: D 1528 THR cc_start: 0.8480 (t) cc_final: 0.8203 (p) REVERT: D 1532 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7928 (m) REVERT: D 1646 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7786 (mmmt) REVERT: D 1684 ASN cc_start: 0.8152 (m110) cc_final: 0.7729 (m110) REVERT: D 2021 ARG cc_start: 0.7490 (mpp-170) cc_final: 0.7209 (mpp-170) REVERT: D 2027 ASP cc_start: 0.8071 (m-30) cc_final: 0.7809 (m-30) REVERT: D 2529 LYS cc_start: 0.8223 (tttp) cc_final: 0.7967 (ttmm) REVERT: D 2610 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (tp) outliers start: 149 outliers final: 85 residues processed: 1518 average time/residue: 3.1053 time to fit residues: 6374.3657 Evaluate side-chains 1511 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1408 time to evaluate : 8.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1502 LEU Chi-restraints excluded: chain B residue 1507 ARG Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 2006 SER Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2600 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1427 GLU Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 498 optimal weight: 2.9990 chunk 638 optimal weight: 2.9990 chunk 494 optimal weight: 2.9990 chunk 736 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 871 optimal weight: 9.9990 chunk 545 optimal weight: 2.9990 chunk 531 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 467 ASN A1285 HIS ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 299 HIS B 976 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B1900 ASN ** B2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2528 GLN C 299 HIS C 399 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D1094 GLN D1284 GLN D2145 GLN D2528 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 75396 Z= 0.463 Angle : 0.536 6.601 101764 Z= 0.290 Chirality : 0.040 0.171 11572 Planarity : 0.004 0.104 12844 Dihedral : 8.527 144.978 10903 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.18 % Allowed : 13.76 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.09), residues: 8952 helix: 2.13 (0.07), residues: 5676 sheet: -0.48 (0.19), residues: 676 loop : -0.21 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1127 HIS 0.013 0.001 HIS B 551 PHE 0.019 0.002 PHE D1286 TYR 0.016 0.002 TYR C2496 ARG 0.011 0.000 ARG D1507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1645 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1469 time to evaluate : 9.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8441 (mtmm) REVERT: A 511 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 608 LYS cc_start: 0.8222 (tppp) cc_final: 0.8021 (tppt) REVERT: A 764 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7916 (ttm) REVERT: A 1193 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7244 (mm-40) REVERT: A 1305 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 1528 THR cc_start: 0.8555 (t) cc_final: 0.8322 (p) REVERT: A 1646 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7818 (mmmt) REVERT: A 1684 ASN cc_start: 0.8138 (m110) cc_final: 0.7813 (m110) REVERT: A 1735 LYS cc_start: 0.8478 (tttm) cc_final: 0.8234 (tttt) REVERT: A 1784 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7785 (mpp80) REVERT: A 1900 ASN cc_start: 0.8349 (m110) cc_final: 0.8026 (m-40) REVERT: A 2014 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 2027 ASP cc_start: 0.8030 (m-30) cc_final: 0.7725 (m-30) REVERT: B 98 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7964 (mt0) REVERT: B 109 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8454 (mtmm) REVERT: B 399 GLN cc_start: 0.8008 (mt0) cc_final: 0.7763 (mt0) REVERT: B 511 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 588 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: B 608 LYS cc_start: 0.8304 (tptm) cc_final: 0.8081 (tppp) REVERT: B 610 ILE cc_start: 0.8734 (mm) cc_final: 0.8467 (mp) REVERT: B 653 CYS cc_start: 0.7420 (m) cc_final: 0.7141 (m) REVERT: B 1103 ASP cc_start: 0.8013 (m-30) cc_final: 0.7790 (m-30) REVERT: B 1193 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7713 (mm-40) REVERT: B 1208 ASP cc_start: 0.7584 (m-30) cc_final: 0.7063 (m-30) REVERT: B 1319 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: B 1377 GLU cc_start: 0.7221 (tt0) cc_final: 0.6956 (tt0) REVERT: B 1448 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: B 1463 THR cc_start: 0.8358 (p) cc_final: 0.8150 (t) REVERT: B 1507 ARG cc_start: 0.7960 (ptm-80) cc_final: 0.7588 (ttt-90) REVERT: B 1646 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7882 (mmmt) REVERT: B 1684 ASN cc_start: 0.8136 (m-40) cc_final: 0.7875 (m110) REVERT: B 1783 GLU cc_start: 0.8048 (tt0) cc_final: 0.7791 (tt0) REVERT: B 2014 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 2021 ARG cc_start: 0.7502 (mpp-170) cc_final: 0.7029 (mtm-85) REVERT: B 2024 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 2027 ASP cc_start: 0.8059 (m-30) cc_final: 0.7736 (m-30) REVERT: B 2150 GLU cc_start: 0.7946 (pm20) cc_final: 0.7739 (mp0) REVERT: B 2282 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7570 (mp) REVERT: B 2531 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7396 (mm-30) REVERT: C 109 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8468 (mtmm) REVERT: C 353 CYS cc_start: 0.8380 (m) cc_final: 0.7982 (t) REVERT: C 511 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7833 (mm-30) REVERT: C 604 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7866 (mttm) REVERT: C 1193 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7541 (mm-40) REVERT: C 1208 ASP cc_start: 0.7623 (m-30) cc_final: 0.7069 (m-30) REVERT: C 1280 GLU cc_start: 0.7747 (mp0) cc_final: 0.7175 (mp0) REVERT: C 1284 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: C 1305 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 1484 PHE cc_start: 0.8616 (m-10) cc_final: 0.8246 (m-80) REVERT: C 1532 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8113 (m) REVERT: C 1646 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7875 (mmmt) REVERT: C 1684 ASN cc_start: 0.8167 (m110) cc_final: 0.7815 (m110) REVERT: C 1783 GLU cc_start: 0.8057 (tt0) cc_final: 0.7806 (tt0) REVERT: C 2027 ASP cc_start: 0.8069 (m-30) cc_final: 0.7780 (m-30) REVERT: C 2460 MET cc_start: 0.8950 (mmm) cc_final: 0.8685 (mmp) REVERT: C 2529 LYS cc_start: 0.8161 (tttp) cc_final: 0.7874 (ttmm) REVERT: C 2531 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7370 (mm-30) REVERT: D 109 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8393 (mtmm) REVERT: D 399 GLN cc_start: 0.7918 (mt0) cc_final: 0.7695 (mt0) REVERT: D 746 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8623 (tt) REVERT: D 793 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (mp) REVERT: D 838 GLU cc_start: 0.7889 (tt0) cc_final: 0.7687 (tt0) REVERT: D 1048 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: D 1208 ASP cc_start: 0.7562 (m-30) cc_final: 0.7006 (m-30) REVERT: D 1305 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8412 (p) REVERT: D 1395 ASP cc_start: 0.7626 (m-30) cc_final: 0.7405 (m-30) REVERT: D 1507 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7568 (ttt-90) REVERT: D 1528 THR cc_start: 0.8449 (t) cc_final: 0.8217 (p) REVERT: D 1532 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8041 (m) REVERT: D 1646 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7821 (mmmt) REVERT: D 1684 ASN cc_start: 0.8138 (m110) cc_final: 0.7716 (m110) REVERT: D 2027 ASP cc_start: 0.8064 (m-30) cc_final: 0.7838 (m-30) REVERT: D 2529 LYS cc_start: 0.8193 (tttp) cc_final: 0.7941 (ttmm) REVERT: D 2610 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8604 (tp) outliers start: 176 outliers final: 103 residues processed: 1560 average time/residue: 3.2268 time to fit residues: 6913.3518 Evaluate side-chains 1541 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1423 time to evaluate : 8.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1358 ASP Chi-restraints excluded: chain A residue 1387 CYS Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 2006 SER Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1048 ASP Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1319 ASP Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 2006 SER Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2537 THR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 961 ASP Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1463 THR Chi-restraints excluded: chain C residue 1481 SER Chi-restraints excluded: chain C residue 1508 LEU Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 2183 GLU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2600 ASP Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1431 ILE Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1463 THR Chi-restraints excluded: chain D residue 1481 SER Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2537 THR Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 0.9990 chunk 347 optimal weight: 0.1980 chunk 520 optimal weight: 3.9990 chunk 262 optimal weight: 0.0980 chunk 171 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 chunk 553 optimal weight: 2.9990 chunk 593 optimal weight: 2.9990 chunk 430 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 684 optimal weight: 2.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 609 HIS ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2337 HIS A2528 GLN B 299 HIS B 460 ASN B 754 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B2337 HIS B2528 GLN C 289 HIS C 290 HIS C 299 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 713 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2528 GLN D 299 HIS D 460 ASN D 601 ASN D1284 GLN D1685 GLN D2145 GLN D2528 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 75396 Z= 0.145 Angle : 0.441 6.475 101764 Z= 0.235 Chirality : 0.035 0.158 11572 Planarity : 0.004 0.083 12844 Dihedral : 7.752 143.184 10901 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.39 % Allowed : 15.08 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.42 (0.09), residues: 8952 helix: 2.51 (0.07), residues: 5684 sheet: -0.33 (0.19), residues: 668 loop : 0.12 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2566 HIS 0.004 0.001 HIS A 609 PHE 0.011 0.001 PHE B 553 TYR 0.011 0.001 TYR B 633 ARG 0.011 0.000 ARG D1507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1562 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1450 time to evaluate : 8.975 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 109 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8405 (mtmm) REVERT: A 511 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 608 LYS cc_start: 0.8201 (tppp) cc_final: 0.7995 (tppt) REVERT: A 1193 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7274 (mm-40) REVERT: A 1305 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8351 (p) REVERT: A 1313 TYR cc_start: 0.8085 (m-80) cc_final: 0.6866 (m-80) REVERT: A 1377 GLU cc_start: 0.7158 (tt0) cc_final: 0.6931 (tt0) REVERT: A 1471 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (m) REVERT: A 1528 THR cc_start: 0.8444 (t) cc_final: 0.8146 (p) REVERT: A 1646 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7777 (mmmt) REVERT: A 1684 ASN cc_start: 0.8128 (m110) cc_final: 0.7802 (m110) REVERT: A 1735 LYS cc_start: 0.8464 (tttm) cc_final: 0.8222 (tttt) REVERT: A 1900 ASN cc_start: 0.8319 (m110) cc_final: 0.8044 (m110) REVERT: A 2005 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6703 (tt0) REVERT: A 2014 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 2027 ASP cc_start: 0.8033 (m-30) cc_final: 0.7711 (m-30) REVERT: B 98 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7922 (mt0) REVERT: B 109 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8434 (mtmm) REVERT: B 399 GLN cc_start: 0.7904 (mt0) cc_final: 0.7670 (mt0) REVERT: B 511 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 588 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: B 604 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7914 (mttm) REVERT: B 608 LYS cc_start: 0.8233 (tptm) cc_final: 0.7980 (tppt) REVERT: B 610 ILE cc_start: 0.8685 (mm) cc_final: 0.8418 (mp) REVERT: B 653 CYS cc_start: 0.7400 (m) cc_final: 0.7095 (m) REVERT: B 1193 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7512 (mm-40) REVERT: B 1208 ASP cc_start: 0.7584 (m-30) cc_final: 0.7083 (m-30) REVERT: B 1305 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 1319 ASP cc_start: 0.8323 (m-30) cc_final: 0.8077 (m-30) REVERT: B 1448 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7924 (mtt) REVERT: B 1507 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7436 (tmt90) REVERT: B 1684 ASN cc_start: 0.8158 (m-40) cc_final: 0.7866 (m110) REVERT: B 1783 GLU cc_start: 0.7973 (tt0) cc_final: 0.7741 (tt0) REVERT: B 2014 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 2021 ARG cc_start: 0.7486 (mpp-170) cc_final: 0.7185 (mpp-170) REVERT: B 2024 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 2027 ASP cc_start: 0.8057 (m-30) cc_final: 0.7728 (m-30) REVERT: B 2150 GLU cc_start: 0.7931 (pm20) cc_final: 0.7715 (mp0) REVERT: B 2282 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 2531 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 2581 THR cc_start: 0.8800 (m) cc_final: 0.8499 (p) REVERT: C 94 GLN cc_start: 0.8281 (tt0) cc_final: 0.7446 (tt0) REVERT: C 109 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8470 (mtmm) REVERT: C 511 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7810 (mm-30) REVERT: C 581 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7716 (mtp) REVERT: C 802 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8194 (tt) REVERT: C 843 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8133 (t0) REVERT: C 966 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7649 (mm-30) REVERT: C 1193 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7509 (mm-40) REVERT: C 1208 ASP cc_start: 0.7590 (m-30) cc_final: 0.7037 (m-30) REVERT: C 1305 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 1427 GLU cc_start: 0.6508 (mp0) cc_final: 0.6029 (mp0) REVERT: C 1507 ARG cc_start: 0.7798 (ttt-90) cc_final: 0.7558 (ttt-90) REVERT: C 1532 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8045 (m) REVERT: C 1684 ASN cc_start: 0.8161 (m110) cc_final: 0.7817 (m110) REVERT: C 1783 GLU cc_start: 0.7992 (tt0) cc_final: 0.7761 (tt0) REVERT: C 2027 ASP cc_start: 0.8077 (m-30) cc_final: 0.7777 (m-30) REVERT: C 2460 MET cc_start: 0.8938 (mmm) cc_final: 0.8652 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8154 (tttp) cc_final: 0.7876 (ttmm) REVERT: C 2531 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7300 (mm-30) REVERT: D 109 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8409 (mtmm) REVERT: D 793 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8686 (mp) REVERT: D 838 GLU cc_start: 0.7852 (tt0) cc_final: 0.7651 (tt0) REVERT: D 1048 ASP cc_start: 0.7946 (t0) cc_final: 0.7715 (m-30) REVERT: D 1208 ASP cc_start: 0.7569 (m-30) cc_final: 0.7025 (m-30) REVERT: D 1284 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: D 1305 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8362 (p) REVERT: D 1324 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7730 (mm-30) REVERT: D 1395 ASP cc_start: 0.7520 (m-30) cc_final: 0.7274 (m-30) REVERT: D 1528 THR cc_start: 0.8423 (t) cc_final: 0.8162 (p) REVERT: D 1531 MET cc_start: 0.7115 (mpm) cc_final: 0.6846 (mpm) REVERT: D 1532 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.7977 (m) REVERT: D 1646 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7764 (mmmt) REVERT: D 1684 ASN cc_start: 0.8168 (m110) cc_final: 0.7743 (m110) REVERT: D 2005 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6706 (tt0) REVERT: D 2027 ASP cc_start: 0.8069 (m-30) cc_final: 0.7803 (m-30) REVERT: D 2529 LYS cc_start: 0.8222 (tttp) cc_final: 0.7967 (ttmm) REVERT: D 2610 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (tp) outliers start: 112 outliers final: 69 residues processed: 1505 average time/residue: 3.1172 time to fit residues: 6377.2847 Evaluate side-chains 1496 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1409 time to evaluate : 8.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1385 ILE Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1507 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2327 ILE Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1284 GLN Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1385 ILE Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1986 MET Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1284 GLN Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1689 MET Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 1.9990 chunk 834 optimal weight: 3.9990 chunk 761 optimal weight: 4.9990 chunk 811 optimal weight: 3.9990 chunk 488 optimal weight: 4.9990 chunk 353 optimal weight: 0.8980 chunk 637 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 733 optimal weight: 4.9990 chunk 767 optimal weight: 4.9990 chunk 809 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 460 ASN A 467 ASN A 976 GLN ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 299 HIS B 460 ASN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B2528 GLN C 299 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D1284 GLN D1685 GLN D1900 ASN D2145 GLN D2528 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 75396 Z= 0.299 Angle : 0.479 6.571 101764 Z= 0.256 Chirality : 0.036 0.177 11572 Planarity : 0.004 0.099 12844 Dihedral : 7.859 145.038 10898 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.32 % Allowed : 15.62 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.28 (0.09), residues: 8952 helix: 2.42 (0.07), residues: 5684 sheet: -0.40 (0.19), residues: 668 loop : 0.02 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C2601 HIS 0.008 0.001 HIS B 551 PHE 0.020 0.001 PHE D1286 TYR 0.015 0.001 TYR C2496 ARG 0.012 0.000 ARG D1507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1538 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1431 time to evaluate : 9.073 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 109 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8431 (mtmm) REVERT: A 511 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 608 LYS cc_start: 0.8229 (tppp) cc_final: 0.8020 (tppt) REVERT: A 1193 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7313 (mm-40) REVERT: A 1305 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 1528 THR cc_start: 0.8500 (t) cc_final: 0.8266 (p) REVERT: A 1646 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7794 (mmmt) REVERT: A 1684 ASN cc_start: 0.8131 (m110) cc_final: 0.7800 (m110) REVERT: A 1735 LYS cc_start: 0.8474 (tttm) cc_final: 0.8235 (tttt) REVERT: A 1784 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7767 (mpp80) REVERT: A 1900 ASN cc_start: 0.8314 (m110) cc_final: 0.8031 (m-40) REVERT: A 2005 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: A 2014 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7915 (mm-30) REVERT: A 2027 ASP cc_start: 0.8035 (m-30) cc_final: 0.7722 (m-30) REVERT: B 98 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7923 (mt0) REVERT: B 109 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8444 (mtmm) REVERT: B 399 GLN cc_start: 0.7913 (mt0) cc_final: 0.7666 (mt0) REVERT: B 511 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 588 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: B 604 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7915 (mttm) REVERT: B 608 LYS cc_start: 0.8255 (tptm) cc_final: 0.8038 (tppp) REVERT: B 610 ILE cc_start: 0.8698 (mm) cc_final: 0.8441 (mp) REVERT: B 653 CYS cc_start: 0.7399 (m) cc_final: 0.7106 (m) REVERT: B 1193 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7535 (mm-40) REVERT: B 1208 ASP cc_start: 0.7593 (m-30) cc_final: 0.7075 (m-30) REVERT: B 1305 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 1319 ASP cc_start: 0.8344 (m-30) cc_final: 0.8074 (m-30) REVERT: B 1448 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: B 1464 LEU cc_start: 0.8911 (tm) cc_final: 0.8669 (tt) REVERT: B 1507 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7312 (ttt-90) REVERT: B 1513 TRP cc_start: 0.6703 (p-90) cc_final: 0.6107 (p-90) REVERT: B 1684 ASN cc_start: 0.8150 (m-40) cc_final: 0.7895 (m110) REVERT: B 1744 THR cc_start: 0.8690 (t) cc_final: 0.8470 (t) REVERT: B 1783 GLU cc_start: 0.8012 (tt0) cc_final: 0.7756 (tt0) REVERT: B 2005 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7030 (tt0) REVERT: B 2014 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 2021 ARG cc_start: 0.7471 (mpp-170) cc_final: 0.7143 (mpp-170) REVERT: B 2024 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7115 (mt-10) REVERT: B 2027 ASP cc_start: 0.8065 (m-30) cc_final: 0.7741 (m-30) REVERT: B 2150 GLU cc_start: 0.7939 (pm20) cc_final: 0.7726 (mp0) REVERT: B 2282 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 2531 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 2581 THR cc_start: 0.8795 (m) cc_final: 0.8514 (p) REVERT: C 109 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8468 (mtmm) REVERT: C 399 GLN cc_start: 0.8124 (mt0) cc_final: 0.7553 (mt0) REVERT: C 511 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 764 MET cc_start: 0.8089 (mtp) cc_final: 0.7871 (ttm) REVERT: C 802 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 843 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8179 (t0) REVERT: C 1193 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7513 (mm-40) REVERT: C 1208 ASP cc_start: 0.7611 (m-30) cc_final: 0.7063 (m-30) REVERT: C 1305 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8427 (p) REVERT: C 1507 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.7563 (ttt-90) REVERT: C 1532 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8087 (m) REVERT: C 1646 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7862 (mmmt) REVERT: C 1684 ASN cc_start: 0.8179 (m110) cc_final: 0.7826 (m110) REVERT: C 1783 GLU cc_start: 0.8022 (tt0) cc_final: 0.7793 (tt0) REVERT: C 2027 ASP cc_start: 0.8074 (m-30) cc_final: 0.7771 (m-30) REVERT: C 2460 MET cc_start: 0.8948 (mmm) cc_final: 0.8667 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8171 (tttp) cc_final: 0.7877 (ttmm) REVERT: C 2531 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7310 (mm-30) REVERT: D 109 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8406 (mtmm) REVERT: D 319 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8167 (mm-30) REVERT: D 838 GLU cc_start: 0.7882 (tt0) cc_final: 0.7682 (tt0) REVERT: D 1048 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: D 1208 ASP cc_start: 0.7555 (m-30) cc_final: 0.7003 (m-30) REVERT: D 1284 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7907 (mm110) REVERT: D 1305 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8386 (p) REVERT: D 1395 ASP cc_start: 0.7583 (m-30) cc_final: 0.7367 (m-30) REVERT: D 1528 THR cc_start: 0.8442 (t) cc_final: 0.8139 (p) REVERT: D 1531 MET cc_start: 0.7165 (mpm) cc_final: 0.6955 (mpm) REVERT: D 1532 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7967 (m) REVERT: D 1646 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7785 (mmmt) REVERT: D 1684 ASN cc_start: 0.8156 (m110) cc_final: 0.7719 (m110) REVERT: D 2005 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: D 2027 ASP cc_start: 0.8072 (m-30) cc_final: 0.7817 (m-30) REVERT: D 2529 LYS cc_start: 0.8194 (tttp) cc_final: 0.7940 (ttmm) REVERT: D 2610 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8526 (tp) outliers start: 107 outliers final: 70 residues processed: 1485 average time/residue: 3.0984 time to fit residues: 6277.3775 Evaluate side-chains 1501 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1414 time to evaluate : 8.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2580 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1507 ARG Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2327 ILE Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1452 CYS Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1986 MET Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1048 ASP Chi-restraints excluded: chain D residue 1284 GLN Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1502 LEU Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 1.9990 chunk 858 optimal weight: 1.9990 chunk 524 optimal weight: 0.7980 chunk 407 optimal weight: 1.9990 chunk 596 optimal weight: 4.9990 chunk 900 optimal weight: 0.0980 chunk 828 optimal weight: 4.9990 chunk 717 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 553 optimal weight: 0.7980 chunk 439 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 460 ASN A 467 ASN ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 289 HIS B 299 HIS B 460 ASN B 492 ASN B 976 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B1900 ASN B2528 GLN C 289 HIS C 299 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D1685 GLN D1900 ASN D2145 GLN D2528 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 75396 Z= 0.224 Angle : 0.459 7.052 101764 Z= 0.245 Chirality : 0.035 0.169 11572 Planarity : 0.004 0.094 12844 Dihedral : 7.663 145.870 10895 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.24 % Allowed : 15.65 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.38 (0.09), residues: 8952 helix: 2.49 (0.07), residues: 5680 sheet: -0.37 (0.19), residues: 668 loop : 0.09 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2601 HIS 0.005 0.001 HIS B 551 PHE 0.013 0.001 PHE D1235 TYR 0.016 0.001 TYR B1313 ARG 0.011 0.000 ARG D1507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1040 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 LYS 1040 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 LYS 1040 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 LYS 1040 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. Evaluate side-chains 1526 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1426 time to evaluate : 9.000 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: A 109 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8411 (mtmm) REVERT: A 511 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 608 LYS cc_start: 0.8226 (tppp) cc_final: 0.8019 (tppt) REVERT: A 1193 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7267 (mm-40) REVERT: A 1305 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 1528 THR cc_start: 0.8465 (t) cc_final: 0.8249 (p) REVERT: A 1646 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7784 (mmmt) REVERT: A 1684 ASN cc_start: 0.8126 (m110) cc_final: 0.7797 (m110) REVERT: A 1735 LYS cc_start: 0.8469 (tttm) cc_final: 0.8228 (tttt) REVERT: A 1784 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7773 (mpp80) REVERT: A 1900 ASN cc_start: 0.8314 (m110) cc_final: 0.8033 (m110) REVERT: A 2005 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: A 2014 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 2027 ASP cc_start: 0.8037 (m-30) cc_final: 0.7713 (m-30) REVERT: B 98 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7932 (mt0) REVERT: B 109 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8439 (mtmm) REVERT: B 399 GLN cc_start: 0.7904 (mt0) cc_final: 0.7660 (mt0) REVERT: B 511 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 588 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: B 604 LYS cc_start: 0.8144 (ttmm) cc_final: 0.7919 (mttm) REVERT: B 608 LYS cc_start: 0.8241 (tptm) cc_final: 0.7991 (tppt) REVERT: B 610 ILE cc_start: 0.8686 (mm) cc_final: 0.8433 (mp) REVERT: B 653 CYS cc_start: 0.7395 (m) cc_final: 0.7099 (m) REVERT: B 1193 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7485 (mm-40) REVERT: B 1208 ASP cc_start: 0.7590 (m-30) cc_final: 0.7068 (m-30) REVERT: B 1305 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 1319 ASP cc_start: 0.8333 (m-30) cc_final: 0.8082 (m-30) REVERT: B 1448 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7968 (mtt) REVERT: B 1464 LEU cc_start: 0.8911 (tm) cc_final: 0.8662 (tt) REVERT: B 1507 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7449 (tmt90) REVERT: B 1513 TRP cc_start: 0.6658 (p-90) cc_final: 0.6118 (p-90) REVERT: B 1684 ASN cc_start: 0.8155 (m-40) cc_final: 0.7890 (m110) REVERT: B 1735 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8228 (ttpp) REVERT: B 1783 GLU cc_start: 0.8008 (tt0) cc_final: 0.7755 (tt0) REVERT: B 2005 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: B 2014 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 2021 ARG cc_start: 0.7460 (mpp-170) cc_final: 0.7124 (mpp-170) REVERT: B 2024 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7105 (mt-10) REVERT: B 2027 ASP cc_start: 0.8065 (m-30) cc_final: 0.7744 (m-30) REVERT: B 2150 GLU cc_start: 0.7936 (pm20) cc_final: 0.7721 (mp0) REVERT: B 2282 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7585 (mp) REVERT: B 2531 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 2581 THR cc_start: 0.8804 (m) cc_final: 0.8533 (p) REVERT: C 109 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8464 (mtmm) REVERT: C 511 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7820 (mm-30) REVERT: C 540 GLU cc_start: 0.6855 (tt0) cc_final: 0.6067 (tt0) REVERT: C 764 MET cc_start: 0.8064 (mtp) cc_final: 0.7856 (ttm) REVERT: C 802 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (tt) REVERT: C 843 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (t0) REVERT: C 1193 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7519 (mm-40) REVERT: C 1208 ASP cc_start: 0.7595 (m-30) cc_final: 0.7046 (m-30) REVERT: C 1305 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8417 (p) REVERT: C 1339 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8410 (tmmm) REVERT: C 1507 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: C 1532 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8054 (m) REVERT: C 1646 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7858 (mmmt) REVERT: C 1684 ASN cc_start: 0.8173 (m110) cc_final: 0.7822 (m110) REVERT: C 1783 GLU cc_start: 0.8012 (tt0) cc_final: 0.7768 (tt0) REVERT: C 2027 ASP cc_start: 0.8080 (m-30) cc_final: 0.7779 (m-30) REVERT: C 2460 MET cc_start: 0.8945 (mmm) cc_final: 0.8665 (OUTLIER) REVERT: C 2529 LYS cc_start: 0.8158 (tttp) cc_final: 0.7869 (ttmm) REVERT: C 2531 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 109 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8410 (mtmm) REVERT: D 319 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 544 GLN cc_start: 0.7040 (tm-30) cc_final: 0.5683 (tt0) REVERT: D 793 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 838 GLU cc_start: 0.7880 (tt0) cc_final: 0.7679 (tt0) REVERT: D 1208 ASP cc_start: 0.7558 (m-30) cc_final: 0.7006 (m-30) REVERT: D 1305 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8382 (p) REVERT: D 1395 ASP cc_start: 0.7538 (m-30) cc_final: 0.7295 (m-30) REVERT: D 1528 THR cc_start: 0.8421 (t) cc_final: 0.8108 (p) REVERT: D 1531 MET cc_start: 0.7161 (mpm) cc_final: 0.6949 (mpm) REVERT: D 1532 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.7994 (m) REVERT: D 1646 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7775 (mmmt) REVERT: D 1684 ASN cc_start: 0.8150 (m110) cc_final: 0.7704 (m110) REVERT: D 2005 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: D 2027 ASP cc_start: 0.8065 (m-30) cc_final: 0.7811 (m-30) REVERT: D 2529 LYS cc_start: 0.8200 (tttp) cc_final: 0.7950 (ttmm) REVERT: D 2610 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (tp) outliers start: 100 outliers final: 73 residues processed: 1483 average time/residue: 3.2014 time to fit residues: 6493.6923 Evaluate side-chains 1494 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1404 time to evaluate : 8.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1395 ASP Chi-restraints excluded: chain A residue 1452 CYS Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1481 SER Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1986 MET Chi-restraints excluded: chain A residue 2005 GLU Chi-restraints excluded: chain A residue 2169 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2282 LEU Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2577 VAL Chi-restraints excluded: chain A residue 2580 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 1305 THR Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1448 MET Chi-restraints excluded: chain B residue 1481 SER Chi-restraints excluded: chain B residue 1507 ARG Chi-restraints excluded: chain B residue 1640 SER Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2282 LEU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2327 ILE Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 843 ASN Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 993 VAL Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1305 THR Chi-restraints excluded: chain C residue 1339 LYS Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1431 ILE Chi-restraints excluded: chain C residue 1532 VAL Chi-restraints excluded: chain C residue 1743 SER Chi-restraints excluded: chain C residue 1986 MET Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 793 LEU Chi-restraints excluded: chain D residue 993 VAL Chi-restraints excluded: chain D residue 1305 THR Chi-restraints excluded: chain D residue 1388 THR Chi-restraints excluded: chain D residue 1452 CYS Chi-restraints excluded: chain D residue 1532 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 2005 GLU Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 1.9990 chunk 763 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 661 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 718 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 737 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 132 optimal weight: 0.1980 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 460 ASN A 467 ASN A 609 HIS ** A1288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN B 289 HIS B 299 HIS B 460 ASN B 976 GLN ** B1284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN B2528 GLN C 289 HIS C 299 HIS ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 976 GLN C1685 GLN C1900 ASN C2145 GLN ** C2337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS D 460 ASN D 601 ASN D1685 GLN D1900 ASN D2145 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112337 restraints weight = 312224.305| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.09 r_work: 0.3217 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 75396 Z= 0.279 Angle : 0.474 6.749 101764 Z= 0.254 Chirality : 0.036 0.157 11572 Planarity : 0.004 0.108 12844 Dihedral : 7.714 148.586 10895 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.42 % Allowed : 15.56 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 2.30 (0.09), residues: 8952 helix: 2.44 (0.07), residues: 5680 sheet: -0.40 (0.19), residues: 668 loop : 0.03 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1127 HIS 0.007 0.001 HIS B 551 PHE 0.018 0.001 PHE A1484 TYR 0.016 0.001 TYR B 633 ARG 0.012 0.000 ARG D1507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 83344.72 seconds wall clock time: 1417 minutes 24.40 seconds (85044.40 seconds total)