Starting phenix.real_space_refine on Fri Mar 22 20:18:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkh_41351/03_2024/8tkh_41351_trim_updated.pdb" } resolution = 3.5 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= -0.001 sd= 0.036 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 24 5.49 5 S 460 5.16 5 C 46468 2.51 5 N 12484 2.21 5 O 13532 1.98 5 H 72844 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 105": "OD1" <-> "OD2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A GLU 1033": "OE1" <-> "OE2" Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1910": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1942": "OE1" <-> "OE2" Residue "A GLU 1946": "OE1" <-> "OE2" Residue "A GLU 1954": "OE1" <-> "OE2" Residue "A GLU 2043": "OE1" <-> "OE2" Residue "A GLU 2160": "OE1" <-> "OE2" Residue "A PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2398": "OE1" <-> "OE2" Residue "A GLU 2452": "OE1" <-> "OE2" Residue "A PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1033": "OE1" <-> "OE2" Residue "B GLU 1050": "OE1" <-> "OE2" Residue "B PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1604": "OE1" <-> "OE2" Residue "B GLU 1783": "OE1" <-> "OE2" Residue "B GLU 1954": "OE1" <-> "OE2" Residue "B GLU 2014": "OE1" <-> "OE2" Residue "B GLU 2043": "OE1" <-> "OE2" Residue "B GLU 2118": "OE1" <-> "OE2" Residue "B GLU 2183": "OE1" <-> "OE2" Residue "B PHE 2388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2398": "OE1" <-> "OE2" Residue "B ASP 2478": "OD1" <-> "OD2" Residue "B GLU 2487": "OE1" <-> "OE2" Residue "B GLU 2532": "OE1" <-> "OE2" Residue "B GLU 2562": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C GLU 616": "OE1" <-> "OE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C GLU 880": "OE1" <-> "OE2" Residue "C GLU 973": "OE1" <-> "OE2" Residue "C TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1066": "OD1" <-> "OD2" Residue "C ASP 1762": "OD1" <-> "OD2" Residue "C PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1931": "OE1" <-> "OE2" Residue "C GLU 1954": "OE1" <-> "OE2" Residue "C GLU 2014": "OE1" <-> "OE2" Residue "C GLU 2118": "OE1" <-> "OE2" Residue "C GLU 2183": "OE1" <-> "OE2" Residue "C GLU 2398": "OE1" <-> "OE2" Residue "C GLU 2562": "OE1" <-> "OE2" Residue "C ASP 2582": "OD1" <-> "OD2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 485": "OD1" <-> "OD2" Residue "D PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 966": "OE1" <-> "OE2" Residue "D GLU 1033": "OE1" <-> "OE2" Residue "D PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 1910": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1912": "OD1" <-> "OD2" Residue "D TYR 1928": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1954": "OE1" <-> "OE2" Residue "D ASP 1977": "OD1" <-> "OD2" Residue "D ASP 1987": "OD1" <-> "OD2" Residue "D GLU 2014": "OE1" <-> "OE2" Residue "D ASP 2027": "OD1" <-> "OD2" Residue "D GLU 2043": "OE1" <-> "OE2" Residue "D GLU 2118": "OE1" <-> "OE2" Residue "D GLU 2149": "OE1" <-> "OE2" Residue "D GLU 2163": "OE1" <-> "OE2" Residue "D GLU 2183": "OE1" <-> "OE2" Residue "D PHE 2222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2398": "OE1" <-> "OE2" Residue "D ASP 2478": "OD1" <-> "OD2" Residue "D GLU 2557": "OE1" <-> "OE2" Residue "D GLU 2562": "OE1" <-> "OE2" Residue "D PHE 2571": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 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: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 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: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 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: 36398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2268, 36398 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34872 SG CYS A2538 155.199 138.469 109.002 1.00 54.92 S ATOM 34921 SG CYS A2541 153.236 139.520 106.926 1.00 31.87 S ATOM 71270 SG CYS B2538 131.923 154.158 109.014 1.00 53.52 S ATOM 71319 SG CYS B2541 130.850 152.199 106.944 1.00 46.72 S ATOM A05X0 SG CYS C2538 115.707 130.792 109.010 1.00 56.53 S ATOM A05YD SG CYS C2541 117.670 129.740 106.934 1.00 39.14 S ATOM A0Y02 SG CYS D2538 139.012 115.087 109.018 1.00 55.58 S ATOM A0Y1F SG CYS D2541 140.082 117.047 106.949 1.00 47.41 S Time building chain proxies: 45.51, per 1000 atoms: 0.31 Number of scatterers: 145816 At special positions: 0 Unit cell: (271.754, 270.102, 193.284, 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 24 15.00 O 13532 8.00 N 12484 7.00 C 46468 6.00 H 72844 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 95.09 Conformation dependent library (CDL) restraints added in 9.5 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 B3001 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2541 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2538 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C3001 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2541 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2538 " pdb=" ZN D3001 " pdb="ZN ZN D3001 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D3001 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2541 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " Number of angles added : 5 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: 416 helices and 36 sheets defined 71.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.06 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 5.321A 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: 4.154A pdb=" N CYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.922A 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: 5.254A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.798A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.220A 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 removed outlier: 3.683A pdb=" N ASN A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.661A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 Proline residue: A 548 - end of helix removed outlier: 3.683A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.296A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.530A pdb=" N GLN A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 586' 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 removed outlier: 3.582A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.800A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 658 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.977A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.097A 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 756 removed outlier: 4.020A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 5.282A pdb=" N GLU A 767 " --> pdb=" O CYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 820 removed outlier: 4.229A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 5.203A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 Processing helix chain 'A' and resid 877 through 893 removed outlier: 4.017A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1003 removed outlier: 3.575A pdb=" N MET A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Proline residue: A1003 - end of helix Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.733A pdb=" N MET A1035 " --> pdb=" O GLN A1031 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 4.300A pdb=" N SER A1043 " --> pdb=" O GLY A1039 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU A1045 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1065 removed outlier: 3.911A pdb=" N MET A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.888A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1096 removed outlier: 5.444A pdb=" N GLN A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1124 Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 3.686A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A1172 " --> pdb=" O ASN A1168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 removed outlier: 4.930A pdb=" N ARG A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1212 removed outlier: 3.692A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 6.261A pdb=" N MET A1222 " --> pdb=" O ASP A1218 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU A1223 " --> pdb=" O ALA A1219 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A1230 " --> pdb=" O ARG A1226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A1237 " --> pdb=" O GLN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 4.389A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 removed outlier: 4.521A pdb=" N ALA A1261 " --> pdb=" O GLY A1257 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.751A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.853A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.875A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.902A pdb=" N ASN A1327 " --> pdb=" O THR A1323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A1328 " --> pdb=" O GLU A1324 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 3.866A pdb=" N ALA A1351 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A1352 " --> pdb=" O MET A1348 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A1353 " --> pdb=" O MET A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 3.771A pdb=" N ALA A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 4.125A pdb=" N GLU A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A1389 " --> pdb=" O ILE A1385 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.978A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 removed outlier: 4.953A pdb=" N THR A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A1458 " --> pdb=" O LYS A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.612A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1488 removed outlier: 4.551A pdb=" N ASN A1487 " --> pdb=" O PRO A1483 " (cutoff:3.500A) removed outlier: 4.774A 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: 4.048A pdb=" N HIS A1494 " --> pdb=" O SER A1490 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN A1495 " --> pdb=" O LEU A1491 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A1496 " --> pdb=" O GLN A1492 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) removed outlier: 5.459A 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: 4.149A pdb=" N GLY A1520 " --> pdb=" O GLN A1516 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1522 " --> pdb=" O HIS A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 removed outlier: 3.842A pdb=" N MET A1551 " --> pdb=" O HIS A1547 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A1553 " --> pdb=" O SER A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1624 removed outlier: 3.813A 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: 3.746A pdb=" N LYS A1652 " --> pdb=" O ILE A1648 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A1653 " --> pdb=" O GLN A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 5.011A 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: 3.756A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 Processing helix chain 'A' and resid 1902 through 1916 removed outlier: 3.624A pdb=" N GLU A1906 " --> pdb=" O ASN A1902 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A1916 " --> pdb=" O ASP A1912 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 4.198A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 3.777A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1931 through 1949 removed outlier: 4.551A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 5.121A 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: 3.925A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 3.776A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 removed outlier: 3.755A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 3.572A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 removed outlier: 3.978A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG A2039 " --> pdb=" O GLN A2035 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU A2040 " --> pdb=" O GLU A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2065 removed outlier: 4.179A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A2064 " --> pdb=" O LEU A2060 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS A2065 " --> pdb=" O SER A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2073 Proline residue: A2073 - end of helix Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 3.998A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.356A 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 2172 through 2190 removed outlier: 4.462A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2191 through 2223 removed outlier: 3.691A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) Processing helix chain 'A' and resid 2261 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.247A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2318 removed outlier: 5.650A 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: 4.686A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.828A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2390 Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 4.020A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.599A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.584A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.187A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2549' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2607 through 2648 removed outlier: 4.984A pdb=" N ASN A2613 " --> pdb=" O SER A2609 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 5.320A 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: 4.154A pdb=" N CYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.922A 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: 5.254A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.799A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.220A 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 removed outlier: 3.683A pdb=" N ASN B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.662A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 565 Proline residue: B 548 - end of helix removed outlier: 3.683A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.297A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 removed outlier: 3.529A pdb=" N GLN B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 586' 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 removed outlier: 3.582A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.799A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 658 Processing helix chain 'B' and resid 661 through 666 removed outlier: 3.977A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.097A 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 756 removed outlier: 4.021A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 5.282A pdb=" N GLU B 767 " --> pdb=" O CYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 811 through 820 removed outlier: 4.230A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 828 Processing helix chain 'B' and resid 830 through 848 removed outlier: 5.203A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 Processing helix chain 'B' and resid 877 through 893 removed outlier: 4.017A pdb=" N ARG B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1003 removed outlier: 3.576A pdb=" N MET B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Proline residue: B1003 - end of helix Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.733A pdb=" N MET B1035 " --> pdb=" O GLN B1031 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1047 removed outlier: 4.300A pdb=" N SER B1043 " --> pdb=" O GLY B1039 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B1045 " --> pdb=" O THR B1041 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL B1047 " --> pdb=" O SER B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1065 removed outlier: 3.911A pdb=" N MET B1064 " --> pdb=" O ILE B1060 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.889A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1096 removed outlier: 5.444A pdb=" N GLN B1096 " --> pdb=" O PHE B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1124 Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 3.687A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B1171 " --> pdb=" O GLU B1167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B1172 " --> pdb=" O ASN B1168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 removed outlier: 4.930A pdb=" N ARG B1190 " --> pdb=" O GLY B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1212 removed outlier: 3.692A pdb=" N ILE B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1237 removed outlier: 6.262A pdb=" N MET B1222 " --> pdb=" O ASP B1218 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU B1223 " --> pdb=" O ALA B1219 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE B1224 " --> pdb=" O LYS B1220 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN B1230 " --> pdb=" O ARG B1226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS B1236 " --> pdb=" O LEU B1232 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B1237 " --> pdb=" O GLN B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 4.390A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 removed outlier: 4.522A pdb=" N ALA B1261 " --> pdb=" O GLY B1257 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B1262 " --> pdb=" O LEU B1258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B1263 " --> pdb=" O LEU B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1271 through 1278 removed outlier: 3.751A pdb=" N GLU B1277 " --> pdb=" O GLN B1273 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.853A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 3.875A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B1307 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.902A pdb=" N ASN B1327 " --> pdb=" O THR B1323 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B1328 " --> pdb=" O GLU B1324 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 removed outlier: 3.866A pdb=" N ALA B1351 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B1352 " --> pdb=" O MET B1348 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B1353 " --> pdb=" O MET B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 3.770A pdb=" N ALA B1376 " --> pdb=" O LEU B1372 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B1377 " --> pdb=" O ALA B1373 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 4.126A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B1389 " --> pdb=" O ILE B1385 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU B1390 " --> pdb=" O LYS B1386 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.502A 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: 3.979A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 removed outlier: 4.953A pdb=" N THR B1439 " --> pdb=" O ASN B1435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B1458 " --> pdb=" O LYS B1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.612A pdb=" N VAL B1471 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B1482 " --> pdb=" O ALA B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1488 removed outlier: 4.551A pdb=" N ASN B1487 " --> pdb=" O PRO B1483 " (cutoff:3.500A) removed outlier: 4.774A 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: 4.048A pdb=" N HIS B1494 " --> pdb=" O SER B1490 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN B1495 " --> pdb=" O LEU B1491 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B1496 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 5.459A 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: 4.150A pdb=" N GLY B1520 " --> pdb=" O GLN B1516 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER B1521 " --> pdb=" O GLN B1517 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B1522 " --> pdb=" O HIS B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 removed outlier: 3.841A pdb=" N MET B1551 " --> pdb=" O HIS B1547 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B1553 " --> pdb=" O SER B1549 " (cutoff:3.500A) Processing helix chain 'B' and resid 1587 through 1624 removed outlier: 3.813A 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: 3.745A pdb=" N LYS B1652 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 5.011A 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: 3.756A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 Processing helix chain 'B' and resid 1902 through 1916 removed outlier: 3.624A pdb=" N GLU B1906 " --> pdb=" O ASN B1902 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B1916 " --> pdb=" O ASP B1912 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 4.198A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 3.777A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1931 through 1949 removed outlier: 4.551A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 5.122A 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: 3.925A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 3.776A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 removed outlier: 3.755A pdb=" N MET B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 3.572A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2040 removed outlier: 3.978A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B2037 " --> pdb=" O TYR B2033 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B2039 " --> pdb=" O GLN B2035 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU B2040 " --> pdb=" O GLU B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2065 removed outlier: 4.179A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B2064 " --> pdb=" O LEU B2060 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B2065 " --> pdb=" O SER B2061 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2073 Proline residue: B2073 - end of helix Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 3.997A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.356A 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 2172 through 2190 removed outlier: 4.461A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) Processing helix chain 'B' and resid 2191 through 2223 removed outlier: 3.692A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2261 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.246A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2318 removed outlier: 5.649A 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: 4.687A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 3.828A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2390 Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 4.021A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.599A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.584A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.187A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2607 through 2648 removed outlier: 4.983A pdb=" N ASN B2613 " --> pdb=" O SER B2609 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B2614 " --> pdb=" O LEU B2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.320A 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: 4.154A pdb=" N CYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.921A 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: 5.254A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.798A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.220A 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 removed outlier: 3.683A pdb=" N ASN C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.661A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 Proline residue: C 548 - end of helix removed outlier: 3.684A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.297A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 removed outlier: 3.530A pdb=" N GLN C 584 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 585 " --> pdb=" O MET C 581 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY C 586 " --> pdb=" O GLN C 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 580 through 586' 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 removed outlier: 3.583A pdb=" N VAL C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.800A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 658 Processing helix chain 'C' and resid 661 through 666 removed outlier: 3.977A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.097A 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 756 removed outlier: 4.020A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 756 " --> pdb=" O SER C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 5.282A pdb=" N GLU C 767 " --> pdb=" O CYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 820 removed outlier: 4.229A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 828 Processing helix chain 'C' and resid 830 through 848 removed outlier: 5.203A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 874 Processing helix chain 'C' and resid 877 through 893 removed outlier: 4.017A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1003 removed outlier: 3.574A pdb=" N MET C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Proline residue: C1003 - end of helix Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.732A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1047 removed outlier: 4.300A pdb=" N SER C1043 " --> pdb=" O GLY C1039 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET C1044 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU C1045 " --> pdb=" O THR C1041 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL C1047 " --> pdb=" O SER C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1065 removed outlier: 3.911A pdb=" N MET C1064 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.888A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1096 removed outlier: 5.444A pdb=" N GLN C1096 " --> pdb=" O PHE C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1124 Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 3.686A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 removed outlier: 4.930A pdb=" N ARG C1190 " --> pdb=" O GLY C1186 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1212 removed outlier: 3.692A pdb=" N ILE C1212 " --> pdb=" O ASP C1208 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 6.261A pdb=" N MET C1222 " --> pdb=" O ASP C1218 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU C1223 " --> pdb=" O ALA C1219 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C1224 " --> pdb=" O LYS C1220 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN C1230 " --> pdb=" O ARG C1226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C1236 " --> pdb=" O LEU C1232 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C1237 " --> pdb=" O GLN C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 4.389A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 removed outlier: 4.521A pdb=" N ALA C1261 " --> pdb=" O GLY C1257 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C1263 " --> pdb=" O LEU C1259 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1278 removed outlier: 3.751A pdb=" N GLU C1277 " --> pdb=" O GLN C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.853A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.875A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.902A pdb=" N ASN C1327 " --> pdb=" O THR C1323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C1328 " --> pdb=" O GLU C1324 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 removed outlier: 3.865A pdb=" N ALA C1351 " --> pdb=" O ASP C1347 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA C1352 " --> pdb=" O MET C1348 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C1353 " --> pdb=" O MET C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 3.771A pdb=" N ALA C1376 " --> pdb=" O LEU C1372 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C1377 " --> pdb=" O ALA C1373 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1392 removed outlier: 4.125A pdb=" N GLU C1384 " --> pdb=" O ASN C1380 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C1385 " --> pdb=" O VAL C1381 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C1389 " --> pdb=" O ILE C1385 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU C1390 " --> pdb=" O LYS C1386 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.502A 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: 3.978A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 removed outlier: 4.953A pdb=" N THR C1439 " --> pdb=" O ASN C1435 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C1458 " --> pdb=" O LYS C1454 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.613A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C1482 " --> pdb=" O ALA C1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 1483 through 1488 removed outlier: 4.551A pdb=" N ASN C1487 " --> pdb=" O PRO C1483 " (cutoff:3.500A) removed outlier: 4.773A 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: 4.048A pdb=" N HIS C1494 " --> pdb=" O SER C1490 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN C1495 " --> pdb=" O LEU C1491 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) removed outlier: 5.458A 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: 4.150A pdb=" N GLY C1520 " --> pdb=" O GLN C1516 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C1522 " --> pdb=" O HIS C1518 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1553 removed outlier: 3.842A pdb=" N MET C1551 " --> pdb=" O HIS C1547 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER C1553 " --> pdb=" O SER C1549 " (cutoff:3.500A) Processing helix chain 'C' and resid 1587 through 1624 removed outlier: 3.813A 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: 3.746A pdb=" N LYS C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C1653 " --> pdb=" O GLN C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 5.011A 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: 3.755A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 removed outlier: 3.625A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C1916 " --> pdb=" O ASP C1912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 4.198A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 3.777A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1931 through 1949 removed outlier: 4.551A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 5.122A 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: 3.925A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 3.776A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 removed outlier: 3.754A pdb=" N MET C2004 " --> pdb=" O LEU C2000 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 3.572A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2040 removed outlier: 3.978A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG C2039 " --> pdb=" O GLN C2035 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU C2040 " --> pdb=" O GLU C2036 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2065 removed outlier: 4.178A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C2064 " --> pdb=" O LEU C2060 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS C2065 " --> pdb=" O SER C2061 " (cutoff:3.500A) Processing helix chain 'C' and resid 2066 through 2073 Proline residue: C2073 - end of helix Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 3.998A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.356A 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 2172 through 2190 removed outlier: 4.462A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) Processing helix chain 'C' and resid 2191 through 2223 removed outlier: 3.691A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) Processing helix chain 'C' and resid 2261 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.247A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2318 removed outlier: 5.649A 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: 4.687A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 3.829A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 4.020A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.599A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.584A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.187A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2607 through 2648 removed outlier: 4.984A pdb=" N ASN C2613 " --> pdb=" O SER C2609 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 4.220A pdb=" N GLY D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.320A 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: 4.155A pdb=" N CYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.922A 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: 5.254A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.799A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.220A 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 removed outlier: 3.683A pdb=" N ASN D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.662A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 Proline residue: D 548 - end of helix removed outlier: 3.684A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.297A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 removed outlier: 3.530A pdb=" N GLN D 584 " --> pdb=" O MET D 580 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLY D 586 " --> pdb=" O GLN D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 580 through 586' 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 removed outlier: 3.581A pdb=" N VAL D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.800A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 658 Processing helix chain 'D' and resid 661 through 666 removed outlier: 3.977A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.096A 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 756 removed outlier: 4.020A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY D 756 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 5.283A pdb=" N GLU D 767 " --> pdb=" O CYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 820 removed outlier: 4.229A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 828 Processing helix chain 'D' and resid 830 through 848 removed outlier: 5.203A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 874 Processing helix chain 'D' and resid 877 through 893 removed outlier: 4.017A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1003 removed outlier: 3.575A pdb=" N MET D 965 " --> pdb=" O ASP D 961 " (cutoff:3.500A) Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1037 removed outlier: 3.733A pdb=" N MET D1035 " --> pdb=" O GLN D1031 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY D1037 " --> pdb=" O GLU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1047 removed outlier: 4.299A pdb=" N SER D1043 " --> pdb=" O GLY D1039 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET D1044 " --> pdb=" O LYS D1040 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU D1045 " --> pdb=" O THR D1041 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL D1047 " --> pdb=" O SER D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1065 removed outlier: 3.911A pdb=" N MET D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.888A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1096 removed outlier: 5.444A pdb=" N GLN D1096 " --> pdb=" O PHE D1092 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1124 Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 3.686A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE D1171 " --> pdb=" O GLU D1167 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL D1172 " --> pdb=" O ASN D1168 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 removed outlier: 4.930A pdb=" N ARG D1190 " --> pdb=" O GLY D1186 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 removed outlier: 3.693A pdb=" N ILE D1212 " --> pdb=" O ASP D1208 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 6.261A pdb=" N MET D1222 " --> pdb=" O ASP D1218 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU D1223 " --> pdb=" O ALA D1219 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE D1224 " --> pdb=" O LYS D1220 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D1230 " --> pdb=" O ARG D1226 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS D1236 " --> pdb=" O LEU D1232 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D1237 " --> pdb=" O GLN D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 4.389A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 removed outlier: 4.521A pdb=" N ALA D1261 " --> pdb=" O GLY D1257 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D1262 " --> pdb=" O LEU D1258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D1263 " --> pdb=" O LEU D1259 " (cutoff:3.500A) Processing helix chain 'D' and resid 1271 through 1278 removed outlier: 3.750A pdb=" N GLU D1277 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.852A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 3.875A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.901A pdb=" N ASN D1327 " --> pdb=" O THR D1323 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D1328 " --> pdb=" O GLU D1324 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 removed outlier: 3.866A pdb=" N ALA D1351 " --> pdb=" O ASP D1347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D1352 " --> pdb=" O MET D1348 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D1353 " --> pdb=" O MET D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.771A pdb=" N ALA D1376 " --> pdb=" O LEU D1372 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D1377 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 removed outlier: 4.126A pdb=" N GLU D1384 " --> pdb=" O ASN D1380 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE D1385 " --> pdb=" O VAL D1381 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D1389 " --> pdb=" O ILE D1385 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D1390 " --> pdb=" O LYS D1386 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.978A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 4.953A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D1458 " --> pdb=" O LYS D1454 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.612A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D1482 " --> pdb=" O ALA D1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 1483 through 1488 removed outlier: 4.551A pdb=" N ASN D1487 " --> pdb=" O PRO D1483 " (cutoff:3.500A) removed outlier: 4.774A 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: 4.048A pdb=" N HIS D1494 " --> pdb=" O SER D1490 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN D1495 " --> pdb=" O LEU D1491 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) removed outlier: 5.458A 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: 4.149A pdb=" N GLY D1520 " --> pdb=" O GLN D1516 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D1522 " --> pdb=" O HIS D1518 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1553 removed outlier: 3.842A pdb=" N MET D1551 " --> pdb=" O HIS D1547 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D1553 " --> pdb=" O SER D1549 " (cutoff:3.500A) Processing helix chain 'D' and resid 1587 through 1624 removed outlier: 3.813A 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: 3.746A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.011A 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: 3.755A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1902 through 1916 removed outlier: 3.624A pdb=" N GLU D1906 " --> pdb=" O ASN D1902 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D1916 " --> pdb=" O ASP D1912 " (cutoff:3.500A) Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 4.198A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.777A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1931 through 1949 removed outlier: 4.551A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 5.122A 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: 3.925A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 3.776A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 removed outlier: 3.755A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 3.572A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2040 removed outlier: 3.978A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG D2039 " --> pdb=" O GLN D2035 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU D2040 " --> pdb=" O GLU D2036 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2065 removed outlier: 4.179A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D2064 " --> pdb=" O LEU D2060 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D2065 " --> pdb=" O SER D2061 " (cutoff:3.500A) Processing helix chain 'D' and resid 2066 through 2073 Proline residue: D2073 - end of helix Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 3.997A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.356A 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 2172 through 2190 removed outlier: 4.461A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) Processing helix chain 'D' and resid 2191 through 2223 removed outlier: 3.691A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) Processing helix chain 'D' and resid 2261 through 2276 Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.247A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2318 removed outlier: 5.649A 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: 4.686A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.585A 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: 3.951A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 3.828A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2390 Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 4.020A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.599A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.584A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.187A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2549' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2607 through 2648 removed outlier: 4.984A pdb=" N ASN D2613 " --> pdb=" O SER D2609 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 19 removed outlier: 4.969A pdb=" N SER A 218 " --> pdb=" O GLU A 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 221 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP A 181 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS A 182 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 167 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TRP A 161 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 57 through 61 removed outlier: 13.700A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.577A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 239 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU A 282 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 309 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 367 through 371 Processing sheet with id= 5, first strand: chain 'A' and resid 396 through 401 removed outlier: 3.812A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 667 through 672 removed outlier: 4.128A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.250A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 7.094A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 240 through 245 removed outlier: 5.617A pdb=" N VAL A 240 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 14 through 19 removed outlier: 4.969A pdb=" N SER B 218 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 221 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP B 181 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS B 182 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 167 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TRP B 161 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 57 through 61 removed outlier: 13.700A pdb=" N ILE B 122 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N VAL B 135 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 131 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.577A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 239 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU B 282 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 309 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 367 through 371 Processing sheet with id= 14, first strand: chain 'B' and resid 396 through 401 removed outlier: 3.812A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 667 through 672 removed outlier: 4.128A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.249A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 7.094A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 240 through 245 removed outlier: 5.617A pdb=" N VAL B 240 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 14 through 19 removed outlier: 4.969A pdb=" N SER C 218 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 221 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP C 181 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS C 182 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 167 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TRP C 161 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 57 through 61 removed outlier: 13.700A pdb=" N ILE C 122 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N VAL C 135 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 131 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.578A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 239 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU C 282 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 309 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 367 through 371 Processing sheet with id= 23, first strand: chain 'C' and resid 396 through 401 removed outlier: 3.812A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 667 through 672 removed outlier: 4.129A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.249A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 2395 through 2399 removed outlier: 7.094A pdb=" N PHE C2395 " --> pdb=" O ALA C2454 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER C2450 " --> pdb=" O VAL C2399 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 240 through 245 removed outlier: 5.617A pdb=" N VAL C 240 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 14 through 19 removed outlier: 4.970A pdb=" N SER D 218 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D 221 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP D 181 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS D 182 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 167 " --> pdb=" O LYS D 182 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TRP D 161 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 57 through 61 removed outlier: 13.700A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.577A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 239 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 367 through 371 Processing sheet with id= 32, first strand: chain 'D' and resid 396 through 401 removed outlier: 3.812A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 667 through 672 removed outlier: 4.129A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.250A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 7.094A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 240 through 245 removed outlier: 5.617A pdb=" N VAL D 240 " --> pdb=" O VAL D 434 " (cutoff:3.500A) 4328 hydrogen bonds defined for protein. 12960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 70.02 Time building geometry restraints manager: 100.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 72676 1.03 - 1.23: 830 1.23 - 1.43: 29910 1.43 - 1.62: 42992 1.62 - 1.82: 748 Bond restraints: 147156 Sorted by residual: bond pdb=" N PRO B 487 " pdb=" CD PRO B 487 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" N PRO D 790 " pdb=" CD PRO D 790 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO D 404 " pdb=" CD PRO D 404 " ideal model delta sigma weight residual 1.473 1.491 -0.018 1.40e-02 5.10e+03 1.74e+00 bond pdb=" N PRO B 404 " pdb=" CD PRO B 404 " ideal model delta sigma weight residual 1.473 1.490 -0.017 1.40e-02 5.10e+03 1.50e+00 bond pdb=" N SER D1917 " pdb=" CA SER D1917 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 ... (remaining 147151 not shown) Histogram of bond angle deviations from ideal: 99.94 - 107.92: 21151 107.92 - 115.90: 169478 115.90 - 123.89: 64624 123.89 - 131.87: 10815 131.87 - 139.85: 96 Bond angle restraints: 266164 Sorted by residual: angle pdb=" CB MET B1206 " pdb=" CG MET B1206 " pdb=" SD MET B1206 " ideal model delta sigma weight residual 112.70 125.11 -12.41 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET A1206 " pdb=" CG MET A1206 " pdb=" SD MET A1206 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET C1206 " pdb=" CG MET C1206 " pdb=" SD MET C1206 " ideal model delta sigma weight residual 112.70 125.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB MET D1206 " pdb=" CG MET D1206 " pdb=" SD MET D1206 " ideal model delta sigma weight residual 112.70 125.09 -12.39 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CG MET D1206 " pdb=" SD MET D1206 " pdb=" CE MET D1206 " ideal model delta sigma weight residual 100.90 107.12 -6.22 2.20e+00 2.07e-01 7.99e+00 ... (remaining 266159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 64717 24.54 - 49.07: 3429 49.07 - 73.61: 632 73.61 - 98.15: 82 98.15 - 122.68: 16 Dihedral angle restraints: 68876 sinusoidal: 37668 harmonic: 31208 Sorted by residual: dihedral pdb=" C4 I3P C3002 " pdb=" C2 I3P C3002 " pdb=" C3 I3P C3002 " pdb=" O2 I3P C3002 " ideal model delta sinusoidal sigma weight residual 65.28 -172.04 -122.68 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C1 I3P B3002 " pdb=" C2 I3P B3002 " pdb=" C3 I3P B3002 " pdb=" C4 I3P B3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.86 122.67 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C4 I3P B3002 " pdb=" C2 I3P B3002 " pdb=" C3 I3P B3002 " pdb=" O2 I3P B3002 " ideal model delta sinusoidal sigma weight residual 65.28 -172.07 -122.65 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 68873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 10319 0.058 - 0.117: 1141 0.117 - 0.175: 76 0.175 - 0.234: 0 0.234 - 0.292: 12 Chirality restraints: 11548 Sorted by residual: chirality pdb=" C3' ATP B3003 " pdb=" C2' ATP B3003 " pdb=" C4' ATP B3003 " pdb=" O3' ATP B3003 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' ATP C3003 " pdb=" C2' ATP C3003 " pdb=" C4' ATP C3003 " pdb=" O3' ATP C3003 " 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 B3003 " pdb=" C1' ATP B3003 " pdb=" C3' ATP B3003 " pdb=" O2' ATP B3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 11545 not shown) Planarity restraints: 21516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 403 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO B 404 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 403 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO D 404 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D2482 " 0.046 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO D2483 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D2483 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D2483 " 0.039 5.00e-02 4.00e+02 ... (remaining 21513 not shown) Histogram of nonbonded interaction distances: 0.23 - 1.10: 40 1.10 - 1.98: 1344 1.98 - 2.85: 361640 2.85 - 3.73: 622224 3.73 - 4.60: 1075618 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2060866 Sorted by model distance: nonbonded pdb="HH12 ARG B 138 " pdb=" NE2 HIS C1288 " model vdw 0.225 2.600 nonbonded pdb=" HE3 MET B 99 " pdb="HD11 LEU C1922 " model vdw 0.484 2.440 nonbonded pdb=" NH1 ARG A 138 " pdb=" NE2 HIS B1288 " model vdw 0.530 3.100 nonbonded pdb=" NH1 ARG C 138 " pdb=" NE2 HIS D1288 " model vdw 0.554 3.100 nonbonded pdb="HH12 ARG C 138 " pdb=" NE2 HIS D1288 " model vdw 0.566 2.600 ... (remaining 2060861 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.500 Extract box with map and model: 30.190 Check model and map are aligned: 1.550 Set scattering table: 0.960 Process input model: 428.680 Find NCS groups from input model: 5.150 Set up NCS constraints: 0.590 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:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 477.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.063 74312 Z= 0.123 Angle : 0.444 12.406 100488 Z= 0.230 Chirality : 0.035 0.292 11548 Planarity : 0.002 0.073 12756 Dihedral : 15.910 122.682 27860 Min Nonbonded Distance : 0.530 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.09 % Allowed : 13.61 % Favored : 86.31 % 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: 3.61 (0.09), residues: 8952 helix: 3.34 (0.07), residues: 5488 sheet: 0.44 (0.22), residues: 608 loop : 0.97 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1438 HIS 0.016 0.001 HIS A1288 PHE 0.020 0.001 PHE A 777 TYR 0.007 0.001 TYR A 257 ARG 0.004 0.000 ARG C 730 *********************** 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 1312 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1305 time to evaluate : 8.571 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 806 ILE cc_start: 0.8551 (mt) cc_final: 0.8201 (mm) REVERT: A 1206 MET cc_start: 0.8557 (mmm) cc_final: 0.8312 (mmm) REVERT: B 1035 MET cc_start: 0.7391 (ptp) cc_final: 0.7041 (ptp) REVERT: B 1058 VAL cc_start: 0.9262 (t) cc_final: 0.8784 (p) REVERT: B 1208 ASP cc_start: 0.8618 (m-30) cc_final: 0.8363 (m-30) REVERT: B 1364 TYR cc_start: 0.8447 (t80) cc_final: 0.8158 (t80) REVERT: B 1606 LEU cc_start: 0.9137 (mt) cc_final: 0.8913 (mm) REVERT: B 1739 ASP cc_start: 0.7983 (m-30) cc_final: 0.7638 (m-30) REVERT: B 1911 LEU cc_start: 0.9005 (tp) cc_final: 0.8656 (tt) REVERT: C 806 ILE cc_start: 0.8561 (mt) cc_final: 0.8324 (mm) REVERT: C 1551 MET cc_start: 0.5975 (mmt) cc_final: 0.4630 (ptt) REVERT: C 2133 MET cc_start: 0.8321 (mtp) cc_final: 0.7986 (mmm) REVERT: C 2318 MET cc_start: 0.7555 (ppp) cc_final: 0.7143 (ppp) REVERT: D 739 MET cc_start: 0.8912 (mtp) cc_final: 0.8514 (mtp) REVERT: D 1058 VAL cc_start: 0.9187 (t) cc_final: 0.8690 (p) REVERT: D 1273 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 1322 MET cc_start: 0.8652 (tpp) cc_final: 0.8399 (tpp) REVERT: D 1364 TYR cc_start: 0.8529 (t80) cc_final: 0.8274 (t80) REVERT: D 1690 LEU cc_start: 0.9364 (mt) cc_final: 0.9098 (mt) REVERT: D 1739 ASP cc_start: 0.8169 (m-30) cc_final: 0.7832 (m-30) REVERT: D 2318 MET cc_start: 0.8234 (mtt) cc_final: 0.7887 (ppp) outliers start: 7 outliers final: 3 residues processed: 1309 average time/residue: 1.7524 time to fit residues: 3896.2212 Evaluate side-chains 781 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 778 time to evaluate : 7.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain C residue 289 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 10.0000 chunk 685 optimal weight: 8.9990 chunk 380 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 462 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 chunk 708 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 527 optimal weight: 9.9990 chunk 820 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** A1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1884 HIS ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2365 ASN A2468 HIS ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 299 HIS B 843 ASN ** B 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1884 HIS B1939 GLN ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2337 HIS ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS C 198 ASN ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1065 HIS ** C1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1650 HIS ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1884 HIS ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 299 HIS D 601 ASN ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1884 HIS ** D1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 74312 Z= 0.396 Angle : 0.594 7.213 100488 Z= 0.326 Chirality : 0.037 0.201 11548 Planarity : 0.004 0.052 12756 Dihedral : 5.613 83.496 9998 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.50 % Allowed : 15.22 % Favored : 82.29 % 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: 2.80 (0.09), residues: 8952 helix: 2.70 (0.07), residues: 5608 sheet: 0.13 (0.22), residues: 584 loop : 0.52 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 161 HIS 0.012 0.001 HIS C1288 PHE 0.025 0.002 PHE B1786 TYR 0.017 0.001 TYR B 989 ARG 0.066 0.001 ARG A 138 *********************** 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 919 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 717 time to evaluate : 8.602 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 538 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7406 (mt) REVERT: A 1064 MET cc_start: 0.8379 (ppp) cc_final: 0.8067 (ppp) REVERT: A 1348 MET cc_start: 0.7190 (ptm) cc_final: 0.6675 (ptm) REVERT: A 2460 MET cc_start: 0.7869 (tpp) cc_final: 0.7638 (tpp) REVERT: B 625 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8632 (m110) REVERT: B 739 MET cc_start: 0.8893 (mtp) cc_final: 0.8562 (mtp) REVERT: B 1035 MET cc_start: 0.7534 (ptp) cc_final: 0.6957 (ptp) REVERT: B 1208 ASP cc_start: 0.8832 (m-30) cc_final: 0.8562 (m-30) REVERT: B 1739 ASP cc_start: 0.8211 (m-30) cc_final: 0.7878 (m-30) REVERT: B 2316 MET cc_start: 0.8093 (tpp) cc_final: 0.7786 (tpp) REVERT: C 1551 MET cc_start: 0.5951 (mmt) cc_final: 0.4559 (ptt) REVERT: C 2133 MET cc_start: 0.8216 (mtp) cc_final: 0.7970 (mmm) REVERT: D 601 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8085 (t0) REVERT: D 739 MET cc_start: 0.9039 (mtp) cc_final: 0.8651 (mtp) REVERT: D 1206 MET cc_start: 0.9222 (mmm) cc_final: 0.9011 (mmp) REVERT: D 1322 MET cc_start: 0.8835 (tpp) cc_final: 0.8572 (tpp) REVERT: D 1363 MET cc_start: 0.8303 (tpp) cc_final: 0.8097 (tpp) REVERT: D 1697 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7096 (t0) outliers start: 202 outliers final: 92 residues processed: 891 average time/residue: 1.6531 time to fit residues: 2553.0510 Evaluate side-chains 722 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 626 time to evaluate : 8.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1280 GLU Chi-restraints excluded: chain A residue 1300 LEU Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1676 LYS Chi-restraints excluded: chain A residue 1724 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1903 LEU Chi-restraints excluded: chain A residue 1940 THR Chi-restraints excluded: chain A residue 2026 VAL Chi-restraints excluded: chain A residue 2121 THR Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2327 ILE Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2600 ASP Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1288 HIS Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1907 THR Chi-restraints excluded: chain B residue 2016 ILE Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 1044 MET Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1656 GLU Chi-restraints excluded: chain C residue 1676 LYS Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1940 THR Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2159 THR Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2600 ASP Chi-restraints excluded: chain C residue 2608 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 601 ASN Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 1332 VAL Chi-restraints excluded: chain D residue 1668 THR Chi-restraints excluded: chain D residue 1697 ASN Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 2016 ILE Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2299 SER Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 683 optimal weight: 0.9990 chunk 559 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 822 optimal weight: 5.9990 chunk 888 optimal weight: 0.7980 chunk 732 optimal weight: 5.9990 chunk 815 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 659 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 HIS ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN D1284 GLN ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 74312 Z= 0.204 Angle : 0.483 6.698 100488 Z= 0.256 Chirality : 0.034 0.161 11548 Planarity : 0.003 0.047 12756 Dihedral : 4.821 87.849 9994 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.65 % Allowed : 15.44 % Favored : 82.92 % 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: 3.04 (0.09), residues: 8952 helix: 2.93 (0.07), residues: 5604 sheet: 0.10 (0.22), residues: 584 loop : 0.54 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1127 HIS 0.006 0.001 HIS D1622 PHE 0.022 0.001 PHE A 526 TYR 0.025 0.001 TYR A1947 ARG 0.005 0.000 ARG B 383 *********************** 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 789 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 656 time to evaluate : 8.743 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8298 (ppp) cc_final: 0.7936 (ppp) REVERT: A 1348 MET cc_start: 0.7066 (ptm) cc_final: 0.6507 (ptm) REVERT: A 2460 MET cc_start: 0.7693 (tpp) cc_final: 0.7482 (tpp) REVERT: B 739 MET cc_start: 0.8928 (mtp) cc_final: 0.8662 (mtp) REVERT: B 1208 ASP cc_start: 0.8773 (m-30) cc_final: 0.8490 (m-30) REVERT: B 1320 MET cc_start: 0.8541 (mtp) cc_final: 0.8258 (mtp) REVERT: B 1739 ASP cc_start: 0.8218 (m-30) cc_final: 0.7895 (m-30) REVERT: B 2316 MET cc_start: 0.8054 (tpp) cc_final: 0.7743 (tpp) REVERT: C 1551 MET cc_start: 0.5925 (mmt) cc_final: 0.4504 (ptt) REVERT: C 2133 MET cc_start: 0.8236 (mtp) cc_final: 0.7998 (mmm) REVERT: D 739 MET cc_start: 0.9004 (mtp) cc_final: 0.8640 (mtp) REVERT: D 1206 MET cc_start: 0.9223 (mmm) cc_final: 0.8993 (mmp) REVERT: D 1322 MET cc_start: 0.8874 (tpp) cc_final: 0.8662 (tpp) REVERT: D 1697 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7222 (t0) outliers start: 133 outliers final: 82 residues processed: 770 average time/residue: 1.5635 time to fit residues: 2068.5804 Evaluate side-chains 694 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 611 time to evaluate : 8.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1656 GLU Chi-restraints excluded: chain C residue 1676 LYS Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1873 ILE Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1697 ASN Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1994 ASP Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2170 ASP Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL 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: 7.9990 chunk 426 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 392 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 825 optimal weight: 8.9990 chunk 873 optimal weight: 8.9990 chunk 431 optimal weight: 2.9990 chunk 782 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 HIS ** A1090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1897 ASN ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 513 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1897 ASN ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN C 513 ASN ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2365 ASN ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 744 GLN D1090 HIS D1759 HIS ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1897 ASN D1939 GLN ** D2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 74312 Z= 0.408 Angle : 0.584 8.245 100488 Z= 0.324 Chirality : 0.036 0.169 11548 Planarity : 0.004 0.046 12756 Dihedral : 5.048 86.226 9992 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.47 % Allowed : 15.99 % Favored : 81.53 % 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: 2.08 (0.09), residues: 8952 helix: 2.32 (0.07), residues: 5628 sheet: -0.70 (0.19), residues: 712 loop : -0.05 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 803 HIS 0.010 0.001 HIS D 600 PHE 0.021 0.002 PHE B1786 TYR 0.027 0.002 TYR A1947 ARG 0.008 0.001 ARG A2047 *********************** 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 793 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 593 time to evaluate : 8.735 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8393 (ppp) cc_final: 0.8021 (ppp) REVERT: B 383 ARG cc_start: 0.7509 (ptm160) cc_final: 0.6920 (ptm160) REVERT: B 739 MET cc_start: 0.8948 (mtp) cc_final: 0.8718 (mtp) REVERT: B 841 LEU cc_start: 0.9449 (mt) cc_final: 0.9153 (mm) REVERT: B 1208 ASP cc_start: 0.8850 (m-30) cc_final: 0.8572 (m-30) REVERT: B 1286 PHE cc_start: 0.8950 (m-80) cc_final: 0.8624 (m-10) REVERT: B 1622 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7730 (m-70) REVERT: B 1739 ASP cc_start: 0.8235 (m-30) cc_final: 0.7969 (m-30) REVERT: B 2355 LEU cc_start: 0.8665 (tp) cc_final: 0.8451 (tp) REVERT: C 1064 MET cc_start: 0.8412 (ppp) cc_final: 0.8081 (ppp) REVERT: C 1551 MET cc_start: 0.6064 (mmt) cc_final: 0.5229 (mpp) REVERT: C 2460 MET cc_start: 0.8029 (tpp) cc_final: 0.7753 (tpp) REVERT: D 739 MET cc_start: 0.9040 (mtp) cc_final: 0.8779 (mtp) REVERT: D 1206 MET cc_start: 0.9244 (mmm) cc_final: 0.8959 (mmp) REVERT: D 1322 MET cc_start: 0.8883 (tpp) cc_final: 0.8651 (tpp) REVERT: D 2299 SER cc_start: 0.9573 (OUTLIER) cc_final: 0.9188 (p) outliers start: 200 outliers final: 144 residues processed: 756 average time/residue: 1.5269 time to fit residues: 1988.3074 Evaluate side-chains 701 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 555 time to evaluate : 8.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 661 ASN Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 988 SER Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1280 GLU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1724 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2314 MET Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1668 THR Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1988 LEU Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 661 ASN Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1089 MET Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1381 VAL Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1676 LYS Chi-restraints excluded: chain C residue 1679 TYR Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2159 THR Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2486 ASP Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 604 LYS Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 877 SER Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1303 LEU Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1668 THR Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1994 ASP Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2299 SER Chi-restraints excluded: chain D residue 2314 MET Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2502 PHE Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 0.7980 chunk 496 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 650 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 745 optimal weight: 10.0000 chunk 604 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 446 optimal weight: 0.8980 chunk 784 optimal weight: 6.9990 chunk 220 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1897 ASN B2180 ASN ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 ASN D 700 ASN ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1897 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 74312 Z= 0.135 Angle : 0.461 6.867 100488 Z= 0.241 Chirality : 0.034 0.157 11548 Planarity : 0.003 0.061 12756 Dihedral : 4.690 87.083 9992 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.32 % Allowed : 16.89 % Favored : 81.79 % 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: 2.88 (0.09), residues: 8952 helix: 2.91 (0.07), residues: 5600 sheet: -0.39 (0.20), residues: 664 loop : 0.36 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1127 HIS 0.005 0.001 HIS B1494 PHE 0.019 0.001 PHE C1055 TYR 0.023 0.001 TYR A1947 ARG 0.004 0.000 ARG B 383 *********************** 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 706 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 599 time to evaluate : 8.691 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8216 (ppp) cc_final: 0.7829 (ppp) REVERT: B 739 MET cc_start: 0.8897 (mtp) cc_final: 0.8643 (mtp) REVERT: B 1035 MET cc_start: 0.7671 (ptp) cc_final: 0.7073 (ptp) REVERT: B 1208 ASP cc_start: 0.8713 (m-30) cc_final: 0.8420 (m-30) REVERT: B 1286 PHE cc_start: 0.8880 (m-80) cc_final: 0.8565 (m-10) REVERT: B 1739 ASP cc_start: 0.8186 (m-30) cc_final: 0.7905 (m-30) REVERT: B 1863 MET cc_start: 0.6924 (mmp) cc_final: 0.6668 (mmp) REVERT: C 1551 MET cc_start: 0.6141 (mmt) cc_final: 0.5415 (mpp) REVERT: D 739 MET cc_start: 0.9019 (mtp) cc_final: 0.8715 (mtp) REVERT: D 1206 MET cc_start: 0.9240 (mmm) cc_final: 0.8956 (mmp) REVERT: D 1322 MET cc_start: 0.8896 (tpp) cc_final: 0.8686 (tpp) outliers start: 107 outliers final: 81 residues processed: 690 average time/residue: 1.5384 time to fit residues: 1831.2696 Evaluate side-chains 648 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 567 time to evaluate : 7.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1967 ILE Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1994 ASP Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 10.0000 chunk 786 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 513 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 874 optimal weight: 5.9990 chunk 726 optimal weight: 5.9990 chunk 404 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 459 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 868 HIS ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1897 ASN ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2180 ASN B2365 ASN ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 74312 Z= 0.326 Angle : 0.522 6.833 100488 Z= 0.286 Chirality : 0.035 0.151 11548 Planarity : 0.003 0.045 12756 Dihedral : 4.812 88.619 9992 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 16.82 % Favored : 81.27 % 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: 2.46 (0.09), residues: 8952 helix: 2.64 (0.07), residues: 5612 sheet: -0.66 (0.20), residues: 664 loop : 0.08 (0.12), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 803 HIS 0.008 0.001 HIS B 868 PHE 0.018 0.001 PHE C1055 TYR 0.017 0.001 TYR A1947 ARG 0.005 0.000 ARG A2047 *********************** 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 710 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 556 time to evaluate : 8.302 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8358 (ppp) cc_final: 0.8088 (ppp) REVERT: A 1348 MET cc_start: 0.7080 (ptm) cc_final: 0.6868 (ptm) REVERT: B 383 ARG cc_start: 0.7315 (ptm160) cc_final: 0.6999 (ptm160) REVERT: B 739 MET cc_start: 0.8923 (mtp) cc_final: 0.8698 (mtp) REVERT: B 1035 MET cc_start: 0.7860 (ptp) cc_final: 0.7242 (ptp) REVERT: B 1208 ASP cc_start: 0.8784 (m-30) cc_final: 0.8506 (m-30) REVERT: B 1264 MET cc_start: 0.9654 (mmm) cc_final: 0.9087 (mmt) REVERT: B 1286 PHE cc_start: 0.8926 (m-80) cc_final: 0.8662 (m-10) REVERT: B 1739 ASP cc_start: 0.8226 (m-30) cc_final: 0.7937 (m-30) REVERT: B 1932 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8341 (t0) REVERT: C 1551 MET cc_start: 0.6299 (mmt) cc_final: 0.5568 (mpp) REVERT: D 739 MET cc_start: 0.9063 (mtp) cc_final: 0.8810 (mtp) REVERT: D 1206 MET cc_start: 0.9225 (mmm) cc_final: 0.8960 (mmp) REVERT: D 1322 MET cc_start: 0.8917 (tpp) cc_final: 0.8710 (tpp) outliers start: 154 outliers final: 132 residues processed: 678 average time/residue: 1.5800 time to fit residues: 1848.6289 Evaluate side-chains 670 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 537 time to evaluate : 8.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1724 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2314 MET Chi-restraints excluded: chain A residue 2347 ASP Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1969 ILE Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2318 MET Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2347 ASP Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2452 GLU Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 877 SER Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1967 ILE Chi-restraints excluded: chain D residue 1969 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1994 ASP Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2314 MET Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2506 ILE 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: 4.9990 chunk 498 optimal weight: 2.9990 chunk 638 optimal weight: 5.9990 chunk 494 optimal weight: 5.9990 chunk 736 optimal weight: 0.7980 chunk 488 optimal weight: 6.9990 chunk 871 optimal weight: 7.9990 chunk 545 optimal weight: 10.0000 chunk 531 optimal weight: 10.0000 chunk 402 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2365 ASN ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 74312 Z= 0.267 Angle : 0.496 8.062 100488 Z= 0.267 Chirality : 0.035 0.149 11548 Planarity : 0.003 0.035 12756 Dihedral : 4.687 86.026 9992 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 16.98 % Favored : 80.95 % 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: 2.48 (0.09), residues: 8952 helix: 2.69 (0.07), residues: 5592 sheet: -0.71 (0.20), residues: 664 loop : 0.04 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1586 HIS 0.005 0.001 HIS B1494 PHE 0.017 0.001 PHE D1055 TYR 0.018 0.001 TYR A1947 ARG 0.004 0.000 ARG B2309 *********************** 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 708 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 541 time to evaluate : 8.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8332 (ppp) cc_final: 0.8095 (ppp) REVERT: A 2605 MET cc_start: 0.8234 (mmm) cc_final: 0.7810 (mmp) REVERT: B 739 MET cc_start: 0.8932 (mtp) cc_final: 0.8709 (mtp) REVERT: B 1208 ASP cc_start: 0.8769 (m-30) cc_final: 0.8495 (m-30) REVERT: B 1286 PHE cc_start: 0.8926 (m-80) cc_final: 0.8685 (m-10) REVERT: B 1739 ASP cc_start: 0.8241 (m-30) cc_final: 0.7951 (m-30) REVERT: B 1932 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (t0) REVERT: B 2316 MET cc_start: 0.7524 (tpp) cc_final: 0.7267 (tpt) REVERT: C 1551 MET cc_start: 0.6270 (mmt) cc_final: 0.5542 (mpp) REVERT: D 289 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7567 (t70) REVERT: D 739 MET cc_start: 0.9060 (mtp) cc_final: 0.8795 (mtp) REVERT: D 1206 MET cc_start: 0.9198 (mmm) cc_final: 0.8946 (mmp) REVERT: D 1322 MET cc_start: 0.8919 (tpp) cc_final: 0.8695 (tpp) outliers start: 167 outliers final: 143 residues processed: 685 average time/residue: 1.5508 time to fit residues: 1841.1881 Evaluate side-chains 674 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 529 time to evaluate : 8.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1967 ILE Chi-restraints excluded: chain B residue 1969 ILE Chi-restraints excluded: chain B residue 1988 LEU Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1662 CYS Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2375 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2452 GLU Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 877 SER Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1252 LEU Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1967 ILE Chi-restraints excluded: chain D residue 1969 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 7.9990 chunk 347 optimal weight: 10.0000 chunk 520 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 553 optimal weight: 10.0000 chunk 593 optimal weight: 0.8980 chunk 430 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 684 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2365 ASN ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 74312 Z= 0.248 Angle : 0.494 9.588 100488 Z= 0.264 Chirality : 0.034 0.152 11548 Planarity : 0.003 0.034 12756 Dihedral : 4.639 88.934 9992 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.93 % Allowed : 17.19 % Favored : 80.88 % 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: 2.52 (0.09), residues: 8952 helix: 2.72 (0.07), residues: 5600 sheet: -0.72 (0.20), residues: 664 loop : 0.05 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2601 HIS 0.005 0.001 HIS B1622 PHE 0.017 0.001 PHE D1055 TYR 0.018 0.001 TYR A1947 ARG 0.003 0.000 ARG A2047 *********************** 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 694 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 538 time to evaluate : 8.642 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 MET cc_start: 0.8927 (mtp) cc_final: 0.8696 (mtp) REVERT: B 1035 MET cc_start: 0.7884 (ptp) cc_final: 0.7505 (ptp) REVERT: B 1208 ASP cc_start: 0.8732 (m-30) cc_final: 0.8461 (m-30) REVERT: B 1286 PHE cc_start: 0.8904 (m-80) cc_final: 0.8677 (m-80) REVERT: B 1739 ASP cc_start: 0.8244 (m-30) cc_final: 0.7961 (m-30) REVERT: B 1932 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8379 (t0) REVERT: B 2201 MET cc_start: 0.8716 (mmm) cc_final: 0.8476 (mmm) REVERT: B 2316 MET cc_start: 0.7565 (tpp) cc_final: 0.7283 (tpt) REVERT: C 1551 MET cc_start: 0.6224 (mmt) cc_final: 0.5481 (mpp) REVERT: D 289 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7550 (t70) REVERT: D 739 MET cc_start: 0.9062 (mtp) cc_final: 0.8781 (mtp) REVERT: D 1206 MET cc_start: 0.9197 (mmm) cc_final: 0.8946 (mmp) REVERT: D 1322 MET cc_start: 0.8915 (tpp) cc_final: 0.8681 (tpp) outliers start: 156 outliers final: 141 residues processed: 674 average time/residue: 1.5567 time to fit residues: 1810.8213 Evaluate side-chains 671 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 528 time to evaluate : 8.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1932 ASP Chi-restraints excluded: chain B residue 1967 ILE Chi-restraints excluded: chain B residue 1969 ILE Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1662 CYS Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2375 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2452 GLU Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1967 ILE Chi-restraints excluded: chain D residue 1969 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2466 MET Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2533 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 0.9990 chunk 834 optimal weight: 8.9990 chunk 761 optimal weight: 3.9990 chunk 811 optimal weight: 8.9990 chunk 488 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 637 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 733 optimal weight: 6.9990 chunk 767 optimal weight: 8.9990 chunk 809 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 818 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1897 ASN ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2164 GLN D2180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 74312 Z= 0.320 Angle : 0.530 10.610 100488 Z= 0.287 Chirality : 0.035 0.149 11548 Planarity : 0.003 0.034 12756 Dihedral : 4.709 80.314 9992 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 17.00 % Favored : 80.81 % 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: 2.24 (0.09), residues: 8952 helix: 2.52 (0.07), residues: 5596 sheet: -0.87 (0.20), residues: 664 loop : -0.09 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A1127 HIS 0.006 0.001 HIS A1249 PHE 0.016 0.001 PHE D1055 TYR 0.017 0.001 TYR B 17 ARG 0.007 0.000 ARG B2309 *********************** 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 699 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 522 time to evaluate : 8.559 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1064 MET cc_start: 0.8251 (ppp) cc_final: 0.7998 (ppp) REVERT: B 739 MET cc_start: 0.8937 (mtp) cc_final: 0.8696 (mtp) REVERT: B 1208 ASP cc_start: 0.8750 (m-30) cc_final: 0.8486 (m-30) REVERT: B 1739 ASP cc_start: 0.8263 (m-30) cc_final: 0.7979 (m-30) REVERT: C 1551 MET cc_start: 0.6162 (mmt) cc_final: 0.5465 (mpp) REVERT: D 739 MET cc_start: 0.9071 (mtp) cc_final: 0.8823 (mtp) REVERT: D 1206 MET cc_start: 0.9199 (mmm) cc_final: 0.8942 (mmp) REVERT: D 1322 MET cc_start: 0.8943 (tpp) cc_final: 0.8688 (tpp) outliers start: 177 outliers final: 159 residues processed: 673 average time/residue: 1.5299 time to fit residues: 1781.1707 Evaluate side-chains 672 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 513 time to evaluate : 8.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1724 THR Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2314 MET Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1214 TYR Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1967 ILE Chi-restraints excluded: chain B residue 1969 ILE Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1442 GLU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1662 CYS Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2347 ASP Chi-restraints excluded: chain C residue 2375 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2452 GLU Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 661 ASN Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 877 SER Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1100 SER Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1672 MET Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1967 ILE Chi-restraints excluded: chain D residue 1969 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2314 MET Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2533 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 9.9990 chunk 858 optimal weight: 10.0000 chunk 524 optimal weight: 6.9990 chunk 407 optimal weight: 5.9990 chunk 596 optimal weight: 5.9990 chunk 900 optimal weight: 3.9990 chunk 828 optimal weight: 10.0000 chunk 717 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 553 optimal weight: 10.0000 chunk 439 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 74312 Z= 0.257 Angle : 0.504 10.164 100488 Z= 0.270 Chirality : 0.035 0.150 11548 Planarity : 0.003 0.036 12756 Dihedral : 4.599 79.899 9992 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.97 % Allowed : 17.24 % Favored : 80.79 % 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: 2.39 (0.09), residues: 8952 helix: 2.65 (0.07), residues: 5592 sheet: -0.86 (0.20), residues: 664 loop : -0.04 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1127 HIS 0.007 0.001 HIS A1249 PHE 0.017 0.001 PHE B1055 TYR 0.018 0.001 TYR A1947 ARG 0.005 0.000 ARG B1190 ********************** 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 682 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 523 time to evaluate : 8.665 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 739 MET cc_start: 0.8914 (mtp) cc_final: 0.8678 (mtp) REVERT: B 1208 ASP cc_start: 0.8702 (m-30) cc_final: 0.8440 (m-30) REVERT: B 1739 ASP cc_start: 0.8257 (m-30) cc_final: 0.7966 (m-30) REVERT: B 2316 MET cc_start: 0.7680 (tpp) cc_final: 0.7296 (tpt) REVERT: C 1551 MET cc_start: 0.6156 (mmt) cc_final: 0.5518 (mpp) REVERT: D 289 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7539 (t70) REVERT: D 739 MET cc_start: 0.9063 (mtp) cc_final: 0.8811 (mtp) REVERT: D 1035 MET cc_start: 0.8271 (ptp) cc_final: 0.8068 (ptp) REVERT: D 1206 MET cc_start: 0.9202 (mmm) cc_final: 0.8947 (mmp) REVERT: D 1322 MET cc_start: 0.8918 (tpp) cc_final: 0.8643 (tpp) outliers start: 159 outliers final: 150 residues processed: 660 average time/residue: 1.5401 time to fit residues: 1765.2939 Evaluate side-chains 665 residues out of total 8248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 514 time to evaluate : 7.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1589 LYS Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1697 ASN Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1758 ILE Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 2289 ASN Chi-restraints excluded: chain A residue 2314 MET Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2495 VAL Chi-restraints excluded: chain A residue 2498 LEU Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1200 MET Chi-restraints excluded: chain B residue 1214 TYR Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1611 GLN Chi-restraints excluded: chain B residue 1758 ILE Chi-restraints excluded: chain B residue 1969 ILE Chi-restraints excluded: chain B residue 2003 LEU Chi-restraints excluded: chain B residue 2068 GLN Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2309 ARG Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2506 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1042 SER Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1303 LEU Chi-restraints excluded: chain C residue 1604 GLU Chi-restraints excluded: chain C residue 1662 CYS Chi-restraints excluded: chain C residue 1697 ASN Chi-restraints excluded: chain C residue 1724 THR Chi-restraints excluded: chain C residue 1758 ILE Chi-restraints excluded: chain C residue 1771 SER Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1887 ASP Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1958 CYS Chi-restraints excluded: chain C residue 2003 LEU Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2299 SER Chi-restraints excluded: chain C residue 2375 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2452 GLU Chi-restraints excluded: chain C residue 2495 VAL Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1331 ASP Chi-restraints excluded: chain D residue 1332 VAL Chi-restraints excluded: chain D residue 1672 MET Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1758 ILE Chi-restraints excluded: chain D residue 1967 ILE Chi-restraints excluded: chain D residue 1969 ILE Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 2003 LEU Chi-restraints excluded: chain D residue 2068 GLN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2157 THR Chi-restraints excluded: chain D residue 2182 MET Chi-restraints excluded: chain D residue 2226 MET Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2494 VAL Chi-restraints excluded: chain D residue 2495 VAL Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2533 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 9.9990 chunk 763 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 661 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 199 optimal weight: 6.9990 chunk 718 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 737 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.068048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047547 restraints weight = 1050752.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049633 restraints weight = 400955.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050856 restraints weight = 229739.703| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 74312 Z= 0.288 Angle : 0.556 59.158 100488 Z= 0.311 Chirality : 0.035 0.287 11548 Planarity : 0.003 0.045 12756 Dihedral : 4.594 79.861 9992 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.93 % Allowed : 17.44 % Favored : 80.63 % 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: 2.65 (0.07), residues: 5592 sheet: -0.86 (0.20), residues: 664 loop : -0.05 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D1127 HIS 0.006 0.001 HIS A1249 PHE 0.017 0.001 PHE B1302 TYR 0.018 0.001 TYR A1947 ARG 0.005 0.000 ARG B2309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31792.70 seconds wall clock time: 549 minutes 56.13 seconds (32996.13 seconds total)