Starting phenix.real_space_refine on Sat Mar 23 20:25:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkg_41350/03_2024/8tkg_41350_trim_updated.pdb" } resolution = 2.5 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= 0.146 sd= 1.901 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 48 5.49 5 S 456 5.16 5 C 46524 2.51 5 N 12272 2.21 5 O 14088 1.98 5 H 71936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A GLU 1177": "OE1" <-> "OE2" Residue "A ASP 1208": "OD1" <-> "OD2" Residue "A TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1319": "OD1" <-> "OD2" Residue "A GLU 1384": "OE1" <-> "OE2" Residue "A GLU 1442": "OE1" <-> "OE2" Residue "A GLU 1639": "OE1" <-> "OE2" Residue "A ASP 1653": "OD1" <-> "OD2" Residue "A TYR 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1954": "OE1" <-> "OE2" Residue "A GLU 2024": "OE1" <-> "OE2" Residue "A GLU 2118": "OE1" <-> "OE2" Residue "A GLU 2149": "OE1" <-> "OE2" Residue "A GLU 2150": "OE1" <-> "OE2" Residue "A GLU 2163": "OE1" <-> "OE2" Residue "A PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2353": "OE1" <-> "OE2" Residue "A GLU 2398": "OE1" <-> "OE2" Residue "A PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2531": "OE1" <-> "OE2" Residue "A ASP 2546": "OD1" <-> "OD2" Residue "B TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 742": "OD1" <-> "OD2" Residue "B ASP 766": "OD1" <-> "OD2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B ASP 814": "OD1" <-> "OD2" Residue "B GLU 880": "OE1" <-> "OE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B GLU 1046": "OE1" <-> "OE2" Residue "B GLU 1177": "OE1" <-> "OE2" Residue "B ASP 1208": "OD1" <-> "OD2" Residue "B TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1319": "OD1" <-> "OD2" Residue "B GLU 1384": "OE1" <-> "OE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B GLU 1639": "OE1" <-> "OE2" Residue "B ASP 1653": "OD1" <-> "OD2" Residue "B GLU 1954": "OE1" <-> "OE2" Residue "B GLU 2024": "OE1" <-> "OE2" Residue "B GLU 2118": "OE1" <-> "OE2" Residue "B GLU 2149": "OE1" <-> "OE2" Residue "B GLU 2150": "OE1" <-> "OE2" Residue "B GLU 2163": "OE1" <-> "OE2" Residue "B PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2353": "OE1" <-> "OE2" Residue "B GLU 2398": "OE1" <-> "OE2" Residue "B PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2531": "OE1" <-> "OE2" Residue "B ASP 2546": "OD1" <-> "OD2" Residue "C TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 742": "OD1" <-> "OD2" Residue "C ASP 766": "OD1" <-> "OD2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 880": "OE1" <-> "OE2" Residue "C GLU 973": "OE1" <-> "OE2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "C GLU 1177": "OE1" <-> "OE2" Residue "C ASP 1208": "OD1" <-> "OD2" Residue "C TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1319": "OD1" <-> "OD2" Residue "C GLU 1384": "OE1" <-> "OE2" Residue "C GLU 1442": "OE1" <-> "OE2" Residue "C GLU 1639": "OE1" <-> "OE2" Residue "C ASP 1653": "OD1" <-> "OD2" Residue "C TYR 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1954": "OE1" <-> "OE2" Residue "C GLU 2024": "OE1" <-> "OE2" Residue "C GLU 2118": "OE1" <-> "OE2" Residue "C GLU 2149": "OE1" <-> "OE2" Residue "C GLU 2150": "OE1" <-> "OE2" Residue "C GLU 2163": "OE1" <-> "OE2" Residue "C PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2353": "OE1" <-> "OE2" Residue "C GLU 2398": "OE1" <-> "OE2" Residue "C PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2531": "OE1" <-> "OE2" Residue "C ASP 2546": "OD1" <-> "OD2" Residue "D TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 742": "OD1" <-> "OD2" Residue "D ASP 766": "OD1" <-> "OD2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D ASP 814": "OD1" <-> "OD2" Residue "D GLU 880": "OE1" <-> "OE2" Residue "D GLU 973": "OE1" <-> "OE2" Residue "D GLU 1046": "OE1" <-> "OE2" Residue "D GLU 1177": "OE1" <-> "OE2" Residue "D ASP 1208": "OD1" <-> "OD2" Residue "D TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 1319": "OD1" <-> "OD2" Residue "D GLU 1384": "OE1" <-> "OE2" Residue "D GLU 1442": "OE1" <-> "OE2" Residue "D GLU 1639": "OE1" <-> "OE2" Residue "D ASP 1653": "OD1" <-> "OD2" Residue "D GLU 1954": "OE1" <-> "OE2" Residue "D GLU 2024": "OE1" <-> "OE2" Residue "D GLU 2118": "OE1" <-> "OE2" Residue "D GLU 2149": "OE1" <-> "OE2" Residue "D GLU 2150": "OE1" <-> "OE2" Residue "D GLU 2163": "OE1" <-> "OE2" Residue "D PHE 2214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2353": "OE1" <-> "OE2" Residue "D GLU 2398": "OE1" <-> "OE2" Residue "D PHE 2502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2531": "OE1" <-> "OE2" Residue "D ASP 2546": "OD1" <-> "OD2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145336 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 35839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2210, 35839 Classifications: {'peptide': 2210} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2146} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 35839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2210, 35839 Classifications: {'peptide': 2210} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2146} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 35839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2210, 35839 Classifications: {'peptide': 2210} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2146} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 35839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2210, 35839 Classifications: {'peptide': 2210} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2146} Chain breaks: 14 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {' CA': 2, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {' CA': 2, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {' CA': 2, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 335 Unusual residues: {' CA': 2, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PCW': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34583 SG CYS A2538 138.391 124.071 93.278 1.00 30.01 S ATOM 34632 SG CYS A2541 136.179 124.831 91.069 1.00 33.32 S ATOM 70422 SG CYS B2538 113.911 138.401 93.231 1.00 30.01 S ATOM 70471 SG CYS B2541 113.150 136.189 91.022 1.00 33.32 S ATOM A04TX SG CYS C2538 99.584 113.912 93.231 1.00 30.01 S ATOM A04VA SG CYS C2541 101.796 113.151 91.022 1.00 33.32 S ATOM A0WHG SG CYS D2538 124.033 99.552 93.215 1.00 30.01 S ATOM A0WIT SG CYS D2541 124.798 101.766 91.009 1.00 33.32 S Time building chain proxies: 46.27, per 1000 atoms: 0.32 Number of scatterers: 145336 At special positions: 0 Unit cell: (239.02, 239.02, 177.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 456 16.00 P 48 15.00 O 14088 8.00 N 12272 7.00 C 46524 6.00 H 71936 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 93.48 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B2702 " pdb="ZN ZN B2702 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2702 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2702 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2702 " - pdb=" SG CYS B2538 " pdb=" ZN C2702 " pdb="ZN ZN C2702 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2702 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2702 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2702 " - pdb=" SG CYS C2538 " pdb=" ZN D2704 " pdb="ZN ZN D2704 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2704 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2704 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2704 " - pdb=" SG CYS D2538 " Number of angles added : 8 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16944 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: 412 helices and 48 sheets defined 70.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 33.86 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.547A pdb=" N CYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.981A 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 76 Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.295A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.671A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.035A 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 362 through 367 removed outlier: 4.228A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.657A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 514 through 525 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.857A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 removed outlier: 3.925A pdb=" N ALA A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Proline residue: A 548 - end of helix removed outlier: 3.919A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.329A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.717A pdb=" N GLN A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 5.795A 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 603 removed outlier: 3.744A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.971A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 removed outlier: 3.593A pdb=" N CYS A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 5.088A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 removed outlier: 3.802A pdb=" N GLU A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 756 removed outlier: 4.021A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 821 removed outlier: 3.831A pdb=" N ASN A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 removed outlier: 4.000A pdb=" N LYS A 829 " --> pdb=" O ASP A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 848 removed outlier: 5.505A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 874 removed outlier: 3.784A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.789A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1003 Proline residue: A1003 - end of helix Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.553A pdb=" N ILE A1028 " --> pdb=" O ASN A1024 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 3.547A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.773A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.541A pdb=" N GLN A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 3.636A pdb=" N LYS A1123 " --> pdb=" O THR A1119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.431A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1202 through 1213 removed outlier: 3.542A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1218 through 1237 Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 4.234A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.890A pdb=" N GLU A1277 " --> pdb=" O GLN A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.862A pdb=" N PHE A1286 " --> pdb=" O VAL A1282 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 3.736A pdb=" N LYS A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.772A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 3.585A pdb=" N ARG A1353 " --> pdb=" O MET A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 5.277A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1392 removed outlier: 3.531A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A1386 " --> pdb=" O TYR A1382 " (cutoff:3.500A) Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1401 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1428 through 1434 removed outlier: 4.392A pdb=" N TYR A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.656A pdb=" N VAL A1471 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1511 removed outlier: 5.933A pdb=" N THR A1496 " --> pdb=" O GLN A1492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A1498 " --> pdb=" O HIS A1494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS A1511 " --> pdb=" O ARG A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1534 Processing helix chain 'A' and resid 1543 through 1557 removed outlier: 4.646A pdb=" N HIS A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1548 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A1550 " --> pdb=" O ALA A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1624 removed outlier: 3.700A pdb=" N LYS A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Proline residue: A1608 - end of helix removed outlier: 3.738A pdb=" N LEU A1617 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 3.967A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 removed outlier: 3.555A pdb=" N MET A1655 " --> pdb=" O THR A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 5.379A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1718 through 1732 Processing helix chain 'A' and resid 1733 through 1744 Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 Processing helix chain 'A' and resid 1781 through 1807 Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 4.241A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 removed outlier: 3.910A pdb=" N ARG A1893 " --> pdb=" O GLN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1902 through 1916 Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 3.663A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 3.980A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1949 Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 4.047A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1985 removed outlier: 3.649A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 removed outlier: 3.595A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2021 removed outlier: 4.024A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2039 removed outlier: 3.868A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2062 removed outlier: 3.814A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2072 removed outlier: 3.527A pdb=" N LYS A2072 " --> pdb=" O GLN A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2121 Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 4.246A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2159 Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 3.896A pdb=" N SER A2175 " --> pdb=" O PHE A2171 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A2191 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Proline residue: A2192 - end of helix Processing helix chain 'A' and resid 2193 through 2223 removed outlier: 3.757A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 6.222A 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: 6.480A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2317 Processing helix chain 'A' and resid 2318 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.736A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.822A 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: 3.992A pdb=" N LEU A2470 " --> pdb=" O MET A2466 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.653A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A2480 " --> pdb=" O VAL A2476 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2475 through 2481' Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.991A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.408A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.783A 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 2612 Processing helix chain 'A' and resid 2598 through 2603 removed outlier: 4.848A pdb=" N TRP A2601 " --> pdb=" O ASN A2598 " (cutoff:3.500A) Proline residue: A2603 - end of helix Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.547A pdb=" N CYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.981A 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 76 Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.295A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.670A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.035A 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 362 through 367 removed outlier: 4.228A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 362 through 367' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.658A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 514 through 525 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.858A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 565 removed outlier: 3.925A pdb=" N ALA B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) Proline residue: B 548 - end of helix removed outlier: 3.919A pdb=" N GLN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.329A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 removed outlier: 3.717A pdb=" N GLN B 584 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 5.795A 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 603 removed outlier: 3.744A pdb=" N THR B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.970A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 removed outlier: 3.593A pdb=" N CYS B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 666 removed outlier: 5.088A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 removed outlier: 3.802A pdb=" N GLU B 723 " --> pdb=" O ASN B 719 " (cutoff:3.500A) 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: 3.806A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 766 Processing helix chain 'B' and resid 770 through 784 Processing helix chain 'B' and resid 811 through 821 removed outlier: 3.831A pdb=" N ASN B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 831 removed outlier: 4.000A pdb=" N LYS B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 848 removed outlier: 5.505A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 874 removed outlier: 3.784A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.789A pdb=" N ARG B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1003 Proline residue: B1003 - end of helix Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.554A pdb=" N ILE B1028 " --> pdb=" O ASN B1024 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 3.546A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.774A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 removed outlier: 3.542A pdb=" N GLN B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 3.637A pdb=" N LYS B1123 " --> pdb=" O THR B1119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B1127 " --> pdb=" O LYS B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.431A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 Processing helix chain 'B' and resid 1202 through 1213 removed outlier: 3.541A pdb=" N ILE B1212 " --> pdb=" O ASP B1208 " (cutoff:3.500A) Proline residue: B1213 - end of helix Processing helix chain 'B' and resid 1218 through 1237 Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 4.233A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1271 through 1278 removed outlier: 3.890A pdb=" N GLU B1277 " --> pdb=" O GLN B1273 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.861A pdb=" N PHE B1286 " --> pdb=" O VAL B1282 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B1287 " --> pdb=" O LEU B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1309 removed outlier: 3.735A pdb=" N LYS B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.771A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 removed outlier: 3.584A pdb=" N ARG B1353 " --> pdb=" O MET B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 5.277A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1392 removed outlier: 3.530A pdb=" N ILE B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B1386 " --> pdb=" O TYR B1382 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1401 Processing helix chain 'B' and resid 1406 through 1420 Processing helix chain 'B' and resid 1428 through 1434 removed outlier: 4.391A pdb=" N TYR B1432 " --> pdb=" O MET B1428 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.657A pdb=" N VAL B1471 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B1474 " --> pdb=" O SER B1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 1490 through 1511 removed outlier: 5.933A pdb=" N THR B1496 " --> pdb=" O GLN B1492 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1534 Processing helix chain 'B' and resid 1543 through 1557 removed outlier: 4.647A pdb=" N HIS B1547 " --> pdb=" O ASP B1543 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B1548 " --> pdb=" O LEU B1544 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B1550 " --> pdb=" O ALA B1546 " (cutoff:3.500A) Processing helix chain 'B' and resid 1587 through 1624 removed outlier: 3.699A pdb=" N LYS B1607 " --> pdb=" O GLU B1603 " (cutoff:3.500A) Proline residue: B1608 - end of helix removed outlier: 3.738A pdb=" N LEU B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B1618 " --> pdb=" O LEU B1614 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 removed outlier: 3.968A pdb=" N GLY B1641 " --> pdb=" O ARG B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.555A pdb=" N MET B1655 " --> pdb=" O THR B1651 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 5.379A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1718 through 1732 Processing helix chain 'B' and resid 1733 through 1744 Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 Processing helix chain 'B' and resid 1781 through 1807 Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 4.241A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 removed outlier: 3.909A pdb=" N ARG B1893 " --> pdb=" O GLN B1889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1902 through 1916 Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 3.663A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 3.980A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1949 Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 4.048A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1985 removed outlier: 3.649A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 removed outlier: 3.594A pdb=" N MET B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2021 removed outlier: 4.024A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2039 removed outlier: 3.868A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU B2037 " --> pdb=" O TYR B2033 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2062 removed outlier: 3.814A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2072 removed outlier: 3.527A pdb=" N LYS B2072 " --> pdb=" O GLN B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2121 Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 4.247A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2159 Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 3.896A pdb=" N SER B2175 " --> pdb=" O PHE B2171 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET B2191 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Proline residue: B2192 - end of helix Processing helix chain 'B' and resid 2193 through 2223 removed outlier: 3.758A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.222A 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: 6.480A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 Processing helix chain 'B' and resid 2318 through 2336 Processing helix chain 'B' and resid 2337 through 2353 removed outlier: 4.736A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 3.822A 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: 3.991A pdb=" N LEU B2470 " --> pdb=" O MET B2466 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.653A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B2480 " --> pdb=" O VAL B2476 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2475 through 2481' Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.991A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.409A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 3.783A 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 2612 Processing helix chain 'B' and resid 2598 through 2603 removed outlier: 4.848A pdb=" N TRP B2601 " --> pdb=" O ASN B2598 " (cutoff:3.500A) Proline residue: B2603 - end of helix Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.547A pdb=" N CYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.981A 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 76 Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.295A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.670A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.035A 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 362 through 367 removed outlier: 4.228A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 367' Processing helix chain 'C' and resid 435 through 462 removed outlier: 3.658A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 514 through 525 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.857A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 removed outlier: 3.925A pdb=" N ALA C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Proline residue: C 548 - end of helix removed outlier: 3.919A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.329A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 removed outlier: 3.717A pdb=" N GLN C 584 " --> pdb=" O MET C 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 585 " --> pdb=" O MET C 581 " (cutoff:3.500A) removed outlier: 5.795A 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 603 removed outlier: 3.744A pdb=" N THR C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.970A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 removed outlier: 3.593A pdb=" N CYS C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 666 removed outlier: 5.088A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 removed outlier: 3.802A pdb=" N GLU C 723 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 756 removed outlier: 4.021A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 756 " --> pdb=" O SER C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 766 Processing helix chain 'C' and resid 770 through 784 Processing helix chain 'C' and resid 811 through 821 removed outlier: 3.830A pdb=" N ASN C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 4.000A pdb=" N LYS C 829 " --> pdb=" O ASP C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 848 removed outlier: 5.505A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 874 removed outlier: 3.784A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.789A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1003 Proline residue: C1003 - end of helix Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.554A pdb=" N ILE C1028 " --> pdb=" O ASN C1024 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 3.546A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.773A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 removed outlier: 3.542A pdb=" N GLN C1094 " --> pdb=" O HIS C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 3.637A pdb=" N LYS C1123 " --> pdb=" O THR C1119 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.431A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 Processing helix chain 'C' and resid 1202 through 1213 removed outlier: 3.541A pdb=" N ILE C1212 " --> pdb=" O ASP C1208 " (cutoff:3.500A) Proline residue: C1213 - end of helix Processing helix chain 'C' and resid 1218 through 1237 Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 4.233A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 Processing helix chain 'C' and resid 1271 through 1278 removed outlier: 3.890A pdb=" N GLU C1277 " --> pdb=" O GLN C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.861A pdb=" N PHE C1286 " --> pdb=" O VAL C1282 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.735A pdb=" N LYS C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.772A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 removed outlier: 3.584A pdb=" N ARG C1353 " --> pdb=" O MET C1349 " (cutoff:3.500A) Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 5.277A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1381 through 1392 removed outlier: 3.530A pdb=" N ILE C1385 " --> pdb=" O VAL C1381 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS C1386 " --> pdb=" O TYR C1382 " (cutoff:3.500A) Proline residue: C1392 - end of helix Processing helix chain 'C' and resid 1393 through 1401 Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1428 through 1434 removed outlier: 4.391A pdb=" N TYR C1432 " --> pdb=" O MET C1428 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER C1434 " --> pdb=" O GLU C1430 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.657A pdb=" N VAL C1471 " --> pdb=" O TYR C1467 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C1474 " --> pdb=" O SER C1470 " (cutoff:3.500A) Processing helix chain 'C' and resid 1490 through 1511 removed outlier: 5.933A pdb=" N THR C1496 " --> pdb=" O GLN C1492 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C1498 " --> pdb=" O HIS C1494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C1511 " --> pdb=" O ARG C1507 " (cutoff:3.500A) Processing helix chain 'C' and resid 1515 through 1534 Processing helix chain 'C' and resid 1543 through 1557 removed outlier: 4.647A pdb=" N HIS C1547 " --> pdb=" O ASP C1543 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1548 " --> pdb=" O LEU C1544 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C1550 " --> pdb=" O ALA C1546 " (cutoff:3.500A) Processing helix chain 'C' and resid 1587 through 1624 removed outlier: 3.699A pdb=" N LYS C1607 " --> pdb=" O GLU C1603 " (cutoff:3.500A) Proline residue: C1608 - end of helix removed outlier: 3.738A pdb=" N LEU C1617 " --> pdb=" O GLU C1613 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C1618 " --> pdb=" O LEU C1614 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 removed outlier: 3.968A pdb=" N GLY C1641 " --> pdb=" O ARG C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1655 removed outlier: 3.555A pdb=" N MET C1655 " --> pdb=" O THR C1651 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 5.379A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1718 through 1732 Processing helix chain 'C' and resid 1733 through 1744 Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1807 Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 4.241A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 removed outlier: 3.910A pdb=" N ARG C1893 " --> pdb=" O GLN C1889 " (cutoff:3.500A) Processing helix chain 'C' and resid 1902 through 1916 Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 3.663A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 3.980A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1949 Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 4.048A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1985 removed outlier: 3.649A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 removed outlier: 3.594A pdb=" N MET C2004 " --> pdb=" O LEU C2000 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2021 removed outlier: 4.024A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2039 removed outlier: 3.868A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2062 removed outlier: 3.814A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2072 removed outlier: 3.527A pdb=" N LYS C2072 " --> pdb=" O GLN C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2121 Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 4.247A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 3.896A pdb=" N SER C2175 " --> pdb=" O PHE C2171 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C2191 " --> pdb=" O LYS C2187 " (cutoff:3.500A) Proline residue: C2192 - end of helix Processing helix chain 'C' and resid 2193 through 2223 removed outlier: 3.758A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.222A 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: 6.480A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2317 Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2337 through 2353 removed outlier: 4.736A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 3.821A 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: 3.991A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.653A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C2480 " --> pdb=" O VAL C2476 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2475 through 2481' Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.991A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.408A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.783A 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 2612 Processing helix chain 'C' and resid 2598 through 2603 removed outlier: 4.848A pdb=" N TRP C2601 " --> pdb=" O ASN C2598 " (cutoff:3.500A) Proline residue: C2603 - end of helix Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.547A pdb=" N CYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.981A 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 76 Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.294A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.671A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.035A 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 362 through 367 removed outlier: 4.228A pdb=" N LEU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE D 367 " --> pdb=" O ILE D 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 362 through 367' Processing helix chain 'D' and resid 435 through 462 removed outlier: 3.657A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 514 through 525 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.857A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 removed outlier: 3.925A pdb=" N ALA D 547 " --> pdb=" O ASP D 543 " (cutoff:3.500A) Proline residue: D 548 - end of helix removed outlier: 3.919A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.329A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 removed outlier: 3.716A pdb=" N GLN D 584 " --> pdb=" O MET D 580 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) removed outlier: 5.795A 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 603 removed outlier: 3.744A pdb=" N THR D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 611 through 626 Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.971A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 removed outlier: 3.593A pdb=" N CYS D 655 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 666 removed outlier: 5.088A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 removed outlier: 3.802A pdb=" N GLU D 723 " --> pdb=" O ASN D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 756 removed outlier: 4.021A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 756 " --> pdb=" O SER D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 766 Processing helix chain 'D' and resid 770 through 784 Processing helix chain 'D' and resid 811 through 821 removed outlier: 3.832A pdb=" N ASN D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 831 removed outlier: 4.000A pdb=" N LYS D 829 " --> pdb=" O ASP D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 848 removed outlier: 5.505A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 874 removed outlier: 3.784A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.790A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1003 Proline residue: D1003 - end of helix Processing helix chain 'D' and resid 1024 through 1037 removed outlier: 3.553A pdb=" N ILE D1028 " --> pdb=" O ASN D1024 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY D1037 " --> pdb=" O GLU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 3.548A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.773A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.541A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.636A pdb=" N LYS D1123 " --> pdb=" O THR D1119 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.431A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 Processing helix chain 'D' and resid 1202 through 1213 removed outlier: 3.542A pdb=" N ILE D1212 " --> pdb=" O ASP D1208 " (cutoff:3.500A) Proline residue: D1213 - end of helix Processing helix chain 'D' and resid 1218 through 1237 Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 4.233A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 Processing helix chain 'D' and resid 1271 through 1278 removed outlier: 3.891A pdb=" N GLU D1277 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.861A pdb=" N PHE D1286 " --> pdb=" O VAL D1282 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D1287 " --> pdb=" O LEU D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1297 through 1309 removed outlier: 3.736A pdb=" N LYS D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.772A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 removed outlier: 3.585A pdb=" N ARG D1353 " --> pdb=" O MET D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 5.278A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1392 removed outlier: 3.531A pdb=" N ILE D1385 " --> pdb=" O VAL D1381 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D1386 " --> pdb=" O TYR D1382 " (cutoff:3.500A) Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1401 Processing helix chain 'D' and resid 1406 through 1420 Processing helix chain 'D' and resid 1428 through 1434 removed outlier: 4.392A pdb=" N TYR D1432 " --> pdb=" O MET D1428 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER D1434 " --> pdb=" O GLU D1430 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.657A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D1474 " --> pdb=" O SER D1470 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1511 removed outlier: 5.934A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D1498 " --> pdb=" O HIS D1494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS D1511 " --> pdb=" O ARG D1507 " (cutoff:3.500A) Processing helix chain 'D' and resid 1515 through 1534 Processing helix chain 'D' and resid 1543 through 1557 removed outlier: 4.646A pdb=" N HIS D1547 " --> pdb=" O ASP D1543 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE D1548 " --> pdb=" O LEU D1544 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D1550 " --> pdb=" O ALA D1546 " (cutoff:3.500A) Processing helix chain 'D' and resid 1587 through 1624 removed outlier: 3.700A pdb=" N LYS D1607 " --> pdb=" O GLU D1603 " (cutoff:3.500A) Proline residue: D1608 - end of helix removed outlier: 3.739A pdb=" N LEU D1617 " --> pdb=" O GLU D1613 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D1618 " --> pdb=" O LEU D1614 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 3.967A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.555A pdb=" N MET D1655 " --> pdb=" O THR D1651 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 5.379A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1718 through 1732 Processing helix chain 'D' and resid 1733 through 1744 Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 Processing helix chain 'D' and resid 1781 through 1807 Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 4.241A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 removed outlier: 3.910A pdb=" N ARG D1893 " --> pdb=" O GLN D1889 " (cutoff:3.500A) Processing helix chain 'D' and resid 1902 through 1916 Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 3.663A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.980A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1933 through 1949 Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 4.047A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) Processing helix chain 'D' and resid 1979 through 1985 removed outlier: 3.649A pdb=" N LYS D1983 " --> pdb=" O SER D1979 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 removed outlier: 3.595A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2021 removed outlier: 4.024A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2039 removed outlier: 3.867A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2062 removed outlier: 3.814A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) Processing helix chain 'D' and resid 2064 through 2072 removed outlier: 3.526A pdb=" N LYS D2072 " --> pdb=" O GLN D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2121 Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 4.246A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2159 Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 3.896A pdb=" N SER D2175 " --> pdb=" O PHE D2171 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET D2191 " --> pdb=" O LYS D2187 " (cutoff:3.500A) Proline residue: D2192 - end of helix Processing helix chain 'D' and resid 2193 through 2223 removed outlier: 3.757A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.222A 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: 6.480A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.736A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 3.821A 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: 3.991A pdb=" N LEU D2470 " --> pdb=" O MET D2466 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.653A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D2480 " --> pdb=" O VAL D2476 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2475 through 2481' Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.991A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.408A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.784A 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 2612 Processing helix chain 'D' and resid 2598 through 2603 removed outlier: 4.848A pdb=" N TRP D2601 " --> pdb=" O ASN D2598 " (cutoff:3.500A) Proline residue: D2603 - end of helix Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 20 removed outlier: 9.233A pdb=" N THR A 217 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 185 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 181 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.182A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.811A pdb=" N GLU A 209 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 252 through 255 Processing sheet with id= 5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.405A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 288 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 309 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU A 282 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 368 through 371 Processing sheet with id= 7, first strand: chain 'A' and resid 396 through 401 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'A' and resid 667 through 672 Processing sheet with id= 9, first strand: chain 'A' and resid 800 through 803 Processing sheet with id= 10, first strand: chain 'A' and resid 2122 through 2128 removed outlier: 4.043A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 2395 through 2399 removed outlier: 6.963A pdb=" N PHE A2395 " --> pdb=" O ALA A2454 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A2450 " --> pdb=" O VAL A2399 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 124 through 127 removed outlier: 5.256A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 14 through 20 removed outlier: 9.233A pdb=" N THR B 217 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 185 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 181 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.181A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 194 through 198 removed outlier: 3.810A pdb=" N GLU B 209 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= 17, first strand: chain 'B' and resid 312 through 315 removed outlier: 4.405A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 288 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 309 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU B 282 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 368 through 371 Processing sheet with id= 19, first strand: chain 'B' and resid 396 through 401 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'B' and resid 667 through 672 Processing sheet with id= 21, first strand: chain 'B' and resid 800 through 803 Processing sheet with id= 22, first strand: chain 'B' and resid 2122 through 2128 removed outlier: 4.044A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 2395 through 2399 removed outlier: 6.962A pdb=" N PHE B2395 " --> pdb=" O ALA B2454 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER B2450 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 124 through 127 removed outlier: 5.257A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 131 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 14 through 20 removed outlier: 9.233A pdb=" N THR C 217 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 185 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 181 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.181A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 194 through 198 removed outlier: 3.810A pdb=" N GLU C 209 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 252 through 255 Processing sheet with id= 29, first strand: chain 'C' and resid 312 through 315 removed outlier: 4.405A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 288 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 309 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU C 282 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 368 through 371 Processing sheet with id= 31, first strand: chain 'C' and resid 396 through 401 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'C' and resid 667 through 672 Processing sheet with id= 33, first strand: chain 'C' and resid 800 through 803 Processing sheet with id= 34, first strand: chain 'C' and resid 2122 through 2128 removed outlier: 4.044A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 2395 through 2399 removed outlier: 6.962A pdb=" N PHE C2395 " --> pdb=" O ALA C2454 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER C2450 " --> pdb=" O VAL C2399 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 124 through 127 removed outlier: 5.257A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 131 " --> pdb=" O HIS C 126 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 14 through 20 removed outlier: 9.233A pdb=" N THR D 217 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU D 185 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP D 181 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 149 through 154 removed outlier: 4.182A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 194 through 198 removed outlier: 3.811A pdb=" N GLU D 209 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 252 through 255 Processing sheet with id= 41, first strand: chain 'D' and resid 312 through 315 removed outlier: 4.405A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 288 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 368 through 371 Processing sheet with id= 43, first strand: chain 'D' and resid 396 through 401 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'D' and resid 667 through 672 Processing sheet with id= 45, first strand: chain 'D' and resid 800 through 803 Processing sheet with id= 46, first strand: chain 'D' and resid 2122 through 2128 removed outlier: 4.044A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'D' and resid 2395 through 2399 removed outlier: 6.962A pdb=" N PHE D2395 " --> pdb=" O ALA D2454 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER D2450 " --> pdb=" O VAL D2399 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'D' and resid 124 through 127 removed outlier: 5.256A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) 4216 hydrogen bonds defined for protein. 12588 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: 69.46 Time building geometry restraints manager: 98.62 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: 71768 1.03 - 1.23: 222 1.23 - 1.42: 30187 1.42 - 1.62: 43031 1.62 - 1.81: 788 Bond restraints: 145996 Sorted by residual: bond pdb=" CB PHE A2502 " pdb=" CG PHE A2502 " ideal model delta sigma weight residual 1.502 1.559 -0.057 2.30e-02 1.89e+03 6.20e+00 bond pdb=" CB PHE D2502 " pdb=" CG PHE D2502 " ideal model delta sigma weight residual 1.502 1.559 -0.057 2.30e-02 1.89e+03 6.15e+00 bond pdb=" CB PHE B2502 " pdb=" CG PHE B2502 " ideal model delta sigma weight residual 1.502 1.559 -0.057 2.30e-02 1.89e+03 6.09e+00 bond pdb=" CB PHE C2502 " pdb=" CG PHE C2502 " ideal model delta sigma weight residual 1.502 1.559 -0.057 2.30e-02 1.89e+03 6.09e+00 bond pdb=" CA MET B2460 " pdb=" CB MET B2460 " ideal model delta sigma weight residual 1.528 1.554 -0.026 1.59e-02 3.96e+03 2.61e+00 ... (remaining 145991 not shown) Histogram of bond angle deviations from ideal: 95.99 - 104.76: 964 104.76 - 113.53: 174861 113.53 - 122.30: 68464 122.30 - 131.07: 18812 131.07 - 139.84: 367 Bond angle restraints: 263468 Sorted by residual: angle pdb=" C PHE C2502 " pdb=" CA PHE C2502 " pdb=" CB PHE C2502 " ideal model delta sigma weight residual 110.95 119.35 -8.40 1.55e+00 4.16e-01 2.94e+01 angle pdb=" C PHE B2502 " pdb=" CA PHE B2502 " pdb=" CB PHE B2502 " ideal model delta sigma weight residual 110.95 119.35 -8.40 1.55e+00 4.16e-01 2.94e+01 angle pdb=" C PHE A2502 " pdb=" CA PHE A2502 " pdb=" CB PHE A2502 " ideal model delta sigma weight residual 110.95 119.33 -8.38 1.55e+00 4.16e-01 2.92e+01 angle pdb=" C PHE D2502 " pdb=" CA PHE D2502 " pdb=" CB PHE D2502 " ideal model delta sigma weight residual 110.95 119.31 -8.36 1.55e+00 4.16e-01 2.91e+01 angle pdb=" CA PHE A2502 " pdb=" CB PHE A2502 " pdb=" HB3 PHE A2502 " ideal model delta sigma weight residual 109.00 121.43 -12.43 3.00e+00 1.11e-01 1.72e+01 ... (remaining 263463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 66129 33.40 - 66.80: 2283 66.80 - 100.19: 168 100.19 - 133.59: 28 133.59 - 166.99: 4 Dihedral angle restraints: 68612 sinusoidal: 38104 harmonic: 30508 Sorted by residual: dihedral pdb=" C33 PCW D2710 " pdb=" C31 PCW D2710 " pdb=" C32 PCW D2710 " pdb=" O2 PCW D2710 " ideal model delta sinusoidal sigma weight residual 191.83 24.84 166.99 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C33 PCW A3007 " pdb=" C31 PCW A3007 " pdb=" C32 PCW A3007 " pdb=" O2 PCW A3007 " ideal model delta sinusoidal sigma weight residual 191.83 24.87 166.96 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C33 PCW B2708 " pdb=" C31 PCW B2708 " pdb=" C32 PCW B2708 " pdb=" O2 PCW B2708 " ideal model delta sinusoidal sigma weight residual 191.83 24.91 166.92 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 68609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 10017 0.058 - 0.116: 1207 0.116 - 0.174: 76 0.174 - 0.232: 4 0.232 - 0.290: 12 Chirality restraints: 11316 Sorted by residual: chirality pdb=" C2' ATP C2706 " pdb=" C1' ATP C2706 " pdb=" C3' ATP C2706 " pdb=" O2' ATP C2706 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' ATP D2708 " pdb=" C1' ATP D2708 " pdb=" C3' ATP D2708 " pdb=" O2' ATP D2708 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ATP B2706 " pdb=" C1' ATP B2706 " pdb=" C3' ATP B2706 " pdb=" O2' ATP B2706 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 11313 not shown) Planarity restraints: 21128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2459 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" N MET A2460 " 0.068 2.00e-02 2.50e+03 pdb=" CA MET A2460 " -0.017 2.00e-02 2.50e+03 pdb=" H MET A2460 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D2459 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.56e+01 pdb=" N MET D2460 " -0.068 2.00e-02 2.50e+03 pdb=" CA MET D2460 " 0.017 2.00e-02 2.50e+03 pdb=" H MET D2460 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B2459 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" N MET B2460 " 0.068 2.00e-02 2.50e+03 pdb=" CA MET B2460 " -0.017 2.00e-02 2.50e+03 pdb=" H MET B2460 " -0.031 2.00e-02 2.50e+03 ... (remaining 21125 not shown) Histogram of nonbonded interaction distances: 0.30 - 1.16: 124 1.16 - 2.02: 1836 2.02 - 2.88: 368808 2.88 - 3.74: 616088 3.74 - 4.60: 1074119 Warning: very small nonbonded interaction distances. Nonbonded interactions: 2060975 Sorted by model distance: nonbonded pdb=" H ASN A 146 " pdb=" HB2 LYS B1534 " model vdw 0.304 2.270 nonbonded pdb=" H ASN B 146 " pdb=" HB2 LYS C1534 " model vdw 0.324 2.270 nonbonded pdb=" H ASN C 146 " pdb=" HB2 LYS D1534 " model vdw 0.369 2.270 nonbonded pdb=" OH TYR C 199 " pdb=" H ARG D1536 " model vdw 0.395 1.850 nonbonded pdb=" HB2 LYS A1534 " pdb=" H ASN D 146 " model vdw 0.395 2.270 ... (remaining 2060970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 2612 or (resid 3009 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name O11 \ or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4 \ P or name P )) or resid 3010 or (resid 3011 and (name N or name C1 or name C11 o \ r name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or n \ ame C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or n \ ame O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or \ name O4P or name P )))) selection = (chain 'B' and (resid 5 through 2612 or (resid 2709 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name O11 \ or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4 \ P or name P )) or (resid 2710 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or \ name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )) or (resid 2711 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) selection = (chain 'C' and (resid 5 through 2612 or (resid 2709 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name O11 \ or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4 \ P or name P )) or (resid 2710 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or \ name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )) or (resid 2711 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) selection = (chain 'D' and (resid 5 through 2612 or (resid 2709 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C4 or name C5 or name C6 or name C7 or name C8 or name O11 \ or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4 \ P or name P )) or (resid 2710 and (name N or name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or \ name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )) or (resid 2711 and (name N or name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name C46 or name C5 or name C6 or name C7 or name C8 or name O11 or name \ O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or nam \ e P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.550 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: 1.640 Extract box with map and model: 59.630 Check model and map are aligned: 1.920 Set scattering table: 1.080 Process input model: 423.130 Find NCS groups from input model: 8.120 Set up NCS constraints: 0.630 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 523.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 0.057 74060 Z= 0.137 Angle : 0.486 8.404 99916 Z= 0.261 Chirality : 0.037 0.290 11316 Planarity : 0.003 0.050 12596 Dihedral : 17.399 166.991 28404 Min Nonbonded Distance : 0.701 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.24 % Allowed : 10.78 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.96 (0.09), residues: 8720 helix: 2.90 (0.07), residues: 5512 sheet: 0.76 (0.22), residues: 600 loop : 0.17 (0.13), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D2196 HIS 0.006 0.001 HIS D1650 PHE 0.022 0.001 PHE D2197 TYR 0.012 0.001 TYR B2326 ARG 0.007 0.000 ARG C1116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1213 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1194 time to evaluate : 8.276 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: A 286 GLU cc_start: 0.7390 (tt0) cc_final: 0.7066 (tm-30) REVERT: A 510 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7627 (tmm-80) REVERT: A 554 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7654 (tpp80) REVERT: A 1182 MET cc_start: 0.8283 (tpp) cc_final: 0.7957 (mmm) REVERT: A 1221 MET cc_start: 0.8122 (tpt) cc_final: 0.7854 (tpt) REVERT: A 1260 GLU cc_start: 0.7431 (mp0) cc_final: 0.7203 (mp0) REVERT: A 1410 LYS cc_start: 0.7764 (mttt) cc_final: 0.7478 (ttmm) REVERT: A 1632 SER cc_start: 0.8354 (m) cc_final: 0.7983 (p) REVERT: A 1658 GLU cc_start: 0.7696 (mp0) cc_final: 0.7469 (mp0) REVERT: B 507 LYS cc_start: 0.8098 (tttt) cc_final: 0.7313 (ttmm) REVERT: B 509 MET cc_start: 0.7718 (mtp) cc_final: 0.7509 (mmm) REVERT: B 810 ILE cc_start: 0.8489 (tp) cc_final: 0.8266 (tp) REVERT: B 1260 GLU cc_start: 0.7598 (mp0) cc_final: 0.7362 (mp0) REVERT: B 1306 VAL cc_start: 0.8290 (t) cc_final: 0.8055 (t) REVERT: B 1632 SER cc_start: 0.8431 (m) cc_final: 0.8158 (p) REVERT: B 1693 ASN cc_start: 0.8227 (t0) cc_final: 0.7869 (t0) REVERT: C 1030 GLU cc_start: 0.7343 (tt0) cc_final: 0.7128 (tt0) REVERT: C 1189 MET cc_start: 0.7861 (tpp) cc_final: 0.7589 (tpp) REVERT: C 1280 GLU cc_start: 0.7378 (tp30) cc_final: 0.6883 (tp30) REVERT: C 1306 VAL cc_start: 0.7412 (t) cc_final: 0.7192 (p) REVERT: C 1320 MET cc_start: 0.7730 (mtt) cc_final: 0.7241 (mtm) REVERT: C 1448 MET cc_start: 0.6055 (mtt) cc_final: 0.5775 (mtt) REVERT: D 507 LYS cc_start: 0.8205 (tttt) cc_final: 0.7383 (ttmm) REVERT: D 564 GLN cc_start: 0.7947 (pp30) cc_final: 0.6971 (pp30) REVERT: D 1177 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 1221 MET cc_start: 0.8023 (tpt) cc_final: 0.7815 (tpt) REVERT: D 1285 HIS cc_start: 0.8341 (t-90) cc_final: 0.7939 (t-170) REVERT: D 1410 LYS cc_start: 0.7854 (mttt) cc_final: 0.7604 (ttmm) REVERT: D 1632 SER cc_start: 0.8313 (m) cc_final: 0.8094 (p) REVERT: D 2531 GLU cc_start: 0.8057 (tp30) cc_final: 0.7809 (mm-30) REVERT: D 2604 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7969 (tpt170) outliers start: 19 outliers final: 9 residues processed: 1202 average time/residue: 2.9320 time to fit residues: 4845.0381 Evaluate side-chains 1024 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1015 time to evaluate : 8.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain D residue 1531 MET Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 746 optimal weight: 1.9990 chunk 670 optimal weight: 50.0000 chunk 371 optimal weight: 1.9990 chunk 228 optimal weight: 50.0000 chunk 451 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 692 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 515 optimal weight: 1.9990 chunk 802 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN A1650 HIS A1685 GLN A1693 ASN A2283 ASN A2550 ASN B 649 GLN B 724 ASN B2283 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN C1168 ASN ** C1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1402 HIS C1443 ASN C1650 HIS ** C2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1211 GLN D1284 GLN D1443 ASN D1650 HIS D1693 ASN D2550 ASN D2592 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.327 74060 Z= 0.638 Angle : 0.599 38.586 99916 Z= 0.323 Chirality : 0.040 0.387 11316 Planarity : 0.004 0.061 12596 Dihedral : 12.407 156.363 10675 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.76 % Rotamer: Outliers : 1.89 % Allowed : 11.34 % Favored : 86.78 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.73 (0.09), residues: 8720 helix: 2.73 (0.07), residues: 5532 sheet: 0.68 (0.22), residues: 600 loop : 0.03 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2566 HIS 0.010 0.001 HIS C1251 PHE 0.017 0.002 PHE D2502 TYR 0.032 0.002 TYR C 199 ARG 0.009 0.000 ARG C1116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1182 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1031 time to evaluate : 8.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7382 (ttm170) REVERT: A 555 LEU cc_start: 0.8312 (mt) cc_final: 0.8001 (mt) REVERT: A 651 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 814 ASP cc_start: 0.7940 (m-30) cc_final: 0.7688 (m-30) REVERT: A 1030 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: A 1105 GLU cc_start: 0.8014 (tt0) cc_final: 0.7800 (mm-30) REVERT: A 1182 MET cc_start: 0.8261 (tpp) cc_final: 0.8008 (tmm) REVERT: A 1410 LYS cc_start: 0.7899 (mttt) cc_final: 0.7620 (ttmm) REVERT: A 1795 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7923 (ttm-80) REVERT: A 2155 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 2338 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: B 627 GLU cc_start: 0.8167 (tt0) cc_final: 0.7753 (tt0) REVERT: B 651 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8303 (mm) REVERT: B 810 ILE cc_start: 0.8676 (tp) cc_final: 0.8441 (tp) REVERT: B 1125 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6856 (mp0) REVERT: B 1260 GLU cc_start: 0.7768 (mp0) cc_final: 0.7556 (mp0) REVERT: B 1289 LEU cc_start: 0.8624 (mp) cc_final: 0.8366 (mm) REVERT: B 1330 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7242 (t0) REVERT: B 1443 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8186 (m110) REVERT: B 1745 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8660 (mppt) REVERT: B 1795 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7916 (ttm-80) REVERT: B 2131 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7437 (mtp-110) REVERT: B 2338 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: C 215 CYS cc_start: 0.3694 (OUTLIER) cc_final: 0.3323 (m) REVERT: C 583 SER cc_start: 0.8794 (t) cc_final: 0.8544 (p) REVERT: C 834 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7529 (mtm) REVERT: C 1189 MET cc_start: 0.7775 (tpp) cc_final: 0.7506 (tpp) REVERT: C 1384 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6380 (mt-10) REVERT: C 1448 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.6002 (mtt) REVERT: C 2129 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: C 2226 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6884 (mtt) REVERT: C 2531 GLU cc_start: 0.8147 (tp30) cc_final: 0.7919 (mm-30) REVERT: D 507 LYS cc_start: 0.8176 (tttt) cc_final: 0.7808 (ttmm) REVERT: D 510 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7430 (ttm170) REVERT: D 554 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7751 (tpp80) REVERT: D 580 MET cc_start: 0.7628 (ppp) cc_final: 0.7317 (ppp) REVERT: D 660 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8820 (ptmm) REVERT: D 724 ASN cc_start: 0.8269 (t0) cc_final: 0.7859 (m-40) REVERT: D 1089 MET cc_start: 0.8519 (mmm) cc_final: 0.8310 (mmp) REVERT: D 1177 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D 1221 MET cc_start: 0.8230 (tpt) cc_final: 0.7903 (tpt) REVERT: D 1248 LYS cc_start: 0.8536 (tppt) cc_final: 0.8301 (mttp) REVERT: D 1285 HIS cc_start: 0.8659 (t-90) cc_final: 0.8288 (t-170) REVERT: D 1297 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6938 (p) REVERT: D 1410 LYS cc_start: 0.7978 (mttt) cc_final: 0.7718 (ttmm) REVERT: D 1783 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: D 1795 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: D 2170 ASP cc_start: 0.8366 (m-30) cc_final: 0.8151 (m-30) REVERT: D 2201 MET cc_start: 0.7671 (ttp) cc_final: 0.7337 (mtp) outliers start: 151 outliers final: 63 residues processed: 1117 average time/residue: 2.8993 time to fit residues: 4436.2832 Evaluate side-chains 1068 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 985 time to evaluate : 8.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1030 GLU Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2338 GLU Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1228 THR Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1443 ASN Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1486 GLU Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1771 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2338 GLU Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 834 MET Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1024 ASN Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1443 ASN Chi-restraints excluded: chain C residue 1448 MET Chi-restraints excluded: chain C residue 1486 GLU Chi-restraints excluded: chain C residue 1681 ASP Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2129 GLN Chi-restraints excluded: chain C residue 2226 MET Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 992 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1783 GLU Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 446 optimal weight: 0.0870 chunk 249 optimal weight: 20.0000 chunk 668 optimal weight: 10.0000 chunk 546 optimal weight: 0.9990 chunk 221 optimal weight: 30.0000 chunk 804 optimal weight: 1.9990 chunk 868 optimal weight: 2.9990 chunk 716 optimal weight: 4.9990 chunk 797 optimal weight: 0.4980 chunk 274 optimal weight: 4.9990 chunk 645 optimal weight: 0.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A1102 GLN ** A1285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 ASN ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1693 ASN A2283 ASN A2550 ASN B 573 HIS B1650 HIS B1693 ASN B2550 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS C1251 HIS C1285 HIS C1327 ASN C1402 HIS C1443 ASN C1650 HIS C1685 GLN C2292 ASN D1180 ASN D1284 GLN ** D1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1443 ASN ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS D1693 ASN D1909 GLN D2035 GLN D2592 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 74060 Z= 0.197 Angle : 0.469 14.160 99916 Z= 0.248 Chirality : 0.036 0.192 11316 Planarity : 0.003 0.073 12596 Dihedral : 10.994 142.054 10671 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 11.96 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.87 (0.09), residues: 8720 helix: 2.88 (0.07), residues: 5528 sheet: 0.66 (0.22), residues: 600 loop : -0.00 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2566 HIS 0.013 0.001 HIS C 195 PHE 0.009 0.001 PHE C2571 TYR 0.012 0.001 TYR C1272 ARG 0.007 0.000 ARG D2199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1125 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1022 time to evaluate : 8.484 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: A 555 LEU cc_start: 0.8318 (mt) cc_final: 0.8026 (mt) REVERT: A 569 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7158 (mttt) REVERT: A 651 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 814 ASP cc_start: 0.7964 (m-30) cc_final: 0.7759 (m-30) REVERT: A 1105 GLU cc_start: 0.7987 (tt0) cc_final: 0.7777 (mm-30) REVERT: A 1410 LYS cc_start: 0.7904 (mttt) cc_final: 0.7609 (ttmm) REVERT: A 1795 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: A 2531 GLU cc_start: 0.8081 (tp30) cc_final: 0.7761 (mm-30) REVERT: B 510 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7588 (tmm160) REVERT: B 651 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 724 ASN cc_start: 0.8338 (t0) cc_final: 0.7960 (m-40) REVERT: B 810 ILE cc_start: 0.8700 (tp) cc_final: 0.8460 (tp) REVERT: B 1125 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6960 (mp0) REVERT: B 1206 MET cc_start: 0.7930 (mmp) cc_final: 0.7619 (mmt) REVERT: B 1330 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7213 (t0) REVERT: B 1443 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8121 (m110) REVERT: B 1745 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8710 (mppt) REVERT: B 1795 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: B 2338 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: C 569 LYS cc_start: 0.7692 (tttt) cc_final: 0.7491 (ttmt) REVERT: C 583 SER cc_start: 0.8788 (t) cc_final: 0.8539 (p) REVERT: C 714 GLU cc_start: 0.8028 (tp30) cc_final: 0.7491 (tp30) REVERT: C 834 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7688 (mtm) REVERT: C 1189 MET cc_start: 0.7686 (tpp) cc_final: 0.7431 (tpp) REVERT: C 1297 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6572 (p) REVERT: C 1384 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6278 (mt-10) REVERT: C 1448 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5999 (mtt) REVERT: C 2021 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7424 (mmm160) REVERT: C 2024 GLU cc_start: 0.7889 (mp0) cc_final: 0.7687 (mp0) REVERT: C 2226 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: C 2531 GLU cc_start: 0.8141 (tp30) cc_final: 0.7929 (mm-30) REVERT: D 510 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7462 (ttm170) REVERT: D 554 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7782 (tpp80) REVERT: D 555 LEU cc_start: 0.8332 (mt) cc_final: 0.8019 (mt) REVERT: D 724 ASN cc_start: 0.8235 (t0) cc_final: 0.7847 (m-40) REVERT: D 1221 MET cc_start: 0.8223 (tpt) cc_final: 0.7906 (tpt) REVERT: D 1248 LYS cc_start: 0.8524 (tppt) cc_final: 0.8265 (mttp) REVERT: D 1396 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7655 (m) REVERT: D 1410 LYS cc_start: 0.7919 (mttt) cc_final: 0.7670 (ttmm) REVERT: D 1487 ASN cc_start: 0.5366 (OUTLIER) cc_final: 0.4858 (m110) REVERT: D 1795 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7868 (ttm-80) REVERT: D 2021 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7229 (mmm160) REVERT: D 2170 ASP cc_start: 0.8356 (m-30) cc_final: 0.8155 (m-30) REVERT: D 2201 MET cc_start: 0.7771 (ttp) cc_final: 0.7480 (mtp) outliers start: 103 outliers final: 46 residues processed: 1068 average time/residue: 2.9428 time to fit residues: 4314.8264 Evaluate side-chains 1036 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 974 time to evaluate : 8.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1487 ASN Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1396 VAL Chi-restraints excluded: chain B residue 1443 ASN Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1886 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2338 GLU Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 834 MET Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1276 SER Chi-restraints excluded: chain C residue 1278 ILE Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1448 MET Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2226 MET Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2354 THR Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1487 ASN Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 794 optimal weight: 4.9990 chunk 604 optimal weight: 2.9990 chunk 417 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 540 optimal weight: 6.9990 chunk 807 optimal weight: 2.9990 chunk 854 optimal weight: 0.9980 chunk 421 optimal weight: 1.9990 chunk 764 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 ASN ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1685 GLN A1693 ASN A2283 ASN B 195 HIS B1650 HIS B1693 ASN B2179 HIS C 562 HIS C1251 HIS C1402 HIS C1650 HIS C1684 ASN C2179 HIS D1443 ASN ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1693 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 74060 Z= 0.345 Angle : 0.525 9.826 99916 Z= 0.277 Chirality : 0.039 0.192 11316 Planarity : 0.004 0.091 12596 Dihedral : 10.628 144.951 10668 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.65 % Favored : 97.34 % Rotamer: Outliers : 2.00 % Allowed : 11.71 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.47 (0.09), residues: 8720 helix: 2.59 (0.07), residues: 5480 sheet: 0.41 (0.21), residues: 604 loop : -0.12 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2566 HIS 0.012 0.001 HIS B1285 PHE 0.021 0.002 PHE C1444 TYR 0.018 0.001 TYR B1421 ARG 0.008 0.001 ARG D1116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1191 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1031 time to evaluate : 8.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.8383 (mt) cc_final: 0.8099 (mt) REVERT: A 564 GLN cc_start: 0.8356 (pp30) cc_final: 0.7811 (pp30) REVERT: A 569 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7354 (mttt) REVERT: A 604 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7782 (ttmm) REVERT: A 627 GLU cc_start: 0.8108 (tt0) cc_final: 0.7872 (tt0) REVERT: A 749 ASP cc_start: 0.8073 (m-30) cc_final: 0.7827 (m-30) REVERT: A 862 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8370 (mp0) REVERT: A 1204 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8088 (mtpm) REVERT: A 1297 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7218 (p) REVERT: A 1410 LYS cc_start: 0.8048 (mttt) cc_final: 0.7789 (ttmm) REVERT: A 1795 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7926 (ttm-80) REVERT: A 2338 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: A 2531 GLU cc_start: 0.8107 (tp30) cc_final: 0.7833 (mm-30) REVERT: B 564 GLN cc_start: 0.8284 (pp30) cc_final: 0.8043 (pp30) REVERT: B 569 LYS cc_start: 0.7735 (mttp) cc_final: 0.7484 (mttp) REVERT: B 627 GLU cc_start: 0.8140 (tt0) cc_final: 0.7854 (tt0) REVERT: B 724 ASN cc_start: 0.8306 (t0) cc_final: 0.7949 (m-40) REVERT: B 810 ILE cc_start: 0.8756 (tp) cc_final: 0.8500 (tp) REVERT: B 1206 MET cc_start: 0.7982 (mmp) cc_final: 0.7756 (mmt) REVERT: B 1330 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7304 (t0) REVERT: B 1784 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.8020 (mtp85) REVERT: B 1795 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: B 1914 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8461 (ttp) REVERT: B 1978 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8029 (mm) REVERT: B 2170 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: B 2226 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7297 (mtt) REVERT: B 2338 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: C 565 GLU cc_start: 0.8241 (tt0) cc_final: 0.7993 (tt0) REVERT: C 583 SER cc_start: 0.8861 (t) cc_final: 0.8605 (p) REVERT: C 705 GLU cc_start: 0.7748 (pm20) cc_final: 0.7346 (pt0) REVERT: C 714 GLU cc_start: 0.8023 (tp30) cc_final: 0.7455 (tp30) REVERT: C 749 ASP cc_start: 0.7532 (m-30) cc_final: 0.7305 (m-30) REVERT: C 1176 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 1189 MET cc_start: 0.7658 (tpp) cc_final: 0.7383 (tpp) REVERT: C 1319 ASP cc_start: 0.7350 (m-30) cc_final: 0.7099 (m-30) REVERT: C 1384 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6524 (mt-10) REVERT: C 1470 SER cc_start: 0.7925 (t) cc_final: 0.7600 (p) REVERT: C 1637 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7332 (mtp180) REVERT: C 2021 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7512 (mmm160) REVERT: C 2024 GLU cc_start: 0.7970 (mp0) cc_final: 0.7729 (mp0) REVERT: C 2170 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8103 (m-30) REVERT: C 2226 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: D 555 LEU cc_start: 0.8380 (mt) cc_final: 0.8093 (mt) REVERT: D 564 GLN cc_start: 0.8410 (pp30) cc_final: 0.8120 (pp30) REVERT: D 581 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: D 627 GLU cc_start: 0.8076 (tt0) cc_final: 0.7704 (tt0) REVERT: D 724 ASN cc_start: 0.8200 (t0) cc_final: 0.7865 (m-40) REVERT: D 1182 MET cc_start: 0.8302 (tpp) cc_final: 0.8074 (tpp) REVERT: D 1200 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: D 1221 MET cc_start: 0.8219 (tpt) cc_final: 0.7860 (tpt) REVERT: D 1297 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7253 (p) REVERT: D 1410 LYS cc_start: 0.8052 (mttt) cc_final: 0.7779 (ttmm) REVERT: D 1795 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: D 2557 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7740 (tt0) outliers start: 160 outliers final: 83 residues processed: 1119 average time/residue: 2.9168 time to fit residues: 4500.2976 Evaluate side-chains 1095 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 994 time to evaluate : 7.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1443 ASN Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1486 GLU Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2338 GLU Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1472 VAL Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1646 LYS Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1886 ARG Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1978 ILE Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2226 MET Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2338 GLU Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1276 SER Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2226 MET Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 992 SER Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1200 MET Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 1931 GLU Chi-restraints excluded: chain D residue 1976 ASN Chi-restraints excluded: chain D residue 2019 SER Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2188 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 711 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 636 optimal weight: 5.9990 chunk 352 optimal weight: 4.9990 chunk 729 optimal weight: 0.6980 chunk 590 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 436 optimal weight: 1.9990 chunk 766 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 ASN ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1693 ASN B1296 HIS B2283 ASN C 562 HIS C1239 ASN C1285 HIS C1443 ASN C1650 HIS C1684 ASN C1900 ASN D1296 HIS D1443 ASN ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1650 HIS D1693 ASN D1798 GLN D1976 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 74060 Z= 0.256 Angle : 0.470 6.897 99916 Z= 0.250 Chirality : 0.036 0.182 11316 Planarity : 0.003 0.081 12596 Dihedral : 10.255 146.528 10668 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.62 % Allowed : 12.52 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 2.53 (0.09), residues: 8720 helix: 2.64 (0.07), residues: 5504 sheet: 0.30 (0.20), residues: 652 loop : -0.10 (0.13), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2566 HIS 0.012 0.001 HIS D1293 PHE 0.013 0.001 PHE D1002 TYR 0.016 0.001 TYR C1272 ARG 0.007 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1158 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1028 time to evaluate : 8.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7180 (mp0) REVERT: A 555 LEU cc_start: 0.8394 (mt) cc_final: 0.8112 (mt) REVERT: A 564 GLN cc_start: 0.8402 (pp30) cc_final: 0.7693 (pp30) REVERT: A 569 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7448 (mttt) REVERT: A 604 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7816 (ttmm) REVERT: A 627 GLU cc_start: 0.8023 (tt0) cc_final: 0.7787 (tt0) REVERT: A 749 ASP cc_start: 0.8073 (m-30) cc_final: 0.7790 (m-30) REVERT: A 1204 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8038 (mtpm) REVERT: A 1297 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7115 (p) REVERT: A 1410 LYS cc_start: 0.8079 (mttt) cc_final: 0.7758 (ttmm) REVERT: A 1795 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7926 (ttm-80) REVERT: A 2531 GLU cc_start: 0.8089 (tp30) cc_final: 0.7817 (mm-30) REVERT: B 564 GLN cc_start: 0.8352 (pp30) cc_final: 0.7446 (pp30) REVERT: B 569 LYS cc_start: 0.7751 (mttp) cc_final: 0.7542 (mttp) REVERT: B 627 GLU cc_start: 0.8084 (tt0) cc_final: 0.7856 (tt0) REVERT: B 724 ASN cc_start: 0.8232 (t0) cc_final: 0.7894 (m-40) REVERT: B 810 ILE cc_start: 0.8765 (tp) cc_final: 0.8492 (tp) REVERT: B 814 ASP cc_start: 0.8062 (m-30) cc_final: 0.7740 (m-30) REVERT: B 1330 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 1783 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: B 1784 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7961 (mtm180) REVERT: B 1795 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7954 (ttm-80) REVERT: B 1914 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: B 2131 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7396 (mtp-110) REVERT: C 563 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8004 (t) REVERT: C 583 SER cc_start: 0.8867 (t) cc_final: 0.8648 (p) REVERT: C 705 GLU cc_start: 0.7766 (pm20) cc_final: 0.7411 (pt0) REVERT: C 714 GLU cc_start: 0.7988 (tp30) cc_final: 0.7449 (tp30) REVERT: C 749 ASP cc_start: 0.7641 (m-30) cc_final: 0.7393 (m-30) REVERT: C 1189 MET cc_start: 0.7612 (tpp) cc_final: 0.7371 (tpp) REVERT: C 1204 LYS cc_start: 0.8545 (mtpm) cc_final: 0.8327 (mtpt) REVERT: C 1297 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7005 (p) REVERT: C 1313 TYR cc_start: 0.7907 (m-80) cc_final: 0.6566 (m-80) REVERT: C 1319 ASP cc_start: 0.7329 (m-30) cc_final: 0.7084 (m-30) REVERT: C 1470 SER cc_start: 0.7978 (t) cc_final: 0.7649 (p) REVERT: C 1637 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7339 (mtp180) REVERT: C 2021 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7491 (mmm160) REVERT: C 2024 GLU cc_start: 0.7999 (mp0) cc_final: 0.7745 (mp0) REVERT: D 555 LEU cc_start: 0.8368 (mt) cc_final: 0.8099 (mt) REVERT: D 564 GLN cc_start: 0.8476 (pp30) cc_final: 0.8049 (pp30) REVERT: D 581 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7937 (ttp) REVERT: D 627 GLU cc_start: 0.8064 (tt0) cc_final: 0.7770 (tt0) REVERT: D 724 ASN cc_start: 0.8168 (t0) cc_final: 0.7855 (m-40) REVERT: D 1182 MET cc_start: 0.8290 (tpp) cc_final: 0.8043 (tpp) REVERT: D 1221 MET cc_start: 0.8196 (tpt) cc_final: 0.7844 (tpt) REVERT: D 1287 VAL cc_start: 0.8467 (t) cc_final: 0.8251 (m) REVERT: D 1297 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7191 (p) REVERT: D 1402 HIS cc_start: 0.7130 (t70) cc_final: 0.6798 (t-90) REVERT: D 1410 LYS cc_start: 0.8068 (mttt) cc_final: 0.7785 (ttmm) REVERT: D 1795 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8017 (ttm-80) REVERT: D 2024 GLU cc_start: 0.7974 (mp0) cc_final: 0.7754 (mp0) REVERT: D 2170 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: D 2557 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7740 (tt0) outliers start: 130 outliers final: 74 residues processed: 1100 average time/residue: 2.9340 time to fit residues: 4428.3349 Evaluate side-chains 1085 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 997 time to evaluate : 8.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1783 GLU Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1886 ARG Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1276 SER Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 1914 MET Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1120 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1486 GLU Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1931 GLU Chi-restraints excluded: chain D residue 1976 ASN Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2170 ASP Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 287 optimal weight: 2.9990 chunk 769 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 501 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 855 optimal weight: 2.9990 chunk 710 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 449 optimal weight: 50.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1487 ASN A1650 HIS A1685 GLN A1693 ASN B1798 GLN B2283 ASN C 562 HIS C1239 ASN C1443 ASN C1650 HIS C1900 ASN D1443 ASN D1487 ASN D1650 HIS D1693 ASN D1798 GLN D1976 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 74060 Z= 0.226 Angle : 0.461 7.039 99916 Z= 0.243 Chirality : 0.036 0.161 11316 Planarity : 0.003 0.078 12596 Dihedral : 10.031 145.902 10668 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 1.70 % Allowed : 12.69 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 2.61 (0.09), residues: 8720 helix: 2.72 (0.07), residues: 5496 sheet: 0.28 (0.20), residues: 652 loop : -0.08 (0.13), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2566 HIS 0.010 0.001 HIS D1293 PHE 0.022 0.001 PHE C1484 TYR 0.014 0.001 TYR C1272 ARG 0.008 0.000 ARG A2199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1157 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1021 time to evaluate : 8.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.8417 (mt) cc_final: 0.8133 (mt) REVERT: A 564 GLN cc_start: 0.8430 (pp30) cc_final: 0.7692 (pp30) REVERT: A 569 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7488 (mttt) REVERT: A 604 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7828 (ttmm) REVERT: A 749 ASP cc_start: 0.8073 (m-30) cc_final: 0.7794 (m-30) REVERT: A 1204 LYS cc_start: 0.8300 (mtmt) cc_final: 0.8017 (mtpm) REVERT: A 1273 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: A 1297 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.7077 (p) REVERT: A 1410 LYS cc_start: 0.8060 (mttt) cc_final: 0.7740 (ttmm) REVERT: A 1487 ASN cc_start: 0.4709 (OUTLIER) cc_final: 0.4472 (m110) REVERT: A 1795 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7930 (ttm-80) REVERT: B 564 GLN cc_start: 0.8399 (pp30) cc_final: 0.7429 (pp30) REVERT: B 627 GLU cc_start: 0.8045 (tt0) cc_final: 0.7820 (tt0) REVERT: B 724 ASN cc_start: 0.8190 (t0) cc_final: 0.7866 (m-40) REVERT: B 749 ASP cc_start: 0.8034 (m-30) cc_final: 0.7756 (m-30) REVERT: B 810 ILE cc_start: 0.8769 (tp) cc_final: 0.8497 (tp) REVERT: B 814 ASP cc_start: 0.8078 (m-30) cc_final: 0.7710 (m-30) REVERT: B 1245 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 1330 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7212 (t0) REVERT: B 1784 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7955 (mtm180) REVERT: B 1795 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7961 (ttm-80) REVERT: B 1978 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8032 (mm) REVERT: B 2131 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7384 (mtp-110) REVERT: B 2170 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: C 563 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (t) REVERT: C 583 SER cc_start: 0.8883 (t) cc_final: 0.8667 (p) REVERT: C 627 GLU cc_start: 0.7931 (tt0) cc_final: 0.7683 (tt0) REVERT: C 705 GLU cc_start: 0.7773 (pm20) cc_final: 0.7443 (pt0) REVERT: C 714 GLU cc_start: 0.7981 (tp30) cc_final: 0.7407 (tp30) REVERT: C 1116 ARG cc_start: 0.8281 (mtp85) cc_final: 0.8014 (ttt90) REVERT: C 1189 MET cc_start: 0.7585 (tpp) cc_final: 0.7338 (tpp) REVERT: C 1297 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7008 (p) REVERT: C 1319 ASP cc_start: 0.7302 (m-30) cc_final: 0.7056 (m-30) REVERT: C 1470 SER cc_start: 0.8045 (t) cc_final: 0.7713 (p) REVERT: C 1637 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7318 (mtp180) REVERT: C 2021 ARG cc_start: 0.7828 (mmm160) cc_final: 0.7509 (mmm160) REVERT: C 2024 GLU cc_start: 0.8018 (mp0) cc_final: 0.7753 (mp0) REVERT: D 555 LEU cc_start: 0.8375 (mt) cc_final: 0.8110 (mt) REVERT: D 564 GLN cc_start: 0.8501 (pp30) cc_final: 0.8073 (pp30) REVERT: D 627 GLU cc_start: 0.8047 (tt0) cc_final: 0.7715 (tt0) REVERT: D 749 ASP cc_start: 0.8052 (m-30) cc_final: 0.7823 (m-30) REVERT: D 1206 MET cc_start: 0.8093 (mmt) cc_final: 0.7884 (mmt) REVERT: D 1221 MET cc_start: 0.8196 (tpt) cc_final: 0.7825 (tpt) REVERT: D 1273 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: D 1287 VAL cc_start: 0.8458 (t) cc_final: 0.8241 (m) REVERT: D 1297 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7172 (p) REVERT: D 1410 LYS cc_start: 0.8076 (mttt) cc_final: 0.7779 (ttmm) REVERT: D 1470 SER cc_start: 0.8430 (t) cc_final: 0.8002 (p) REVERT: D 1783 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: D 1795 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8025 (ttm-80) REVERT: D 2024 GLU cc_start: 0.7984 (mp0) cc_final: 0.7651 (mp0) REVERT: D 2170 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8106 (m-30) REVERT: D 2557 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7738 (tt0) outliers start: 136 outliers final: 75 residues processed: 1098 average time/residue: 2.9291 time to fit residues: 4432.1915 Evaluate side-chains 1086 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 993 time to evaluate : 8.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1273 GLN Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1487 ASN Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1245 LEU Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1978 ILE Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1276 SER Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1443 ASN Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1120 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1443 ASN Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1783 GLU Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2170 ASP Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 824 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 487 optimal weight: 1.9990 chunk 624 optimal weight: 2.9990 chunk 483 optimal weight: 5.9990 chunk 719 optimal weight: 0.9990 chunk 477 optimal weight: 9.9990 chunk 852 optimal weight: 1.9990 chunk 533 optimal weight: 1.9990 chunk 519 optimal weight: 0.9980 chunk 393 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 ASN A1650 HIS A1685 GLN A1693 ASN A1900 ASN B1798 GLN B2283 ASN C 550 GLN C1180 ASN C1239 ASN C1443 ASN C1650 HIS C1897 ASN C1900 ASN D1650 HIS D1693 ASN D1798 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 74060 Z= 0.283 Angle : 0.481 7.613 99916 Z= 0.254 Chirality : 0.037 0.176 11316 Planarity : 0.003 0.081 12596 Dihedral : 9.962 144.434 10668 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.76 % Allowed : 12.89 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.09), residues: 8720 helix: 2.67 (0.07), residues: 5472 sheet: 0.25 (0.20), residues: 652 loop : -0.06 (0.13), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2566 HIS 0.013 0.001 HIS D 195 PHE 0.013 0.001 PHE D1444 TYR 0.016 0.001 TYR C1272 ARG 0.012 0.000 ARG C2199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1159 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1018 time to evaluate : 8.486 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: A 511 GLU cc_start: 0.7434 (mp0) cc_final: 0.7194 (mp0) REVERT: A 564 GLN cc_start: 0.8470 (pp30) cc_final: 0.7732 (pp30) REVERT: A 569 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7531 (mttt) REVERT: A 604 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7853 (ttmm) REVERT: A 660 LYS cc_start: 0.9141 (ptmm) cc_final: 0.8927 (ptmm) REVERT: A 749 ASP cc_start: 0.8090 (m-30) cc_final: 0.7855 (m-30) REVERT: A 1204 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8019 (mtpm) REVERT: A 1273 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: A 1297 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.7095 (p) REVERT: A 1410 LYS cc_start: 0.8089 (mttt) cc_final: 0.7812 (ttmm) REVERT: A 1681 ASP cc_start: 0.8057 (m-30) cc_final: 0.7778 (m-30) REVERT: A 1795 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: B 564 GLN cc_start: 0.8453 (pp30) cc_final: 0.7746 (pp30) REVERT: B 627 GLU cc_start: 0.8037 (tt0) cc_final: 0.7822 (tt0) REVERT: B 724 ASN cc_start: 0.8176 (t0) cc_final: 0.7858 (m-40) REVERT: B 749 ASP cc_start: 0.8072 (m-30) cc_final: 0.7792 (m-30) REVERT: B 810 ILE cc_start: 0.8783 (tp) cc_final: 0.8511 (tp) REVERT: B 814 ASP cc_start: 0.8087 (m-30) cc_final: 0.7738 (m-30) REVERT: B 1245 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 1330 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7209 (t0) REVERT: B 1784 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7955 (mtm180) REVERT: B 1795 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7969 (ttm-80) REVERT: B 1978 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8068 (mm) REVERT: B 2131 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7394 (mtp-110) REVERT: C 148 MET cc_start: 0.1383 (OUTLIER) cc_final: 0.1037 (tmt) REVERT: C 280 ASN cc_start: 0.7867 (m-40) cc_final: 0.7615 (t0) REVERT: C 509 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7222 (mtt) REVERT: C 511 GLU cc_start: 0.7202 (mp0) cc_final: 0.6959 (mp0) REVERT: C 583 SER cc_start: 0.8904 (t) cc_final: 0.8690 (p) REVERT: C 627 GLU cc_start: 0.7945 (tt0) cc_final: 0.7675 (tt0) REVERT: C 705 GLU cc_start: 0.7812 (pm20) cc_final: 0.7498 (pt0) REVERT: C 1116 ARG cc_start: 0.8311 (mtp85) cc_final: 0.8087 (ttp80) REVERT: C 1189 MET cc_start: 0.7597 (tpp) cc_final: 0.7337 (tpp) REVERT: C 1297 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7071 (p) REVERT: C 1319 ASP cc_start: 0.7323 (m-30) cc_final: 0.7076 (m-30) REVERT: C 1470 SER cc_start: 0.8088 (t) cc_final: 0.7771 (p) REVERT: C 1637 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7363 (mtp180) REVERT: C 2021 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7501 (mmm160) REVERT: C 2024 GLU cc_start: 0.8025 (mp0) cc_final: 0.7746 (mp0) REVERT: C 2170 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: D 555 LEU cc_start: 0.8403 (mt) cc_final: 0.8135 (mt) REVERT: D 564 GLN cc_start: 0.8533 (pp30) cc_final: 0.7952 (pp30) REVERT: D 627 GLU cc_start: 0.8039 (tt0) cc_final: 0.7729 (tt0) REVERT: D 749 ASP cc_start: 0.8082 (m-30) cc_final: 0.7849 (m-30) REVERT: D 1200 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: D 1221 MET cc_start: 0.8198 (tpt) cc_final: 0.7835 (tpt) REVERT: D 1273 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: D 1287 VAL cc_start: 0.8477 (t) cc_final: 0.8260 (m) REVERT: D 1297 VAL cc_start: 0.7455 (OUTLIER) cc_final: 0.7201 (p) REVERT: D 1402 HIS cc_start: 0.7138 (t70) cc_final: 0.6851 (t-90) REVERT: D 1410 LYS cc_start: 0.8115 (mttt) cc_final: 0.7781 (ttmm) REVERT: D 1470 SER cc_start: 0.8444 (t) cc_final: 0.8010 (p) REVERT: D 1795 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8056 (ttm-80) REVERT: D 2557 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7740 (tt0) outliers start: 141 outliers final: 82 residues processed: 1102 average time/residue: 2.9406 time to fit residues: 4455.6538 Evaluate side-chains 1087 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 988 time to evaluate : 8.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1273 GLN Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1332 VAL Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain B residue 1245 LEU Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1978 ILE Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1120 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1200 MET Chi-restraints excluded: chain D residue 1273 GLN Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1396 VAL Chi-restraints excluded: chain D residue 1439 THR Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 527 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 chunk 508 optimal weight: 0.5980 chunk 256 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 541 optimal weight: 3.9990 chunk 580 optimal weight: 2.9990 chunk 421 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 669 optimal weight: 40.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 ASN ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1650 HIS A1685 GLN A1693 ASN A1900 ASN A2283 ASN B1685 GLN B1798 GLN B2283 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 ASN C1239 ASN C1650 HIS C1684 ASN C1900 ASN D 550 GLN D1650 HIS D1685 GLN D1693 ASN D1798 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 74060 Z= 0.241 Angle : 0.471 7.899 99916 Z= 0.248 Chirality : 0.036 0.156 11316 Planarity : 0.003 0.078 12596 Dihedral : 9.664 144.102 10668 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.54 % Allowed : 13.14 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.58 (0.09), residues: 8720 helix: 2.67 (0.07), residues: 5520 sheet: 0.25 (0.20), residues: 652 loop : -0.05 (0.13), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2566 HIS 0.009 0.001 HIS D1293 PHE 0.016 0.001 PHE C 553 TYR 0.018 0.001 TYR B1432 ARG 0.011 0.000 ARG C2199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1135 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1012 time to evaluate : 8.511 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: A 511 GLU cc_start: 0.7457 (mp0) cc_final: 0.7199 (mp0) REVERT: A 564 GLN cc_start: 0.8503 (pp30) cc_final: 0.7758 (pp30) REVERT: A 569 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7437 (ttmt) REVERT: A 604 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7891 (ttmm) REVERT: A 660 LYS cc_start: 0.9142 (ptmm) cc_final: 0.8929 (ptmm) REVERT: A 749 ASP cc_start: 0.8088 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1204 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7990 (mtpm) REVERT: A 1273 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: A 1297 VAL cc_start: 0.7304 (OUTLIER) cc_final: 0.7046 (p) REVERT: A 1681 ASP cc_start: 0.8051 (m-30) cc_final: 0.7774 (m-30) REVERT: A 1795 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: B 511 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 564 GLN cc_start: 0.8486 (pp30) cc_final: 0.7776 (pp30) REVERT: B 627 GLU cc_start: 0.7982 (tt0) cc_final: 0.7766 (tt0) REVERT: B 724 ASN cc_start: 0.8160 (t0) cc_final: 0.7852 (m-40) REVERT: B 749 ASP cc_start: 0.8090 (m-30) cc_final: 0.7796 (m-30) REVERT: B 810 ILE cc_start: 0.8790 (tp) cc_final: 0.8514 (tp) REVERT: B 814 ASP cc_start: 0.8113 (m-30) cc_final: 0.7757 (m-30) REVERT: B 1330 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7123 (t0) REVERT: B 1383 THR cc_start: 0.6082 (OUTLIER) cc_final: 0.5780 (t) REVERT: B 1596 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7931 (mm-40) REVERT: B 1784 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7944 (mtm180) REVERT: B 1795 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: B 1978 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8081 (mm) REVERT: B 2131 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7393 (mtp-110) REVERT: B 2170 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: C 148 MET cc_start: 0.1185 (OUTLIER) cc_final: 0.0850 (tmt) REVERT: C 280 ASN cc_start: 0.7855 (m-40) cc_final: 0.7618 (t0) REVERT: C 583 SER cc_start: 0.8915 (t) cc_final: 0.8704 (p) REVERT: C 627 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: C 705 GLU cc_start: 0.7812 (pm20) cc_final: 0.7525 (pt0) REVERT: C 1116 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8113 (ttp80) REVERT: C 1189 MET cc_start: 0.7581 (tpp) cc_final: 0.7352 (tpp) REVERT: C 1204 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8277 (mtpm) REVERT: C 1297 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7078 (p) REVERT: C 1319 ASP cc_start: 0.7335 (m-30) cc_final: 0.7087 (m-30) REVERT: C 1470 SER cc_start: 0.8127 (t) cc_final: 0.7808 (p) REVERT: C 1637 ARG cc_start: 0.7838 (tpp80) cc_final: 0.7387 (mtp180) REVERT: C 2021 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7499 (mmm160) REVERT: C 2024 GLU cc_start: 0.8030 (mp0) cc_final: 0.7751 (mp0) REVERT: C 2170 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: C 2531 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7839 (mm-30) REVERT: D 564 GLN cc_start: 0.8559 (pp30) cc_final: 0.7924 (pp30) REVERT: D 604 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8102 (ttmm) REVERT: D 627 GLU cc_start: 0.8019 (tt0) cc_final: 0.7686 (tt0) REVERT: D 749 ASP cc_start: 0.8084 (m-30) cc_final: 0.7860 (m-30) REVERT: D 1221 MET cc_start: 0.8210 (tpt) cc_final: 0.7830 (tpt) REVERT: D 1287 VAL cc_start: 0.8460 (t) cc_final: 0.8234 (m) REVERT: D 1297 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7178 (p) REVERT: D 1402 HIS cc_start: 0.7184 (t70) cc_final: 0.6898 (t-90) REVERT: D 1410 LYS cc_start: 0.8099 (mttt) cc_final: 0.7762 (ttmm) REVERT: D 1470 SER cc_start: 0.8459 (t) cc_final: 0.8023 (p) REVERT: D 1795 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8044 (ttm-80) REVERT: D 2170 ASP cc_start: 0.8402 (m-30) cc_final: 0.8094 (m-30) REVERT: D 2557 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7745 (tt0) outliers start: 123 outliers final: 79 residues processed: 1086 average time/residue: 2.9710 time to fit residues: 4467.3146 Evaluate side-chains 1096 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1000 time to evaluate : 8.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1273 GLN Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1632 SER Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 1978 ILE Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain B residue 2170 ASP Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1332 VAL Chi-restraints excluded: chain C residue 1396 VAL Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1443 ASN Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2170 ASP Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1120 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1439 THR Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 1886 ARG Chi-restraints excluded: chain D residue 1914 MET Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 775 optimal weight: 0.6980 chunk 816 optimal weight: 1.9990 chunk 744 optimal weight: 1.9990 chunk 793 optimal weight: 0.8980 chunk 477 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 623 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 717 optimal weight: 3.9990 chunk 750 optimal weight: 0.0870 chunk 791 optimal weight: 4.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1487 ASN A1650 HIS A1685 GLN A1693 ASN A1900 ASN A2035 GLN B 577 GLN B1443 ASN B1909 GLN B2283 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 ASN C1239 ASN C1650 HIS C1684 ASN C1900 ASN D1650 HIS D1693 ASN D1798 GLN D1976 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 74060 Z= 0.189 Angle : 0.460 8.437 99916 Z= 0.240 Chirality : 0.036 0.210 11316 Planarity : 0.003 0.073 12596 Dihedral : 9.360 143.314 10668 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 13.54 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.71 (0.09), residues: 8720 helix: 2.78 (0.07), residues: 5520 sheet: 0.26 (0.20), residues: 652 loop : -0.01 (0.13), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2566 HIS 0.008 0.001 HIS D1293 PHE 0.017 0.001 PHE C 553 TYR 0.013 0.001 TYR B1432 ARG 0.010 0.000 ARG D2199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1131 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1026 time to evaluate : 8.430 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: A 511 GLU cc_start: 0.7494 (mp0) cc_final: 0.7223 (mp0) REVERT: A 564 GLN cc_start: 0.8505 (pp30) cc_final: 0.7755 (pp30) REVERT: A 569 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7476 (mttt) REVERT: A 602 ASN cc_start: 0.7706 (t0) cc_final: 0.7469 (t0) REVERT: A 604 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7890 (ttmm) REVERT: A 660 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8916 (ptmm) REVERT: A 749 ASP cc_start: 0.8079 (m-30) cc_final: 0.7877 (m-30) REVERT: A 1204 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7967 (mtpm) REVERT: A 1221 MET cc_start: 0.8211 (tpt) cc_final: 0.7817 (tpt) REVERT: A 1297 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.7009 (p) REVERT: A 1681 ASP cc_start: 0.8053 (m-30) cc_final: 0.7776 (m-30) REVERT: A 1795 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7937 (ttm-80) REVERT: B 564 GLN cc_start: 0.8502 (pp30) cc_final: 0.7676 (pp30) REVERT: B 627 GLU cc_start: 0.7940 (tt0) cc_final: 0.7724 (tt0) REVERT: B 724 ASN cc_start: 0.8137 (t0) cc_final: 0.7826 (m110) REVERT: B 749 ASP cc_start: 0.8083 (m-30) cc_final: 0.7783 (m-30) REVERT: B 810 ILE cc_start: 0.8797 (tp) cc_final: 0.8526 (tp) REVERT: B 1596 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7919 (mm-40) REVERT: B 1784 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7925 (mtm180) REVERT: B 1795 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7975 (ttm-80) REVERT: B 2131 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7369 (mtp-110) REVERT: C 148 MET cc_start: 0.1045 (OUTLIER) cc_final: 0.0742 (tmt) REVERT: C 280 ASN cc_start: 0.7829 (m-40) cc_final: 0.7616 (t0) REVERT: C 511 GLU cc_start: 0.7246 (mp0) cc_final: 0.6515 (mp0) REVERT: C 627 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: C 692 VAL cc_start: 0.8872 (p) cc_final: 0.8654 (t) REVERT: C 705 GLU cc_start: 0.7816 (pm20) cc_final: 0.7585 (pt0) REVERT: C 1116 ARG cc_start: 0.8325 (mtp85) cc_final: 0.8100 (ttp80) REVERT: C 1189 MET cc_start: 0.7568 (tpp) cc_final: 0.7289 (tpp) REVERT: C 1204 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8242 (mtpm) REVERT: C 1297 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.7063 (p) REVERT: C 1319 ASP cc_start: 0.7328 (m-30) cc_final: 0.7073 (m-30) REVERT: C 1470 SER cc_start: 0.8135 (t) cc_final: 0.7819 (p) REVERT: C 1637 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7378 (mtp180) REVERT: C 2021 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7542 (mmm160) REVERT: C 2024 GLU cc_start: 0.8032 (mp0) cc_final: 0.7807 (mp0) REVERT: C 2170 ASP cc_start: 0.8331 (m-30) cc_final: 0.8052 (m-30) REVERT: C 2531 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7840 (mm-30) REVERT: D 564 GLN cc_start: 0.8572 (pp30) cc_final: 0.7945 (pp30) REVERT: D 602 ASN cc_start: 0.7783 (t0) cc_final: 0.7579 (t0) REVERT: D 604 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8092 (ttmm) REVERT: D 627 GLU cc_start: 0.7981 (tt0) cc_final: 0.7656 (tt0) REVERT: D 749 ASP cc_start: 0.8078 (m-30) cc_final: 0.7854 (m-30) REVERT: D 1221 MET cc_start: 0.8209 (tpt) cc_final: 0.7842 (tpt) REVERT: D 1287 VAL cc_start: 0.8451 (t) cc_final: 0.8216 (m) REVERT: D 1297 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7130 (p) REVERT: D 1402 HIS cc_start: 0.7165 (t70) cc_final: 0.6893 (t-90) REVERT: D 1410 LYS cc_start: 0.8084 (mttt) cc_final: 0.7739 (ttmm) REVERT: D 1470 SER cc_start: 0.8450 (t) cc_final: 0.8014 (p) REVERT: D 1472 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.6993 (m) REVERT: D 1795 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8040 (ttm-80) REVERT: D 2170 ASP cc_start: 0.8391 (m-30) cc_final: 0.8100 (m-30) REVERT: D 2557 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7729 (tt0) outliers start: 105 outliers final: 68 residues processed: 1088 average time/residue: 2.8885 time to fit residues: 4323.8175 Evaluate side-chains 1075 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 996 time to evaluate : 8.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1330 ASP Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1100 SER Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1120 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1439 THR Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 521 optimal weight: 1.9990 chunk 839 optimal weight: 1.9990 chunk 512 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 583 optimal weight: 0.5980 chunk 880 optimal weight: 1.9990 chunk 810 optimal weight: 1.9990 chunk 701 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 541 optimal weight: 6.9990 chunk 430 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1443 ASN A1650 HIS A1685 GLN A1693 ASN A1900 ASN B2292 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1443 ASN C1684 ASN C1900 ASN D1443 ASN D1650 HIS D1685 GLN D1798 GLN D1976 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 74060 Z= 0.232 Angle : 0.473 7.933 99916 Z= 0.247 Chirality : 0.036 0.227 11316 Planarity : 0.003 0.071 12596 Dihedral : 9.262 140.879 10668 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.19 % Allowed : 13.81 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 2.62 (0.09), residues: 8720 helix: 2.72 (0.07), residues: 5516 sheet: 0.09 (0.19), residues: 712 loop : -0.04 (0.13), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2566 HIS 0.007 0.001 HIS D1293 PHE 0.017 0.001 PHE C1002 TYR 0.012 0.001 TYR B1432 ARG 0.010 0.000 ARG B1116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17440 Ramachandran restraints generated. 8720 Oldfield, 0 Emsley, 8720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Residue MET 1004 is missing expected H atoms. Skipping. Evaluate side-chains 1098 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1003 time to evaluate : 8.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.0837 (tmt) cc_final: 0.0545 (tmt) REVERT: A 511 GLU cc_start: 0.7524 (mp0) cc_final: 0.7271 (mp0) REVERT: A 564 GLN cc_start: 0.8536 (pp30) cc_final: 0.7867 (pp30) REVERT: A 569 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7572 (mttt) REVERT: A 602 ASN cc_start: 0.7734 (t0) cc_final: 0.7499 (t0) REVERT: A 604 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7902 (ttmm) REVERT: A 660 LYS cc_start: 0.9128 (ptmm) cc_final: 0.8922 (ptmm) REVERT: A 749 ASP cc_start: 0.8093 (m-30) cc_final: 0.7870 (m-30) REVERT: A 1178 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: A 1204 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7983 (mtpm) REVERT: A 1221 MET cc_start: 0.8213 (tpt) cc_final: 0.7828 (tpt) REVERT: A 1297 VAL cc_start: 0.7291 (OUTLIER) cc_final: 0.7024 (p) REVERT: A 1681 ASP cc_start: 0.8046 (m-30) cc_final: 0.7766 (m-30) REVERT: A 1795 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (ttm-80) REVERT: B 511 GLU cc_start: 0.7450 (mp0) cc_final: 0.7131 (mp0) REVERT: B 564 GLN cc_start: 0.8534 (pp30) cc_final: 0.7826 (pp30) REVERT: B 627 GLU cc_start: 0.7929 (tt0) cc_final: 0.7711 (tt0) REVERT: B 749 ASP cc_start: 0.8105 (m-30) cc_final: 0.7817 (m-30) REVERT: B 810 ILE cc_start: 0.8788 (tp) cc_final: 0.8518 (tp) REVERT: B 1383 THR cc_start: 0.6131 (OUTLIER) cc_final: 0.5820 (t) REVERT: B 1596 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7835 (mm-40) REVERT: B 1784 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7930 (mtm180) REVERT: B 1795 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7999 (ttm-80) REVERT: B 2131 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7372 (mtp-110) REVERT: C 148 MET cc_start: 0.1028 (OUTLIER) cc_final: 0.0684 (tmt) REVERT: C 280 ASN cc_start: 0.7834 (m-40) cc_final: 0.7619 (t0) REVERT: C 627 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: C 692 VAL cc_start: 0.8884 (p) cc_final: 0.8660 (t) REVERT: C 705 GLU cc_start: 0.7841 (pm20) cc_final: 0.7640 (pt0) REVERT: C 1177 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 1189 MET cc_start: 0.7581 (tpp) cc_final: 0.7289 (tpp) REVERT: C 1200 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8268 (mtp) REVERT: C 1204 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8244 (mtpm) REVERT: C 1297 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7088 (p) REVERT: C 1319 ASP cc_start: 0.7346 (m-30) cc_final: 0.7094 (m-30) REVERT: C 1470 SER cc_start: 0.8174 (t) cc_final: 0.7853 (p) REVERT: C 1637 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7395 (mtp180) REVERT: C 2021 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7457 (mmm160) REVERT: C 2024 GLU cc_start: 0.8032 (mp0) cc_final: 0.7691 (mp0) REVERT: C 2170 ASP cc_start: 0.8343 (m-30) cc_final: 0.8049 (m-30) REVERT: C 2531 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7834 (mm-30) REVERT: D 564 GLN cc_start: 0.8581 (pp30) cc_final: 0.7912 (pp30) REVERT: D 602 ASN cc_start: 0.7821 (t0) cc_final: 0.7615 (t0) REVERT: D 604 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8093 (ttmm) REVERT: D 749 ASP cc_start: 0.8090 (m-30) cc_final: 0.7866 (m-30) REVERT: D 1200 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8248 (mtp) REVERT: D 1221 MET cc_start: 0.8219 (tpt) cc_final: 0.7832 (tpt) REVERT: D 1287 VAL cc_start: 0.8455 (t) cc_final: 0.8225 (m) REVERT: D 1297 VAL cc_start: 0.7395 (OUTLIER) cc_final: 0.7142 (p) REVERT: D 1402 HIS cc_start: 0.7130 (t70) cc_final: 0.6917 (t-90) REVERT: D 1410 LYS cc_start: 0.8123 (mttt) cc_final: 0.7766 (ttmm) REVERT: D 1470 SER cc_start: 0.8446 (t) cc_final: 0.8010 (p) REVERT: D 1472 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7004 (m) REVERT: D 1795 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (ttm-80) REVERT: D 2170 ASP cc_start: 0.8399 (m-30) cc_final: 0.8099 (m-30) REVERT: D 2557 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7735 (tt0) outliers start: 95 outliers final: 68 residues processed: 1061 average time/residue: 3.0018 time to fit residues: 4399.9744 Evaluate side-chains 1074 residues out of total 8028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 992 time to evaluate : 8.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1120 MET Chi-restraints excluded: chain A residue 1183 CYS Chi-restraints excluded: chain A residue 1276 SER Chi-restraints excluded: chain A residue 1297 VAL Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1472 VAL Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1646 LYS Chi-restraints excluded: chain A residue 1771 SER Chi-restraints excluded: chain A residue 1795 ARG Chi-restraints excluded: chain A residue 1802 SER Chi-restraints excluded: chain A residue 1866 SER Chi-restraints excluded: chain A residue 1886 ARG Chi-restraints excluded: chain A residue 1914 MET Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2316 MET Chi-restraints excluded: chain A residue 2461 CYS Chi-restraints excluded: chain A residue 2581 THR Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain B residue 1276 SER Chi-restraints excluded: chain B residue 1306 VAL Chi-restraints excluded: chain B residue 1383 THR Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1632 SER Chi-restraints excluded: chain B residue 1795 ARG Chi-restraints excluded: chain B residue 1802 SER Chi-restraints excluded: chain B residue 2019 SER Chi-restraints excluded: chain B residue 2131 ARG Chi-restraints excluded: chain B residue 2297 VAL Chi-restraints excluded: chain B residue 2461 CYS Chi-restraints excluded: chain B residue 2581 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 611 THR Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 805 GLU Chi-restraints excluded: chain C residue 1183 CYS Chi-restraints excluded: chain C residue 1193 GLN Chi-restraints excluded: chain C residue 1200 MET Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 VAL Chi-restraints excluded: chain C residue 1646 LYS Chi-restraints excluded: chain C residue 1802 SER Chi-restraints excluded: chain C residue 1866 SER Chi-restraints excluded: chain C residue 2019 SER Chi-restraints excluded: chain C residue 2034 LEU Chi-restraints excluded: chain C residue 2297 VAL Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 862 GLU Chi-restraints excluded: chain D residue 1099 ILE Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1183 CYS Chi-restraints excluded: chain D residue 1200 MET Chi-restraints excluded: chain D residue 1276 SER Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1384 GLU Chi-restraints excluded: chain D residue 1439 THR Chi-restraints excluded: chain D residue 1443 ASN Chi-restraints excluded: chain D residue 1472 VAL Chi-restraints excluded: chain D residue 1528 THR Chi-restraints excluded: chain D residue 1632 SER Chi-restraints excluded: chain D residue 1771 SER Chi-restraints excluded: chain D residue 1795 ARG Chi-restraints excluded: chain D residue 1802 SER Chi-restraints excluded: chain D residue 1866 SER Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2297 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 884 random chunks: chunk 557 optimal weight: 0.6980 chunk 747 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 646 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 702 optimal weight: 5.9990 chunk 293 optimal weight: 0.1980 chunk 721 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1650 HIS A1685 GLN A1693 ASN A1900 ASN B1443 ASN ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 ASN C1443 ASN ** C1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1900 ASN D1650 HIS D1685 GLN D1798 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.181403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125600 restraints weight = 292524.904| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.36 r_work: 0.3262 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 74060 Z= 0.240 Angle : 0.530 59.198 99916 Z= 0.292 Chirality : 0.036 0.213 11316 Planarity : 0.003 0.069 12596 Dihedral : 9.262 140.871 10668 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.16 % Allowed : 14.01 % Favored : 84.83 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.23 % 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: 2.62 (0.09), residues: 8720 helix: 2.72 (0.07), residues: 5516 sheet: 0.09 (0.19), residues: 712 loop : -0.04 (0.13), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2566 HIS 0.006 0.001 HIS D1293 PHE 0.015 0.001 PHE C 553 TYR 0.011 0.001 TYR D2496 ARG 0.007 0.000 ARG C2199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 62925.79 seconds wall clock time: 1072 minutes 49.29 seconds (64369.29 seconds total)