Starting phenix.real_space_refine on Mon Apr 15 20:05:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y6o_38993/04_2024/8y6o_38993_trim_updated.pdb" } resolution = 3.38 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= 0.004 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 409 5.49 5 Mg 2 5.21 5 S 502 5.16 5 C 62886 2.51 5 N 17821 2.21 5 O 19866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 759": "OE1" <-> "OE2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "C GLU 848": "OE1" <-> "OE2" Residue "C GLU 862": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 893": "OE1" <-> "OE2" Residue "C GLU 897": "OE1" <-> "OE2" Residue "C GLU 1171": "OE1" <-> "OE2" Residue "C TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1378": "OE1" <-> "OE2" Residue "C GLU 1388": "OE1" <-> "OE2" Residue "C GLU 1395": "OE1" <-> "OE2" Residue "C GLU 1499": "OE1" <-> "OE2" Residue "C GLU 1587": "OE1" <-> "OE2" Residue "C GLU 2236": "OE1" <-> "OE2" Residue "C GLU 2295": "OE1" <-> "OE2" Residue "C GLU 2331": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 593": "OE1" <-> "OE2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 716": "OE1" <-> "OE2" Residue "D GLU 776": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 659": "OE1" <-> "OE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E GLU 767": "OE1" <-> "OE2" Residue "E GLU 1013": "OE1" <-> "OE2" Residue "E GLU 1031": "OE1" <-> "OE2" Residue "E GLU 1050": "OE1" <-> "OE2" Residue "E GLU 1053": "OE1" <-> "OE2" Residue "E GLU 1073": "OE1" <-> "OE2" Residue "E GLU 1151": "OE1" <-> "OE2" Residue "E GLU 1318": "OE1" <-> "OE2" Residue "E GLU 1383": "OE1" <-> "OE2" Residue "E TYR 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1594": "OE1" <-> "OE2" Residue "E GLU 1739": "OE1" <-> "OE2" Residue "E GLU 1807": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G GLU 719": "OE1" <-> "OE2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "I GLU 252": "OE1" <-> "OE2" Residue "I GLU 337": "OE1" <-> "OE2" Residue "I GLU 404": "OE1" <-> "OE2" Residue "I GLU 486": "OE1" <-> "OE2" Residue "I GLU 509": "OE1" <-> "OE2" Residue "I GLU 583": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "c PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 14": "OE1" <-> "OE2" Residue "d GLU 59": "OE1" <-> "OE2" Residue "e GLU 37": "OE1" <-> "OE2" Residue "e GLU 44": "OE1" <-> "OE2" Residue "e ASP 60": "OD1" <-> "OD2" Residue "f TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 8": "OE1" <-> "OE2" Residue "g ASP 14": "OD1" <-> "OD2" Residue "g PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L GLU 319": "OE1" <-> "OE2" Residue "M GLU 409": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 91": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "W GLU 102": "OE1" <-> "OE2" Residue "W GLU 121": "OE1" <-> "OE2" Residue "W GLU 149": "OE1" <-> "OE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X GLU 103": "OE1" <-> "OE2" Residue "Y ARG 81": "NH1" <-> "NH2" Residue "Y GLU 171": "OE1" <-> "OE2" Residue "Z GLU 287": "OE1" <-> "OE2" Residue "o GLU 75": "OE1" <-> "OE2" Residue "p GLU 51": "OE1" <-> "OE2" Residue "p GLU 56": "OE1" <-> "OE2" Residue "q GLU 14": "OE1" <-> "OE2" Residue "q GLU 15": "OE1" <-> "OE2" Residue "q GLU 20": "OE1" <-> "OE2" Residue "q GLU 21": "OE1" <-> "OE2" Residue "q GLU 22": "OE1" <-> "OE2" Residue "q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 12": "OE1" <-> "OE2" Residue "r GLU 34": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "s GLU 63": "OE1" <-> "OE2" Residue "u GLU 8": "OE1" <-> "OE2" Residue "U GLU 404": "OE1" <-> "OE2" Residue "U GLU 465": "OE1" <-> "OE2" Residue "U ASP 556": "OD1" <-> "OD2" Residue "Q GLU 723": "OE1" <-> "OE2" Residue "Q GLU 734": "OE1" <-> "OE2" Residue "Q GLU 825": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 101492 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 268 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2296 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 12, 'rna3p_pur': 39, 'rna3p_pyr': 50} Link IDs: {'rna2p': 20, 'rna3p': 88} Chain breaks: 1 Chain: "C" Number of atoms: 18488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2227, 18488 Classifications: {'peptide': 2227} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 122, 'TRANS': 2100} Chain breaks: 5 Chain: "D" Number of atoms: 6747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6747 Classifications: {'peptide': 855} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 804} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 16077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2001, 16077 Classifications: {'peptide': 2001} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 1917} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2399 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain: "G" Number of atoms: 6229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6229 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 30, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1145 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 4819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4819 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 566} Chain breaks: 3 Chain: "a" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 594 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Chain: "b" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Chain: "d" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "e" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "f" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 567 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "g" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 577 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "J" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2320 Unusual residues: {'M7M': 1} Classifications: {'RNA': 108, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 41, 'rna3p_pyr': 46} Link IDs: {'rna2p': 21, 'rna3p': 86, None: 1} Not linked: pdbres="M7M J 0 " pdbres=" A J 1 " Chain breaks: 3 Chain: "K" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 942 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 22, 'rna3p_pyr': 19} Link IDs: {'rna2p': 3, 'rna3p': 40} Chain breaks: 1 Chain: "L" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2512 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2863 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 345} Chain: "N" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1861 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 960 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "h" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 669 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "i" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "j" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 737 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "k" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 652 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "l" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 631 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "m" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 562 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "n" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 577 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "P" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2647 Classifications: {'RNA': 124} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 15, 'rna3p_pur': 54, 'rna3p_pyr': 44} Link IDs: {'rna2p': 26, 'rna3p': 97} Chain breaks: 2 Chain: "V" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "W" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "X" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1055 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1889 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Chain: "Z" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1727 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain: "o" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 844 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "r" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 643 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "s" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 668 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "t" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "u" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "S" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 1 Chain: "U" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3765 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 434} Chain: "Q" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2626 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 74439 SG CYS R 7 232.824 185.057 220.827 1.00 93.24 S ATOM 74460 SG CYS R 10 230.574 182.940 222.910 1.00 99.21 S ATOM 74932 SG CYS R 66 242.561 182.036 208.544 1.00235.91 S ATOM 74952 SG CYS R 69 245.080 184.866 208.576 1.00233.45 S ATOM 83282 SG CYS V 57 235.398 97.739 120.516 1.00514.80 S ATOM 83355 SG CYS V 66 233.358 95.844 123.028 1.00495.69 S ATOM 83398 SG CYS V 72 234.405 94.215 119.856 1.00507.80 S ATOM 82858 SG CYS V 7 227.850 70.477 122.466 1.00251.03 S ATOM 82884 SG CYS V 10 226.056 73.685 123.113 1.00257.92 S ATOM 86491 SG CYS Y 58 256.206 43.789 70.340 1.00215.77 S ATOM 86645 SG CYS Y 78 254.520 43.196 74.315 1.00181.63 S ATOM 95328 SG CYS U 136 93.289 137.679 140.895 1.00 0.00 S ATOM 95349 SG CYS U 139 96.364 136.208 142.736 1.00 12.65 S Time building chain proxies: 39.41, per 1000 atoms: 0.39 Number of scatterers: 101492 At special positions: 0 Unit cell: (298.628, 258.882, 283.589, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 502 16.00 P 409 15.00 Mg 2 11.99 O 19866 8.00 N 17821 7.00 C 62886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.40 Conformation dependent library (CDL) restraints added in 12.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" ND1 HIS R 26 " pdb="ZN ZN R1001 " - pdb=" NE2 HIS R 20 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 10 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 7 " pdb=" ZN R1002 " pdb="ZN ZN R1002 " - pdb=" NE2 HIS R 92 " pdb="ZN ZN R1002 " - pdb=" ND1 HIS R 98 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 69 " pdb="ZN ZN R1002 " - pdb=" SG CYS R 66 " pdb=" ZN U1000 " pdb="ZN ZN U1000 " - pdb=" ND1 HIS U 161 " pdb="ZN ZN U1000 " - pdb=" NE2 HIS U 155 " pdb="ZN ZN U1000 " - pdb=" SG CYS U 139 " pdb="ZN ZN U1000 " - pdb=" SG CYS U 136 " pdb=" ZN V 301 " pdb="ZN ZN V 301 " - pdb=" SG CYS V 72 " pdb="ZN ZN V 301 " - pdb=" SG CYS V 57 " pdb="ZN ZN V 301 " - pdb=" SG CYS V 66 " pdb="ZN ZN V 301 " - pdb=" NE2 HIS V 76 " pdb=" ZN V 302 " pdb="ZN ZN V 302 " - pdb=" NE2 HIS V 24 " pdb="ZN ZN V 302 " - pdb=" SG CYS V 7 " pdb="ZN ZN V 302 " - pdb=" SG CYS V 10 " pdb="ZN ZN V 302 " - pdb=" ND1 HIS V 30 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" NE2 HIS Y 74 " pdb="ZN ZN Y1001 " - pdb=" ND1 HIS Y 64 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 58 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 78 " Number of angles added : 10 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21808 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: 423 helices and 109 sheets defined 49.3% alpha, 15.9% beta 112 base pairs and 209 stacking pairs defined. Time for finding SS restraints: 77.99 Creating SS restraints... Processing helix chain 'C' and resid 26 through 51 removed outlier: 3.698A pdb=" N LYS C 43 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 4.683A pdb=" N VAL C 66 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.839A pdb=" N ALA C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N MET C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Proline residue: C 96 - end of helix removed outlier: 3.905A pdb=" N MET C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 159 removed outlier: 3.544A pdb=" N ARG C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 5.987A pdb=" N ASP C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 231 through 247 removed outlier: 5.329A pdb=" N GLN C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.657A pdb=" N LYS C 313 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Proline residue: C 317 - end of helix Processing helix chain 'C' and resid 395 through 407 removed outlier: 4.728A pdb=" N ALA C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 434 removed outlier: 3.884A pdb=" N TYR C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU C 433 " --> pdb=" O ASN C 429 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 427 through 434' Processing helix chain 'C' and resid 440 through 461 removed outlier: 3.523A pdb=" N HIS C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 480 removed outlier: 5.101A pdb=" N LYS C 480 " --> pdb=" O PHE C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.094A pdb=" N LYS C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN C 512 " --> pdb=" O ILE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 539 Processing helix chain 'C' and resid 541 through 567 removed outlier: 3.572A pdb=" N TYR C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 590 through 596 removed outlier: 4.765A pdb=" N TYR C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR C 596 " --> pdb=" O TYR C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 removed outlier: 4.241A pdb=" N GLN C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 657 removed outlier: 4.195A pdb=" N ARG C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 680 through 697 Processing helix chain 'C' and resid 704 through 723 removed outlier: 4.355A pdb=" N THR C 708 " --> pdb=" O ASN C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 764 Processing helix chain 'C' and resid 768 through 798 removed outlier: 3.531A pdb=" N GLU C 789 " --> pdb=" O LYS C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 821 Processing helix chain 'C' and resid 834 through 851 removed outlier: 4.322A pdb=" N TYR C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 851 " --> pdb=" O LYS C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 874 removed outlier: 3.833A pdb=" N ARG C 861 " --> pdb=" O ASN C 857 " (cutoff:3.500A) Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 875 through 887 Processing helix chain 'C' and resid 913 through 934 removed outlier: 3.882A pdb=" N ILE C 917 " --> pdb=" O PRO C 913 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR C 918 " --> pdb=" O LEU C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 962 removed outlier: 3.563A pdb=" N LEU C 962 " --> pdb=" O GLY C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 988 removed outlier: 4.122A pdb=" N ILE C 988 " --> pdb=" O MET C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1001 removed outlier: 3.902A pdb=" N LEU C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1015 removed outlier: 3.639A pdb=" N ASP C1007 " --> pdb=" O HIS C1003 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1054 Processing helix chain 'C' and resid 1055 through 1063 Processing helix chain 'C' and resid 1076 through 1083 removed outlier: 3.725A pdb=" N ALA C1082 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS C1083 " --> pdb=" O THR C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1118 removed outlier: 3.595A pdb=" N ALA C1106 " --> pdb=" O THR C1102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C1107 " --> pdb=" O ALA C1103 " (cutoff:3.500A) Proline residue: C1118 - end of helix Processing helix chain 'C' and resid 1135 through 1140 removed outlier: 5.863A pdb=" N MET C1140 " --> pdb=" O ARG C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1162 removed outlier: 3.618A pdb=" N VAL C1147 " --> pdb=" O MET C1143 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C1161 " --> pdb=" O ILE C1157 " (cutoff:3.500A) Proline residue: C1162 - end of helix Processing helix chain 'C' and resid 1169 through 1174 removed outlier: 5.223A pdb=" N PHE C1174 " --> pdb=" O TRP C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1233 through 1251 removed outlier: 3.903A pdb=" N SER C1251 " --> pdb=" O ILE C1247 " (cutoff:3.500A) Processing helix chain 'C' and resid 1255 through 1275 removed outlier: 3.527A pdb=" N ILE C1259 " --> pdb=" O THR C1255 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C1273 " --> pdb=" O GLY C1269 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C1275 " --> pdb=" O MET C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1276 through 1282 removed outlier: 5.175A pdb=" N GLN C1282 " --> pdb=" O VAL C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1304 Processing helix chain 'C' and resid 1312 through 1318 removed outlier: 4.489A pdb=" N PHE C1316 " --> pdb=" O PRO C1312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C1318 " --> pdb=" O VAL C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1336 through 1341 removed outlier: 3.908A pdb=" N LEU C1340 " --> pdb=" O PRO C1336 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG C1341 " --> pdb=" O GLN C1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1336 through 1341' Processing helix chain 'C' and resid 1367 through 1373 removed outlier: 4.087A pdb=" N TYR C1371 " --> pdb=" O ASN C1367 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN C1373 " --> pdb=" O TYR C1369 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1400 Processing helix chain 'C' and resid 1404 through 1409 Processing helix chain 'C' and resid 1418 through 1424 removed outlier: 4.592A pdb=" N LEU C1422 " --> pdb=" O ARG C1418 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE C1423 " --> pdb=" O ILE C1419 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C1424 " --> pdb=" O ASN C1420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1418 through 1424' Processing helix chain 'C' and resid 1426 through 1434 removed outlier: 4.588A pdb=" N TYR C1432 " --> pdb=" O HIS C1428 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C1433 " --> pdb=" O THR C1429 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS C1434 " --> pdb=" O LEU C1430 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1448 removed outlier: 4.624A pdb=" N GLN C1444 " --> pdb=" O THR C1440 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR C1445 " --> pdb=" O ASP C1441 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN C1446 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU C1448 " --> pdb=" O GLN C1444 " (cutoff:3.500A) Processing helix chain 'C' and resid 1467 through 1479 removed outlier: 3.678A pdb=" N GLY C1479 " --> pdb=" O ILE C1475 " (cutoff:3.500A) Processing helix chain 'C' and resid 1480 through 1489 removed outlier: 4.059A pdb=" N HIS C1487 " --> pdb=" O GLY C1483 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C1488 " --> pdb=" O ILE C1484 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU C1489 " --> pdb=" O LEU C1485 " (cutoff:3.500A) Processing helix chain 'C' and resid 1519 through 1543 Proline residue: C1530 - end of helix Proline residue: C1540 - end of helix Processing helix chain 'C' and resid 1544 through 1549 Processing helix chain 'C' and resid 1566 through 1578 Processing helix chain 'C' and resid 1580 through 1605 removed outlier: 5.343A pdb=" N ASP C1602 " --> pdb=" O ASP C1598 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C1603 " --> pdb=" O GLN C1599 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C1604 " --> pdb=" O GLU C1600 " (cutoff:3.500A) Processing helix chain 'C' and resid 1675 through 1690 removed outlier: 3.590A pdb=" N TYR C1679 " --> pdb=" O ASP C1675 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C1689 " --> pdb=" O LEU C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1721 through 1737 removed outlier: 3.897A pdb=" N LEU C1725 " --> pdb=" O GLY C1721 " (cutoff:3.500A) Processing helix chain 'C' and resid 1738 through 1752 Processing helix chain 'C' and resid 1764 through 1774 removed outlier: 5.783A pdb=" N GLY C1769 " --> pdb=" O SER C1765 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU C1770 " --> pdb=" O GLN C1766 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU C1771 " --> pdb=" O ASN C1767 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE C1772 " --> pdb=" O TYR C1768 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER C1773 " --> pdb=" O GLY C1769 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASN C1774 " --> pdb=" O GLU C1770 " (cutoff:3.500A) Processing helix chain 'C' and resid 1823 through 1828 removed outlier: 4.064A pdb=" N TRP C1827 " --> pdb=" O HIS C1823 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1853 removed outlier: 3.512A pdb=" N ALA C1837 " --> pdb=" O LEU C1833 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TRP C1839 " --> pdb=" O GLN C1835 " (cutoff:3.500A) Proline residue: C1853 - end of helix Processing helix chain 'C' and resid 1868 through 1877 removed outlier: 3.861A pdb=" N LEU C1877 " --> pdb=" O GLU C1873 " (cutoff:3.500A) Processing helix chain 'C' and resid 1892 through 1900 removed outlier: 4.586A pdb=" N CYS C1896 " --> pdb=" O PRO C1892 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C1897 " --> pdb=" O PHE C1893 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU C1900 " --> pdb=" O CYS C1896 " (cutoff:3.500A) Processing helix chain 'C' and resid 1901 through 1909 Processing helix chain 'C' and resid 1922 through 1927 removed outlier: 4.226A pdb=" N THR C1926 " --> pdb=" O ASP C1922 " (cutoff:3.500A) Processing helix chain 'C' and resid 1928 through 1946 Processing helix chain 'C' and resid 1947 through 1956 removed outlier: 3.568A pdb=" N LYS C1955 " --> pdb=" O LYS C1951 " (cutoff:3.500A) Proline residue: C1956 - end of helix Processing helix chain 'C' and resid 1972 through 1996 Processing helix chain 'C' and resid 2003 through 2013 Processing helix chain 'C' and resid 2069 through 2090 removed outlier: 4.644A pdb=" N TRP C2073 " --> pdb=" O SER C2069 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG C2074 " --> pdb=" O LYS C2070 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C2082 " --> pdb=" O ILE C2078 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU C2083 " --> pdb=" O SER C2079 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS C2084 " --> pdb=" O ALA C2080 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C2085 " --> pdb=" O ALA C2081 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ARG C2086 " --> pdb=" O ASN C2082 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR C2087 " --> pdb=" O LEU C2083 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN C2088 " --> pdb=" O HIS C2084 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS C2089 " --> pdb=" O LEU C2085 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C2090 " --> pdb=" O ARG C2086 " (cutoff:3.500A) Processing helix chain 'C' and resid 2107 through 2118 removed outlier: 3.559A pdb=" N LEU C2111 " --> pdb=" O PRO C2107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C2118 " --> pdb=" O PHE C2114 " (cutoff:3.500A) Processing helix chain 'C' and resid 2166 through 2173 removed outlier: 4.332A pdb=" N GLU C2171 " --> pdb=" O GLU C2167 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET C2172 " --> pdb=" O TYR C2168 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU C2173 " --> pdb=" O LEU C2169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2204 Proline residue: C2204 - end of helix Processing helix chain 'C' and resid 2231 through 2241 Processing helix chain 'C' and resid 2252 through 2257 removed outlier: 4.915A pdb=" N TYR C2256 " --> pdb=" O LEU C2252 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU C2257 " --> pdb=" O PRO C2253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2252 through 2257' Processing helix chain 'C' and resid 2284 through 2289 removed outlier: 3.634A pdb=" N HIS C2288 " --> pdb=" O MET C2284 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP C2289 " --> pdb=" O GLY C2285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2284 through 2289' Processing helix chain 'C' and resid 2306 through 2311 removed outlier: 3.654A pdb=" N ARG C2310 " --> pdb=" O HIS C2306 " (cutoff:3.500A) Proline residue: C2311 - end of helix No H-bonds generated for 'chain 'C' and resid 2306 through 2311' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.132A pdb=" N ALA C 201 " --> pdb=" O ASP C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 201' Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.621A pdb=" N ASN D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Proline residue: D 155 - end of helix Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 211 through 222 removed outlier: 4.336A pdb=" N VAL D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 250 removed outlier: 3.557A pdb=" N GLU D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 removed outlier: 4.527A pdb=" N LEU D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 293 Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.980A pdb=" N ILE D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.880A pdb=" N LYS D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 343 " --> pdb=" O PHE D 339 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 386 removed outlier: 4.040A pdb=" N LEU D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Proline residue: D 376 - end of helix Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.507A pdb=" N THR D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.963A pdb=" N LYS D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 427 through 437 removed outlier: 3.731A pdb=" N VAL D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 452 removed outlier: 4.826A pdb=" N LYS D 446 " --> pdb=" O LYS D 442 " (cutoff:3.500A) Proline residue: D 447 - end of helix Processing helix chain 'D' and resid 459 through 468 removed outlier: 3.992A pdb=" N ASP D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 560 removed outlier: 4.696A pdb=" N ILE D 559 " --> pdb=" O VAL D 555 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 555 through 560' Processing helix chain 'D' and resid 596 through 615 removed outlier: 4.227A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) Proline residue: D 601 - end of helix removed outlier: 3.678A pdb=" N LYS D 612 " --> pdb=" O ARG D 608 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 633 through 646 Processing helix chain 'D' and resid 695 through 703 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 725 through 732 removed outlier: 3.898A pdb=" N ILE D 732 " --> pdb=" O ALA D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 755 removed outlier: 4.355A pdb=" N ASP D 755 " --> pdb=" O PRO D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 777 removed outlier: 4.562A pdb=" N ASP D 764 " --> pdb=" O GLY D 760 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER D 765 " --> pdb=" O SER D 761 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 777 " --> pdb=" O GLY D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 3.976A pdb=" N ARG D 803 " --> pdb=" O GLU D 799 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY D 804 " --> pdb=" O PRO D 800 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 799 through 804' Processing helix chain 'D' and resid 805 through 824 Proline residue: D 810 - end of helix removed outlier: 4.864A pdb=" N THR D 824 " --> pdb=" O PHE D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 854 removed outlier: 3.772A pdb=" N ARG D 852 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG D 853 " --> pdb=" O VAL D 849 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG D 854 " --> pdb=" O LEU D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 876 through 881 removed outlier: 4.214A pdb=" N PHE D 881 " --> pdb=" O ALA D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 882 through 892 Processing helix chain 'D' and resid 925 through 942 removed outlier: 3.584A pdb=" N LEU D 929 " --> pdb=" O PRO D 925 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG D 931 " --> pdb=" O PRO D 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 86 Processing helix chain 'E' and resid 107 through 125 removed outlier: 4.112A pdb=" N GLU E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 144 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.876A pdb=" N ARG E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.668A pdb=" N ILE E 263 " --> pdb=" O HIS E 259 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP E 264 " --> pdb=" O PRO E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 264' Processing helix chain 'E' and resid 266 through 276 removed outlier: 4.043A pdb=" N ARG E 274 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE E 275 " --> pdb=" O GLN E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 296 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'E' and resid 326 through 337 removed outlier: 3.529A pdb=" N ALA E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 354 removed outlier: 3.566A pdb=" N ASP E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Proline residue: E 354 - end of helix Processing helix chain 'E' and resid 355 through 365 removed outlier: 3.727A pdb=" N PHE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 463 through 468 removed outlier: 3.931A pdb=" N LEU E 467 " --> pdb=" O PRO E 463 " (cutoff:3.500A) Proline residue: E 468 - end of helix No H-bonds generated for 'chain 'E' and resid 463 through 468' Processing helix chain 'E' and resid 469 through 476 removed outlier: 3.666A pdb=" N ALA E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY E 474 " --> pdb=" O TYR E 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 469 through 476' Processing helix chain 'E' and resid 482 through 493 removed outlier: 3.578A pdb=" N LEU E 488 " --> pdb=" O ILE E 484 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG E 490 " --> pdb=" O SER E 486 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA E 491 " --> pdb=" O LYS E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 removed outlier: 3.566A pdb=" N GLU E 520 " --> pdb=" O CYS E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 537 removed outlier: 4.427A pdb=" N PHE E 536 " --> pdb=" O ASN E 532 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS E 537 " --> pdb=" O VAL E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 537' Processing helix chain 'E' and resid 544 through 560 Processing helix chain 'E' and resid 574 through 583 removed outlier: 4.574A pdb=" N GLU E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 579 " --> pdb=" O LEU E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 600 Processing helix chain 'E' and resid 618 through 623 removed outlier: 4.052A pdb=" N ASP E 622 " --> pdb=" O HIS E 618 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 618 through 623' Processing helix chain 'E' and resid 624 through 643 removed outlier: 3.855A pdb=" N LEU E 628 " --> pdb=" O ARG E 624 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 630 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 696 through 716 Processing helix chain 'E' and resid 727 through 746 removed outlier: 3.603A pdb=" N GLY E 732 " --> pdb=" O ARG E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.984A pdb=" N PHE E 751 " --> pdb=" O THR E 747 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 752 " --> pdb=" O LEU E 748 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG E 753 " --> pdb=" O GLY E 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 747 through 753' Processing helix chain 'E' and resid 756 through 770 removed outlier: 3.866A pdb=" N GLU E 760 " --> pdb=" O SER E 756 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS E 770 " --> pdb=" O ALA E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 779 Proline residue: E 779 - end of helix Processing helix chain 'E' and resid 790 through 804 Processing helix chain 'E' and resid 812 through 819 removed outlier: 4.313A pdb=" N ALA E 816 " --> pdb=" O THR E 812 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP E 817 " --> pdb=" O ALA E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 856 removed outlier: 4.163A pdb=" N ALA E 856 " --> pdb=" O MET E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 884 removed outlier: 4.420A pdb=" N GLN E 877 " --> pdb=" O HIS E 873 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR E 878 " --> pdb=" O GLY E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 892 through 908 removed outlier: 4.417A pdb=" N LYS E 896 " --> pdb=" O GLN E 892 " (cutoff:3.500A) Proline residue: E 898 - end of helix Processing helix chain 'E' and resid 912 through 924 removed outlier: 3.700A pdb=" N TYR E 922 " --> pdb=" O ASN E 918 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 923 " --> pdb=" O TRP E 919 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR E 924 " --> pdb=" O LEU E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 932 Processing helix chain 'E' and resid 939 through 947 Proline residue: E 947 - end of helix Processing helix chain 'E' and resid 949 through 968 Processing helix chain 'E' and resid 982 through 992 Processing helix chain 'E' and resid 994 through 1005 removed outlier: 3.815A pdb=" N VAL E 998 " --> pdb=" O THR E 994 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 999 " --> pdb=" O ASN E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1026 removed outlier: 3.856A pdb=" N SER E1021 " --> pdb=" O VAL E1017 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER E1022 " --> pdb=" O PHE E1018 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E1023 " --> pdb=" O SER E1019 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE E1024 " --> pdb=" O LEU E1020 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS E1025 " --> pdb=" O SER E1021 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN E1026 " --> pdb=" O SER E1022 " (cutoff:3.500A) Processing helix chain 'E' and resid 1030 through 1044 removed outlier: 4.397A pdb=" N LEU E1035 " --> pdb=" O GLU E1031 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU E1036 " --> pdb=" O GLU E1032 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU E1042 " --> pdb=" O GLN E1038 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG E1043 " --> pdb=" O LYS E1039 " (cutoff:3.500A) Processing helix chain 'E' and resid 1054 through 1069 Processing helix chain 'E' and resid 1074 through 1103 removed outlier: 3.631A pdb=" N VAL E1082 " --> pdb=" O MET E1078 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E1083 " --> pdb=" O ALA E1079 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY E1089 " --> pdb=" O THR E1085 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG E1090 " --> pdb=" O GLN E1086 " (cutoff:3.500A) Processing helix chain 'E' and resid 1104 through 1121 removed outlier: 3.656A pdb=" N THR E1108 " --> pdb=" O TRP E1104 " (cutoff:3.500A) Processing helix chain 'E' and resid 1127 through 1133 removed outlier: 4.743A pdb=" N GLN E1131 " --> pdb=" O CYS E1127 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE E1132 " --> pdb=" O PRO E1128 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG E1133 " --> pdb=" O LEU E1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1127 through 1133' Processing helix chain 'E' and resid 1136 through 1147 removed outlier: 4.427A pdb=" N ASN E1147 " --> pdb=" O ILE E1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 1149 through 1157 removed outlier: 3.988A pdb=" N LEU E1153 " --> pdb=" O PRO E1149 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR E1154 " --> pdb=" O PHE E1150 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP E1155 " --> pdb=" O GLU E1151 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E1156 " --> pdb=" O ARG E1152 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN E1157 " --> pdb=" O LEU E1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1149 through 1157' Processing helix chain 'E' and resid 1158 through 1166 Processing helix chain 'E' and resid 1167 through 1182 removed outlier: 4.143A pdb=" N GLY E1171 " --> pdb=" O MET E1167 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS E1172 " --> pdb=" O PRO E1168 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR E1173 " --> pdb=" O LYS E1169 " (cutoff:3.500A) Proline residue: E1182 - end of helix Processing helix chain 'E' and resid 1314 through 1323 removed outlier: 4.034A pdb=" N TYR E1321 " --> pdb=" O PHE E1317 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP E1323 " --> pdb=" O SER E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1329 through 1340 removed outlier: 4.798A pdb=" N ASN E1337 " --> pdb=" O THR E1333 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR E1338 " --> pdb=" O GLN E1334 " (cutoff:3.500A) Processing helix chain 'E' and resid 1355 through 1371 removed outlier: 4.245A pdb=" N CYS E1359 " --> pdb=" O GLY E1355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E1360 " --> pdb=" O LYS E1356 " (cutoff:3.500A) Processing helix chain 'E' and resid 1382 through 1397 removed outlier: 4.025A pdb=" N GLU E1395 " --> pdb=" O MET E1391 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS E1396 " --> pdb=" O ASP E1392 " (cutoff:3.500A) Processing helix chain 'E' and resid 1411 through 1422 Processing helix chain 'E' and resid 1428 through 1437 Processing helix chain 'E' and resid 1438 through 1443 removed outlier: 4.906A pdb=" N LYS E1443 " --> pdb=" O TRP E1439 " (cutoff:3.500A) Processing helix chain 'E' and resid 1463 through 1482 removed outlier: 3.576A pdb=" N LEU E1467 " --> pdb=" O ASN E1463 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E1482 " --> pdb=" O SER E1478 " (cutoff:3.500A) Processing helix chain 'E' and resid 1496 through 1505 removed outlier: 3.502A pdb=" N VAL E1500 " --> pdb=" O ASN E1496 " (cutoff:3.500A) Processing helix chain 'E' and resid 1507 through 1512 removed outlier: 5.555A pdb=" N PHE E1512 " --> pdb=" O ALA E1508 " (cutoff:3.500A) Processing helix chain 'E' and resid 1536 through 1553 removed outlier: 3.860A pdb=" N ALA E1543 " --> pdb=" O LEU E1539 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS E1544 " --> pdb=" O LEU E1540 " (cutoff:3.500A) Proline residue: E1545 - end of helix Processing helix chain 'E' and resid 1565 through 1584 removed outlier: 3.825A pdb=" N THR E1569 " --> pdb=" O SER E1565 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG E1570 " --> pdb=" O ARG E1566 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E1571 " --> pdb=" O LYS E1567 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE E1584 " --> pdb=" O CYS E1580 " (cutoff:3.500A) Processing helix chain 'E' and resid 1593 through 1602 removed outlier: 4.009A pdb=" N LEU E1597 " --> pdb=" O THR E1593 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E1598 " --> pdb=" O GLU E1594 " (cutoff:3.500A) Proline residue: E1599 - end of helix Processing helix chain 'E' and resid 1606 through 1616 Processing helix chain 'E' and resid 1625 through 1639 Processing helix chain 'E' and resid 1647 through 1655 removed outlier: 3.849A pdb=" N CYS E1651 " --> pdb=" O SER E1647 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP E1652 " --> pdb=" O ARG E1648 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY E1653 " --> pdb=" O SER E1649 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN E1655 " --> pdb=" O CYS E1651 " (cutoff:3.500A) Processing helix chain 'E' and resid 1680 through 1692 removed outlier: 4.250A pdb=" N ALA E1691 " --> pdb=" O MET E1687 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN E1692 " --> pdb=" O VAL E1688 " (cutoff:3.500A) Processing helix chain 'E' and resid 1707 through 1720 removed outlier: 3.758A pdb=" N LYS E1711 " --> pdb=" O GLN E1707 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP E1712 " --> pdb=" O GLY E1708 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE E1713 " --> pdb=" O SER E1709 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR E1719 " --> pdb=" O LYS E1715 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU E1720 " --> pdb=" O LYS E1716 " (cutoff:3.500A) Processing helix chain 'E' and resid 1727 through 1732 removed outlier: 4.149A pdb=" N CYS E1731 " --> pdb=" O HIS E1727 " (cutoff:3.500A) Processing helix chain 'E' and resid 1733 through 1743 Processing helix chain 'E' and resid 1747 through 1759 removed outlier: 3.617A pdb=" N TRP E1757 " --> pdb=" O ASP E1753 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR E1758 " --> pdb=" O TYR E1754 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE E1759 " --> pdb=" O LEU E1755 " (cutoff:3.500A) Processing helix chain 'E' and resid 1760 through 1767 removed outlier: 3.712A pdb=" N THR E1765 " --> pdb=" O TYR E1761 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E1766 " --> pdb=" O ARG E1762 " (cutoff:3.500A) Processing helix chain 'E' and resid 1777 through 1800 Processing helix chain 'E' and resid 1813 through 1823 Processing helix chain 'E' and resid 1825 through 1836 Processing helix chain 'E' and resid 1841 through 1852 Processing helix chain 'E' and resid 1862 through 1875 removed outlier: 7.015A pdb=" N ASN E1866 " --> pdb=" O HIS E1862 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU E1867 " --> pdb=" O HIS E1863 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E1869 " --> pdb=" O ASP E1865 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN E1870 " --> pdb=" O ASN E1866 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN E1873 " --> pdb=" O ARG E1869 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E1874 " --> pdb=" O GLN E1870 " (cutoff:3.500A) Processing helix chain 'E' and resid 1886 through 1901 removed outlier: 3.744A pdb=" N LYS E1890 " --> pdb=" O ASP E1886 " (cutoff:3.500A) Processing helix chain 'E' and resid 1905 through 1934 removed outlier: 3.588A pdb=" N LYS E1918 " --> pdb=" O GLU E1914 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E1920 " --> pdb=" O LEU E1916 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG E1921 " --> pdb=" O SER E1917 " (cutoff:3.500A) Processing helix chain 'E' and resid 1935 through 1952 Processing helix chain 'E' and resid 1967 through 1978 Processing helix chain 'E' and resid 1981 through 1989 removed outlier: 3.549A pdb=" N ILE E1985 " --> pdb=" O SER E1981 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET E1988 " --> pdb=" O ASP E1984 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU E1989 " --> pdb=" O ILE E1985 " (cutoff:3.500A) Processing helix chain 'E' and resid 1990 through 1997 Processing helix chain 'E' and resid 2000 through 2015 removed outlier: 3.575A pdb=" N ALA E2008 " --> pdb=" O ILE E2004 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG E2009 " --> pdb=" O ALA E2005 " (cutoff:3.500A) Proline residue: E2015 - end of helix Processing helix chain 'E' and resid 1308 through 1313 removed outlier: 3.721A pdb=" N LEU E1312 " --> pdb=" O VAL E1309 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG E1313 " --> pdb=" O SER E1310 " (cutoff:3.500A) Processing helix chain 'E' and resid 1853 through 1858 removed outlier: 4.484A pdb=" N ASN E1857 " --> pdb=" O GLU E1854 " (cutoff:3.500A) Processing helix chain 'E' and resid 1958 through 1964 removed outlier: 3.724A pdb=" N LYS E1961 " --> pdb=" O SER E1958 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN E1962 " --> pdb=" O TYR E1959 " (cutoff:3.500A) Proline residue: E1964 - end of helix Processing helix chain 'E' and resid 668 through 673 Processing helix chain 'E' and resid 1211 through 1216 removed outlier: 3.686A pdb=" N GLY E1216 " --> pdb=" O ASP E1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1211 through 1216' Processing helix chain 'G' and resid 95 through 115 removed outlier: 4.436A pdb=" N ARG G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 136 Proline residue: G 136 - end of helix Processing helix chain 'G' and resid 137 through 151 removed outlier: 4.837A pdb=" N ASP G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU G 145 " --> pdb=" O GLN G 141 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA G 150 " --> pdb=" O LYS G 146 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU G 151 " --> pdb=" O ARG G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 160 removed outlier: 3.696A pdb=" N ILE G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 261 removed outlier: 4.293A pdb=" N ILE G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY G 244 " --> pdb=" O MET G 240 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER G 261 " --> pdb=" O GLN G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 281 removed outlier: 3.674A pdb=" N ILE G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 306 Proline residue: G 306 - end of helix Processing helix chain 'G' and resid 308 through 322 removed outlier: 3.572A pdb=" N TRP G 312 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 339 removed outlier: 3.864A pdb=" N ALA G 328 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 3.774A pdb=" N TRP G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 369 Processing helix chain 'G' and resid 372 through 384 removed outlier: 3.830A pdb=" N THR G 384 " --> pdb=" O ALA G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 401 Proline residue: G 401 - end of helix Processing helix chain 'G' and resid 403 through 414 removed outlier: 3.867A pdb=" N GLU G 412 " --> pdb=" O LYS G 408 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 413 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 414 " --> pdb=" O ALA G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 431 Proline residue: G 431 - end of helix Processing helix chain 'G' and resid 433 through 445 removed outlier: 4.833A pdb=" N THR G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 460 removed outlier: 3.989A pdb=" N LYS G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 478 removed outlier: 4.239A pdb=" N TRP G 467 " --> pdb=" O ASP G 463 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY G 478 " --> pdb=" O GLU G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 498 removed outlier: 3.826A pdb=" N VAL G 483 " --> pdb=" O ASN G 479 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 484 " --> pdb=" O THR G 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 517 removed outlier: 3.897A pdb=" N GLN G 508 " --> pdb=" O GLU G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 533 Processing helix chain 'G' and resid 536 through 554 Processing helix chain 'G' and resid 555 through 571 removed outlier: 3.798A pdb=" N ALA G 559 " --> pdb=" O ALA G 555 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE G 570 " --> pdb=" O ALA G 566 " (cutoff:3.500A) Proline residue: G 571 - end of helix Processing helix chain 'G' and resid 573 through 587 Processing helix chain 'G' and resid 590 through 605 Proline residue: G 605 - end of helix Processing helix chain 'G' and resid 607 through 621 removed outlier: 3.809A pdb=" N TRP G 611 " --> pdb=" O ALA G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 639 Proline residue: G 639 - end of helix Processing helix chain 'G' and resid 644 through 656 removed outlier: 3.502A pdb=" N GLU G 652 " --> pdb=" O ALA G 648 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN G 655 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP G 656 " --> pdb=" O GLU G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 673 Proline residue: G 673 - end of helix Processing helix chain 'G' and resid 674 through 689 removed outlier: 3.547A pdb=" N PHE G 678 " --> pdb=" O THR G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 706 removed outlier: 4.013A pdb=" N GLN G 695 " --> pdb=" O ILE G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 708 through 723 removed outlier: 4.188A pdb=" N TRP G 712 " --> pdb=" O PHE G 708 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS G 722 " --> pdb=" O ILE G 718 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU G 723 " --> pdb=" O GLU G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 739 Processing helix chain 'G' and resid 742 through 757 removed outlier: 3.603A pdb=" N TRP G 746 " --> pdb=" O SER G 742 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY G 757 " --> pdb=" O GLU G 753 " (cutoff:3.500A) Processing helix chain 'G' and resid 758 through 774 removed outlier: 3.728A pdb=" N ALA G 762 " --> pdb=" O GLN G 758 " (cutoff:3.500A) Proline residue: G 774 - end of helix Processing helix chain 'G' and resid 776 through 791 removed outlier: 4.084A pdb=" N TRP G 780 " --> pdb=" O ASN G 776 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 790 " --> pdb=" O LEU G 786 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY G 791 " --> pdb=" O GLU G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 792 through 807 removed outlier: 4.584A pdb=" N ALA G 796 " --> pdb=" O LEU G 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 810 through 821 removed outlier: 4.019A pdb=" N TRP G 814 " --> pdb=" O SER G 810 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE G 819 " --> pdb=" O SER G 815 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 821 " --> pdb=" O ALA G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 837 removed outlier: 3.787A pdb=" N LYS G 829 " --> pdb=" O GLN G 825 " (cutoff:3.500A) Processing helix chain 'G' and resid 840 through 855 Processing helix chain 'G' and resid 856 through 872 removed outlier: 4.250A pdb=" N GLU G 862 " --> pdb=" O THR G 858 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER G 872 " --> pdb=" O VAL G 868 " (cutoff:3.500A) Processing helix chain 'G' and resid 874 through 889 removed outlier: 4.036A pdb=" N TRP G 878 " --> pdb=" O LEU G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 890 through 905 removed outlier: 4.553A pdb=" N VAL G 897 " --> pdb=" O GLN G 893 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG G 898 " --> pdb=" O GLN G 894 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS G 899 " --> pdb=" O GLU G 895 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER G 903 " --> pdb=" O LYS G 899 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 904 " --> pdb=" O ARG G 900 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU G 905 " --> pdb=" O CYS G 901 " (cutoff:3.500A) Processing helix chain 'G' and resid 909 through 917 removed outlier: 3.852A pdb=" N VAL G 915 " --> pdb=" O LEU G 911 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 923 removed outlier: 3.695A pdb=" N TRP G 922 " --> pdb=" O ASP G 918 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN G 923 " --> pdb=" O ILE G 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 918 through 923' Processing helix chain 'G' and resid 925 through 937 removed outlier: 4.257A pdb=" N ARG G 931 " --> pdb=" O GLY G 927 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 937 " --> pdb=" O VAL G 933 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.598A pdb=" N ARG G 23 " --> pdb=" O GLY G 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 21 Processing helix chain 'H' and resid 35 through 53 removed outlier: 4.488A pdb=" N SER H 50 " --> pdb=" O SER H 46 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASP H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.611A pdb=" N THR H 66 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 108 through 126 removed outlier: 3.562A pdb=" N PHE H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 203 Processing helix chain 'I' and resid 241 through 255 removed outlier: 3.860A pdb=" N TYR I 254 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 293 removed outlier: 4.044A pdb=" N ARG I 293 " --> pdb=" O LEU I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 316 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 329 through 355 Processing helix chain 'I' and resid 356 through 361 removed outlier: 4.826A pdb=" N LYS I 361 " --> pdb=" O TRP I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 378 Processing helix chain 'I' and resid 392 through 397 removed outlier: 5.006A pdb=" N SER I 397 " --> pdb=" O TRP I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 410 Processing helix chain 'I' and resid 415 through 426 removed outlier: 3.796A pdb=" N GLN I 420 " --> pdb=" O PRO I 416 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE I 422 " --> pdb=" O GLN I 418 " (cutoff:3.500A) Proline residue: I 423 - end of helix Processing helix chain 'I' and resid 440 through 457 Proline residue: I 448 - end of helix removed outlier: 3.502A pdb=" N THR I 454 " --> pdb=" O LEU I 450 " (cutoff:3.500A) Proline residue: I 457 - end of helix Processing helix chain 'I' and resid 458 through 464 removed outlier: 6.253A pdb=" N GLU I 464 " --> pdb=" O ASP I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 496 removed outlier: 3.510A pdb=" N GLN I 483 " --> pdb=" O GLU I 479 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE I 484 " --> pdb=" O LEU I 480 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 490 " --> pdb=" O GLU I 486 " (cutoff:3.500A) Proline residue: I 494 - end of helix Processing helix chain 'I' and resid 507 through 518 removed outlier: 3.714A pdb=" N LEU I 515 " --> pdb=" O GLN I 511 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET I 517 " --> pdb=" O PHE I 513 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY I 518 " --> pdb=" O ARG I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 536 removed outlier: 3.609A pdb=" N ASP I 531 " --> pdb=" O GLY I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 558 removed outlier: 3.670A pdb=" N ILE I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP I 556 " --> pdb=" O ASP I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 571 Proline residue: I 571 - end of helix Processing helix chain 'I' and resid 579 through 584 removed outlier: 3.974A pdb=" N GLU I 583 " --> pdb=" O THR I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 585 through 595 removed outlier: 3.508A pdb=" N SER I 594 " --> pdb=" O ALA I 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 621 Processing helix chain 'I' and resid 634 through 639 removed outlier: 3.779A pdb=" N ARG I 638 " --> pdb=" O LYS I 634 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 662 removed outlier: 4.788A pdb=" N ARG I 652 " --> pdb=" O GLU I 648 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS I 653 " --> pdb=" O SER I 649 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY I 662 " --> pdb=" O ILE I 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 673 through 688 Processing helix chain 'I' and resid 699 through 713 Processing helix chain 'I' and resid 721 through 726 Processing helix chain 'I' and resid 744 through 755 removed outlier: 3.991A pdb=" N ARG I 754 " --> pdb=" O HIS I 750 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR I 755 " --> pdb=" O ARG I 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 772 through 787 removed outlier: 3.724A pdb=" N PHE I 776 " --> pdb=" O ASP I 772 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR I 777 " --> pdb=" O SER I 773 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU I 778 " --> pdb=" O ALA I 774 " (cutoff:3.500A) Proline residue: I 787 - end of helix Processing helix chain 'I' and resid 792 through 797 Processing helix chain 'I' and resid 798 through 803 removed outlier: 3.732A pdb=" N GLN I 802 " --> pdb=" O HIS I 798 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS I 803 " --> pdb=" O PRO I 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 798 through 803' Processing helix chain 'a' and resid 6 through 13 removed outlier: 3.816A pdb=" N HIS a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE a 13 " --> pdb=" O MET a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 78 removed outlier: 3.889A pdb=" N LEU a 77 " --> pdb=" O ARG a 73 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL a 78 " --> pdb=" O GLY a 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 73 through 78' Processing helix chain 'b' and resid 2 through 11 removed outlier: 3.578A pdb=" N LYS b 9 " --> pdb=" O ARG b 5 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 82 removed outlier: 3.613A pdb=" N VAL b 81 " --> pdb=" O ASP b 77 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP b 82 " --> pdb=" O THR b 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 11 removed outlier: 4.286A pdb=" N PHE i 6 " --> pdb=" O LYS i 2 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU i 7 " --> pdb=" O LEU i 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS i 9 " --> pdb=" O ARG i 5 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU i 10 " --> pdb=" O PHE i 6 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER i 11 " --> pdb=" O LEU i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 82 removed outlier: 3.615A pdb=" N LEU i 79 " --> pdb=" O PRO i 75 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL i 81 " --> pdb=" O ASP i 77 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP i 82 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 27 removed outlier: 4.370A pdb=" N GLU c 22 " --> pdb=" O LYS c 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN c 25 " --> pdb=" O GLU c 21 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR c 26 " --> pdb=" O GLU c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 38 removed outlier: 4.348A pdb=" N LEU c 32 " --> pdb=" O PRO c 28 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER c 35 " --> pdb=" O VAL c 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 14 removed outlier: 3.920A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 81 removed outlier: 4.744A pdb=" N LYS d 78 " --> pdb=" O PRO d 74 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASN d 79 " --> pdb=" O ASP d 75 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA d 80 " --> pdb=" O MET d 76 " (cutoff:3.500A) Proline residue: d 81 - end of helix No H-bonds generated for 'chain 'd' and resid 74 through 81' Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'f' and resid 6 through 15 removed outlier: 3.718A pdb=" N THR f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 removed outlier: 4.251A pdb=" N ILE g 67 " --> pdb=" O ARG g 63 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE g 68 " --> pdb=" O GLY g 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 68' Processing helix chain 'n' and resid 63 through 68 removed outlier: 5.473A pdb=" N ILE n 68 " --> pdb=" O GLY n 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 74 removed outlier: 4.240A pdb=" N ALA L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 118 removed outlier: 4.115A pdb=" N VAL L 92 " --> pdb=" O PRO L 88 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS L 117 " --> pdb=" O PHE L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 4.901A pdb=" N GLU L 126 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER L 127 " --> pdb=" O PRO L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 removed outlier: 4.164A pdb=" N GLY L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 159 Processing helix chain 'L' and resid 160 through 174 removed outlier: 3.711A pdb=" N ILE L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET L 165 " --> pdb=" O ASN L 161 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR L 173 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 216 removed outlier: 4.317A pdb=" N ALA L 194 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU L 195 " --> pdb=" O CYS L 191 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU L 196 " --> pdb=" O ASP L 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 197 " --> pdb=" O MET L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 223 Processing helix chain 'L' and resid 224 through 236 removed outlier: 4.107A pdb=" N ALA L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY L 236 " --> pdb=" O MET L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 245 Proline residue: L 245 - end of helix Processing helix chain 'L' and resid 246 through 252 Processing helix chain 'L' and resid 272 through 277 removed outlier: 3.747A pdb=" N HIS L 276 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 removed outlier: 4.416A pdb=" N LEU L 283 " --> pdb=" O ILE L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 307 removed outlier: 3.605A pdb=" N ARG L 288 " --> pdb=" O PRO L 284 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG L 289 " --> pdb=" O PRO L 285 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LYS L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 333 removed outlier: 3.629A pdb=" N GLN L 332 " --> pdb=" O PHE L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 365 removed outlier: 6.729A pdb=" N TYR L 359 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG L 360 " --> pdb=" O GLY L 356 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU L 364 " --> pdb=" O ARG L 360 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG L 365 " --> pdb=" O LYS L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 378 removed outlier: 5.886A pdb=" N ARG L 377 " --> pdb=" O LYS L 373 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N MET L 378 " --> pdb=" O GLN L 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 373 through 378' Processing helix chain 'L' and resid 145 through 150 removed outlier: 4.565A pdb=" N LYS L 148 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS L 149 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 150 " --> pdb=" O ASP L 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 145 through 150' Processing helix chain 'M' and resid 171 through 202 removed outlier: 3.895A pdb=" N LYS M 175 " --> pdb=" O PRO M 171 " (cutoff:3.500A) Proline residue: M 187 - end of helix removed outlier: 3.520A pdb=" N GLU M 201 " --> pdb=" O ARG M 197 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE M 202 " --> pdb=" O LEU M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 221 removed outlier: 3.542A pdb=" N ARG M 207 " --> pdb=" O PRO M 203 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER M 220 " --> pdb=" O LYS M 216 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 395 removed outlier: 3.894A pdb=" N SER N 392 " --> pdb=" O GLU N 388 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR N 393 " --> pdb=" O TRP N 389 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE N 394 " --> pdb=" O TRP N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 412 removed outlier: 3.967A pdb=" N TYR N 411 " --> pdb=" O LYS N 407 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE N 412 " --> pdb=" O ARG N 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 407 through 412' Processing helix chain 'N' and resid 441 through 467 Processing helix chain 'N' and resid 521 through 540 removed outlier: 4.102A pdb=" N ASP N 536 " --> pdb=" O LYS N 532 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE N 537 " --> pdb=" O LEU N 533 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER N 538 " --> pdb=" O LYS N 534 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN N 539 " --> pdb=" O GLU N 535 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLY N 540 " --> pdb=" O ASP N 536 " (cutoff:3.500A) Processing helix chain 'N' and resid 553 through 568 removed outlier: 3.640A pdb=" N LYS N 557 " --> pdb=" O ASN N 553 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR N 568 " --> pdb=" O ALA N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 587 through 600 Processing helix chain 'N' and resid 653 through 665 removed outlier: 3.764A pdb=" N ALA N 657 " --> pdb=" O THR N 653 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS N 664 " --> pdb=" O HIS N 660 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 683 removed outlier: 3.531A pdb=" N ASP N 671 " --> pdb=" O GLU N 667 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 33 Processing helix chain 'O' and resid 38 through 49 removed outlier: 4.371A pdb=" N GLY O 49 " --> pdb=" O THR O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.665A pdb=" N LEU O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N HIS O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix Processing helix chain 'O' and resid 85 through 94 Processing helix chain 'O' and resid 112 through 128 removed outlier: 3.545A pdb=" N SER O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL O 128 " --> pdb=" O GLU O 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 24 removed outlier: 4.341A pdb=" N TYR R 22 " --> pdb=" O ARG R 18 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG R 24 " --> pdb=" O HIS R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 51 removed outlier: 3.512A pdb=" N GLN R 29 " --> pdb=" O LYS R 25 " (cutoff:3.500A) Proline residue: R 39 - end of helix removed outlier: 4.562A pdb=" N ARG R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 62 removed outlier: 4.154A pdb=" N GLU R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG R 62 " --> pdb=" O PRO R 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 57 through 62' Processing helix chain 'R' and resid 86 through 95 removed outlier: 3.517A pdb=" N GLU R 91 " --> pdb=" O GLY R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 110 removed outlier: 3.642A pdb=" N ASN R 109 " --> pdb=" O PHE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 120 removed outlier: 3.698A pdb=" N LYS R 116 " --> pdb=" O GLU R 112 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS R 118 " --> pdb=" O GLN R 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 120 " --> pdb=" O LYS R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 158 removed outlier: 4.145A pdb=" N ARG R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL R 158 " --> pdb=" O GLN R 154 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 13 removed outlier: 4.089A pdb=" N HIS h 12 " --> pdb=" O LYS h 8 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE h 13 " --> pdb=" O MET h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 8 through 13' Processing helix chain 'h' and resid 73 through 78 removed outlier: 3.948A pdb=" N LEU h 77 " --> pdb=" O ARG h 73 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL h 78 " --> pdb=" O GLY h 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 73 through 78' Processing helix chain 'j' and resid 22 through 27 removed outlier: 4.509A pdb=" N THR j 26 " --> pdb=" O GLU j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 39 Processing helix chain 'j' and resid 102 through 107 removed outlier: 4.220A pdb=" N VAL j 106 " --> pdb=" O ARG j 102 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ILE j 107 " --> pdb=" O GLY j 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 102 through 107' Processing helix chain 'k' and resid 4 through 14 removed outlier: 3.575A pdb=" N GLU k 14 " --> pdb=" O LEU k 10 " (cutoff:3.500A) Processing helix chain 'k' and resid 64 through 69 removed outlier: 3.565A pdb=" N ILE k 68 " --> pdb=" O ARG k 64 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG k 69 " --> pdb=" O GLY k 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 64 through 69' Processing helix chain 'k' and resid 75 through 81 removed outlier: 4.503A pdb=" N ASN k 79 " --> pdb=" O ASP k 75 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA k 80 " --> pdb=" O MET k 76 " (cutoff:3.500A) Proline residue: k 81 - end of helix No H-bonds generated for 'chain 'k' and resid 75 through 81' Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'm' and resid 6 through 15 removed outlier: 3.871A pdb=" N THR m 15 " --> pdb=" O LEU m 11 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 70 removed outlier: 3.843A pdb=" N VAL m 69 " --> pdb=" O ARG m 65 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU m 70 " --> pdb=" O CYS m 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 65 through 70' Processing helix chain 'V' and resid 17 through 27 removed outlier: 3.598A pdb=" N ARG V 21 " --> pdb=" O ASN V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 42 removed outlier: 4.006A pdb=" N MET V 40 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE V 41 " --> pdb=" O TRP V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 Processing helix chain 'V' and resid 57 through 63 Processing helix chain 'V' and resid 78 through 101 removed outlier: 3.577A pdb=" N LEU V 82 " --> pdb=" O SER V 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 19 removed outlier: 3.792A pdb=" N SER W 18 " --> pdb=" O LEU W 14 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ILE W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 37 removed outlier: 3.738A pdb=" N TRP W 32 " --> pdb=" O ASP W 28 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU W 36 " --> pdb=" O TRP W 32 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 73 removed outlier: 4.023A pdb=" N LEU W 67 " --> pdb=" O LYS W 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG W 73 " --> pdb=" O GLU W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 111 removed outlier: 4.115A pdb=" N VAL W 105 " --> pdb=" O GLU W 101 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE W 106 " --> pdb=" O GLU W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 removed outlier: 3.988A pdb=" N THR W 131 " --> pdb=" O GLU W 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.900A pdb=" N GLU X 6 " --> pdb=" O ASP X 2 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP X 14 " --> pdb=" O MET X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 38 removed outlier: 3.584A pdb=" N VAL X 29 " --> pdb=" O THR X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 82 removed outlier: 4.729A pdb=" N GLY X 82 " --> pdb=" O GLN X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 96 Processing helix chain 'X' and resid 111 through 116 removed outlier: 3.654A pdb=" N TYR X 115 " --> pdb=" O LYS X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 20 removed outlier: 4.606A pdb=" N ASP X 19 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU X 20 " --> pdb=" O LEU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 37 Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.989A pdb=" N ASP Y 44 " --> pdb=" O LEU Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 84 removed outlier: 4.029A pdb=" N LEU Y 71 " --> pdb=" O PRO Y 67 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA Y 72 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS Y 74 " --> pdb=" O SER Y 70 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 93 removed outlier: 4.299A pdb=" N GLU Y 92 " --> pdb=" O GLU Y 88 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 101 removed outlier: 3.676A pdb=" N TYR Y 100 " --> pdb=" O PRO Y 96 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU Y 101 " --> pdb=" O GLU Y 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 96 through 101' Processing helix chain 'Y' and resid 111 through 127 Processing helix chain 'Y' and resid 131 through 139 removed outlier: 4.633A pdb=" N GLN Y 135 " --> pdb=" O ASP Y 131 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER Y 139 " --> pdb=" O GLN Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 155 Processing helix chain 'Y' and resid 157 through 179 Processing helix chain 'Y' and resid 229 through 234 Processing helix chain 'Y' and resid 236 through 262 Processing helix chain 'Z' and resid 170 through 199 Processing helix chain 'Z' and resid 202 through 224 removed outlier: 3.588A pdb=" N ALA Z 213 " --> pdb=" O TYR Z 209 " (cutoff:3.500A) Proline residue: Z 214 - end of helix Processing helix chain 'Z' and resid 228 through 325 removed outlier: 4.357A pdb=" N VAL Z 232 " --> pdb=" O GLN Z 228 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU Z 273 " --> pdb=" O GLU Z 269 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS Z 308 " --> pdb=" O GLU Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 332 through 337 Processing helix chain 'Z' and resid 341 through 378 removed outlier: 3.655A pdb=" N ASP Z 345 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 13 Processing helix chain 'p' and resid 2 through 11 removed outlier: 4.276A pdb=" N PHE p 6 " --> pdb=" O LYS p 2 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU p 7 " --> pdb=" O LEU p 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS p 9 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU p 10 " --> pdb=" O PHE p 6 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 82 removed outlier: 3.715A pdb=" N LEU p 79 " --> pdb=" O PRO p 75 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP p 82 " --> pdb=" O THR p 78 " (cutoff:3.500A) Processing helix chain 'q' and resid 7 through 12 removed outlier: 4.299A pdb=" N MET q 11 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR q 12 " --> pdb=" O LYS q 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 7 through 12' Processing helix chain 'q' and resid 13 through 27 Processing helix chain 'q' and resid 28 through 39 removed outlier: 4.783A pdb=" N LEU q 32 " --> pdb=" O PRO q 28 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 14 removed outlier: 4.197A pdb=" N GLU r 14 " --> pdb=" O LEU r 10 " (cutoff:3.500A) Processing helix chain 'r' and resid 64 through 69 removed outlier: 3.800A pdb=" N ILE r 68 " --> pdb=" O ARG r 64 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG r 69 " --> pdb=" O GLY r 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 64 through 69' Processing helix chain 'r' and resid 74 through 80 removed outlier: 3.569A pdb=" N LEU r 77 " --> pdb=" O PRO r 74 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN r 79 " --> pdb=" O MET r 76 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 28 Processing helix chain 't' and resid 6 through 15 Processing helix chain 'S' and resid 554 through 564 removed outlier: 4.726A pdb=" N GLY S 564 " --> pdb=" O CYS S 560 " (cutoff:3.500A) Processing helix chain 'S' and resid 721 through 735 Processing helix chain 'S' and resid 739 through 759 removed outlier: 3.730A pdb=" N THR S 743 " --> pdb=" O GLY S 739 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET S 759 " --> pdb=" O LEU S 755 " (cutoff:3.500A) Processing helix chain 'S' and resid 565 through 571 removed outlier: 5.822A pdb=" N THR S 568 " --> pdb=" O GLU S 565 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR S 569 " --> pdb=" O ILE S 566 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY S 570 " --> pdb=" O PRO S 567 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 117 removed outlier: 4.052A pdb=" N LEU U 116 " --> pdb=" O ASN U 112 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP U 117 " --> pdb=" O ARG U 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 112 through 117' Processing helix chain 'U' and resid 150 through 159 Processing helix chain 'U' and resid 183 through 195 removed outlier: 4.360A pdb=" N GLU U 187 " --> pdb=" O ASP U 183 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP U 188 " --> pdb=" O SER U 184 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE U 189 " --> pdb=" O SER U 185 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) Proline residue: U 195 - end of helix Processing helix chain 'U' and resid 198 through 205 Processing helix chain 'U' and resid 233 through 246 removed outlier: 3.864A pdb=" N VAL U 239 " --> pdb=" O TYR U 235 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN U 245 " --> pdb=" O GLN U 241 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL U 246 " --> pdb=" O ALA U 242 " (cutoff:3.500A) Processing helix chain 'U' and resid 247 through 255 removed outlier: 3.991A pdb=" N GLU U 255 " --> pdb=" O ASN U 251 " (cutoff:3.500A) Processing helix chain 'U' and resid 269 through 286 removed outlier: 4.484A pdb=" N LEU U 273 " --> pdb=" O ILE U 269 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL U 274 " --> pdb=" O MET U 270 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN U 286 " --> pdb=" O ARG U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 296 through 308 removed outlier: 4.623A pdb=" N LYS U 308 " --> pdb=" O VAL U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 336 removed outlier: 3.957A pdb=" N GLY U 336 " --> pdb=" O SER U 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 343 through 349 Processing helix chain 'U' and resid 366 through 377 removed outlier: 4.023A pdb=" N ASP U 377 " --> pdb=" O LEU U 373 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 421 removed outlier: 3.678A pdb=" N ILE U 418 " --> pdb=" O PRO U 414 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LYS U 421 " --> pdb=" O ASN U 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 480 through 485 removed outlier: 3.657A pdb=" N LEU U 484 " --> pdb=" O LEU U 480 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER U 485 " --> pdb=" O ARG U 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 480 through 485' Processing helix chain 'U' and resid 486 through 493 removed outlier: 4.440A pdb=" N ALA U 490 " --> pdb=" O GLU U 486 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL U 491 " --> pdb=" O GLU U 487 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS U 493 " --> pdb=" O GLN U 489 " (cutoff:3.500A) Processing helix chain 'U' and resid 538 through 543 removed outlier: 3.958A pdb=" N ILE U 542 " --> pdb=" O LEU U 538 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR U 543 " --> pdb=" O PRO U 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 538 through 543' Processing helix chain 'U' and resid 105 through 111 removed outlier: 3.808A pdb=" N LEU U 108 " --> pdb=" O CYS U 105 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP U 109 " --> pdb=" O PRO U 106 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE U 111 " --> pdb=" O LEU U 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 722 through 744 removed outlier: 3.534A pdb=" N THR Q 728 " --> pdb=" O LEU Q 724 " (cutoff:3.500A) Proline residue: Q 744 - end of helix Processing helix chain 'Q' and resid 773 through 782 removed outlier: 3.540A pdb=" N GLY Q 782 " --> pdb=" O LEU Q 778 " (cutoff:3.500A) Processing helix chain 'Q' and resid 788 through 810 Processing helix chain 'Q' and resid 817 through 822 removed outlier: 5.163A pdb=" N LEU Q 822 " --> pdb=" O PRO Q 818 " (cutoff:3.500A) Processing helix chain 'Q' and resid 857 through 863 removed outlier: 3.573A pdb=" N ILE Q 861 " --> pdb=" O ALA Q 857 " (cutoff:3.500A) Processing helix chain 'Q' and resid 867 through 885 removed outlier: 4.304A pdb=" N ASP Q 871 " --> pdb=" O ASP Q 867 " (cutoff:3.500A) Processing helix chain 'Q' and resid 893 through 906 removed outlier: 3.522A pdb=" N LEU Q 904 " --> pdb=" O LEU Q 900 " (cutoff:3.500A) Processing helix chain 'Q' and resid 909 through 917 removed outlier: 5.731A pdb=" N VAL Q 917 " --> pdb=" O ILE Q 913 " (cutoff:3.500A) Processing helix chain 'Q' and resid 918 through 923 removed outlier: 3.818A pdb=" N HIS Q 922 " --> pdb=" O PHE Q 918 " (cutoff:3.500A) Processing helix chain 'Q' and resid 954 through 959 removed outlier: 3.811A pdb=" N LEU Q 959 " --> pdb=" O LEU Q 955 " (cutoff:3.500A) Processing helix chain 'Q' and resid 966 through 985 removed outlier: 3.775A pdb=" N MET Q 985 " --> pdb=" O ASP Q 981 " (cutoff:3.500A) Processing helix chain 'Q' and resid 987 through 992 removed outlier: 5.656A pdb=" N ILE Q 992 " --> pdb=" O PRO Q 988 " (cutoff:3.500A) Processing helix chain 'Q' and resid 993 through 1000 Processing sheet with id= 1, first strand: chain 'C' and resid 127 through 130 Processing sheet with id= 2, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.952A pdb=" N GLN C 226 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 418 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG C 414 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 894 through 900 removed outlier: 3.699A pdb=" N GLY C 895 " --> pdb=" O ASP C 910 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 3.548A pdb=" N LEU C1087 " --> pdb=" O PHE C1098 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C1095 " --> pdb=" O SER C 979 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 1184 through 1188 removed outlier: 3.544A pdb=" N ALA C1226 " --> pdb=" O LEU C1216 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 1342 through 1346 Processing sheet with id= 7, first strand: chain 'C' and resid 1500 through 1503 removed outlier: 7.807A pdb=" N GLY C1500 " --> pdb=" O SER C1756 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 1552 through 1555 removed outlier: 4.859A pdb=" N ILE C1560 " --> pdb=" O LEU C1555 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 1607 through 1612 removed outlier: 3.579A pdb=" N GLU C1612 " --> pdb=" O ASP C1628 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASP C1628 " --> pdb=" O GLU C1612 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR C1699 " --> pdb=" O LYS C1659 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 1785 through 1792 removed outlier: 6.092A pdb=" N VAL C1785 " --> pdb=" O GLY C1805 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C1805 " --> pdb=" O VAL C1785 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG C1787 " --> pdb=" O ILE C1803 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP C1782 " --> pdb=" O THR C1864 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C1863 " --> pdb=" O LYS C1885 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 1912 through 1918 Processing sheet with id= 12, first strand: chain 'C' and resid 2138 through 2142 removed outlier: 4.457A pdb=" N GLN C2260 " --> pdb=" O TYR C2102 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 2222 through 2229 removed outlier: 3.824A pdb=" N GLY C2176 " --> pdb=" O LEU C2128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE C2124 " --> pdb=" O THR C2180 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 1805 through 1812 removed outlier: 3.654A pdb=" N GLN C1816 " --> pdb=" O ASN C1811 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 183 through 189 removed outlier: 3.684A pdb=" N THR D 184 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 204 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS D 135 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS D 137 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP D 230 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN D 306 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 347 through 351 Processing sheet with id= 17, first strand: chain 'D' and resid 480 through 484 removed outlier: 6.105A pdb=" N GLN D 489 " --> pdb=" O THR D 484 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 474 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU D 567 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP D 521 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 499 through 502 removed outlier: 6.968A pdb=" N GLY D 499 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 530 through 534 removed outlier: 4.080A pdb=" N LEU D 530 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 537 " --> pdb=" O VAL D 534 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 617 through 622 removed outlier: 3.749A pdb=" N THR D 618 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS D 627 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS D 589 " --> pdb=" O PRO D 658 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA D 591 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP D 652 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 39.570A pdb=" N ILE D 653 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 35.241A pdb=" N ALA D 838 " --> pdb=" O ILE D 653 " (cutoff:3.500A) removed outlier: 32.094A pdb=" N VAL D 655 " --> pdb=" O VAL D 836 " (cutoff:3.500A) removed outlier: 28.543A pdb=" N VAL D 836 " --> pdb=" O VAL D 655 " (cutoff:3.500A) removed outlier: 25.286A pdb=" N ASP D 657 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 20.925A pdb=" N VAL D 834 " --> pdb=" O ASP D 657 " (cutoff:3.500A) removed outlier: 15.997A pdb=" N VAL D 659 " --> pdb=" O TYR D 832 " (cutoff:3.500A) removed outlier: 12.524A pdb=" N TYR D 832 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR D 661 " --> pdb=" O PRO D 830 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 838 " --> pdb=" O TYR D 869 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS D 872 " --> pdb=" O THR D 858 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 673 through 678 removed outlier: 5.674A pdb=" N ASN D 683 " --> pdb=" O THR D 678 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 686 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 787 " --> pdb=" O PRO D 742 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN D 743 " --> pdb=" O GLY D 736 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 734 " --> pdb=" O LEU D 745 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 491 through 497 removed outlier: 3.939A pdb=" N ASN D 548 " --> pdb=" O VAL D 496 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 682 through 686 removed outlier: 8.725A pdb=" N LYS D 682 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA D 797 " --> pdb=" O LYS D 682 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP D 793 " --> pdb=" O THR D 686 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 832 through 838 Processing sheet with id= 25, first strand: chain 'D' and resid 827 through 832 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'D' and resid 859 through 863 removed outlier: 5.416A pdb=" N LEU D 868 " --> pdb=" O ILE D 863 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 434 through 438 removed outlier: 4.642A pdb=" N PHE E 435 " --> pdb=" O HIS E 446 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS E 446 " --> pdb=" O PHE E 435 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 499 through 503 Processing sheet with id= 29, first strand: chain 'E' and resid 683 through 692 removed outlier: 3.806A pdb=" N LYS E 829 " --> pdb=" O PHE E 724 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 831 through 834 removed outlier: 8.499A pdb=" N THR E 831 " --> pdb=" O LEU E 844 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 970 through 974 removed outlier: 3.722A pdb=" N ASN E 978 " --> pdb=" O ASP E 973 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'E' and resid 1183 through 1192 removed outlier: 4.998A pdb=" N LYS E1183 " --> pdb=" O ASP E1207 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 1235 through 1243 removed outlier: 3.661A pdb=" N HIS E1235 " --> pdb=" O VAL E1225 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N SER E1217 " --> pdb=" O ALA E1243 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA E1220 " --> pdb=" O ASP E1273 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS E1278 " --> pdb=" O SER E1272 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 4.152A pdb=" N LEU E1450 " --> pdb=" O ARG E1375 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 1522 through 1529 Processing sheet with id= 36, first strand: chain 'E' and resid 1666 through 1671 removed outlier: 8.438A pdb=" N THR E1666 " --> pdb=" O TYR E1679 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 1802 through 1805 Processing sheet with id= 38, first strand: chain 'E' and resid 2016 through 2024 removed outlier: 6.770A pdb=" N ASN E2016 " --> pdb=" O GLU E2044 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU E2044 " --> pdb=" O ASN E2016 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E2042 " --> pdb=" O GLU E2018 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E2024 " --> pdb=" O VAL E2036 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL E2036 " --> pdb=" O VAL E2024 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY E2033 " --> pdb=" O ALA E2096 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E2092 " --> pdb=" O VAL E2037 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 2078 through 2083 removed outlier: 4.129A pdb=" N TRP E2065 " --> pdb=" O MET E2109 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET E2109 " --> pdb=" O TRP E2065 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR E2107 " --> pdb=" O VAL E2067 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N HIS E2102 " --> pdb=" O VAL E2124 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL E2124 " --> pdb=" O HIS E2102 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN E2118 " --> pdb=" O PHE E2108 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'F' and resid 58 through 62 removed outlier: 4.193A pdb=" N MET F 353 " --> pdb=" O MET F 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU F 351 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE F 341 " --> pdb=" O HIS F 336 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'F' and resid 70 through 75 removed outlier: 3.545A pdb=" N HIS F 75 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR F 80 " --> pdb=" O HIS F 75 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER F 79 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY F 85 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA F 103 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'F' and resid 113 through 117 removed outlier: 4.335A pdb=" N THR F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 145 " --> pdb=" O VAL F 135 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'F' and resid 156 through 160 removed outlier: 4.629A pdb=" N LEU F 166 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN F 188 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'F' and resid 197 through 202 removed outlier: 6.306A pdb=" N GLN F 207 " --> pdb=" O ASN F 202 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ASP F 206 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'F' and resid 240 through 244 removed outlier: 6.218A pdb=" N TYR F 249 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER F 248 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 290 through 294 removed outlier: 5.361A pdb=" N ARG F 290 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 301 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS F 299 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N SER F 298 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR F 310 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 311 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG F 318 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'F' and resid 308 through 311 Processing sheet with id= 48, first strand: chain 'H' and resid 55 through 61 removed outlier: 3.553A pdb=" N ALA H 57 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL H 27 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY H 31 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 90 through 94 Processing sheet with id= 50, first strand: chain 'I' and resid 498 through 502 removed outlier: 3.999A pdb=" N ASP I 549 " --> pdb=" O LEU I 474 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 640 through 646 removed outlier: 3.555A pdb=" N LEU I 768 " --> pdb=" O PHE I 644 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL I 763 " --> pdb=" O SER I 734 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I 668 " --> pdb=" O MET I 735 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'a' and resid 62 through 67 removed outlier: 5.944A pdb=" N CYS a 45 " --> pdb=" O LEU a 67 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG a 25 " --> pdb=" O LEU a 21 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 36 through 41 removed outlier: 5.917A pdb=" N MET b 36 " --> pdb=" O GLY b 62 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY b 62 " --> pdb=" O MET b 36 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'b' and resid 49 through 54 removed outlier: 5.832A pdb=" N LYS b 48 " --> pdb=" O ASN b 49 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU b 51 " --> pdb=" O THR b 46 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR b 46 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL b 53 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS b 44 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY b 22 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY b 27 " --> pdb=" O VAL b 15 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR b 16 " --> pdb=" O ILE b 69 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 36 through 41 removed outlier: 6.164A pdb=" N MET i 36 " --> pdb=" O GLY i 62 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY i 62 " --> pdb=" O MET i 36 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 49 through 54 removed outlier: 6.137A pdb=" N LYS i 48 " --> pdb=" O ASN i 49 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU i 51 " --> pdb=" O THR i 46 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR i 46 " --> pdb=" O GLU i 51 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL i 53 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS i 44 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS i 48 " --> pdb=" O GLY i 22 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY i 22 " --> pdb=" O LYS i 48 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'c' and resid 50 through 54 removed outlier: 4.090A pdb=" N LYS c 50 " --> pdb=" O CYS c 46 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLN c 41 " --> pdb=" O ASN c 112 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL c 108 " --> pdb=" O ASN c 45 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'c' and resid 63 through 66 removed outlier: 5.783A pdb=" N CYS c 63 " --> pdb=" O GLY c 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY c 103 " --> pdb=" O CYS c 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'c' and resid 70 through 77 Processing sheet with id= 60, first strand: chain 'd' and resid 39 through 44 removed outlier: 5.042A pdb=" N MET d 39 " --> pdb=" O GLY d 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY d 65 " --> pdb=" O MET d 39 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'd' and resid 54 through 59 removed outlier: 5.299A pdb=" N ARG d 54 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN d 45 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS d 31 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE d 70 " --> pdb=" O GLU d 21 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'e' and resid 70 through 75 removed outlier: 5.186A pdb=" N ASP e 60 " --> pdb=" O CYS e 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS e 46 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET e 41 " --> pdb=" O LEU e 35 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU e 35 " --> pdb=" O MET e 41 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE e 43 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG e 30 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU e 86 " --> pdb=" O TRP e 34 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 41 through 45 Processing sheet with id= 64, first strand: chain 'f' and resid 47 through 51 Processing sheet with id= 65, first strand: chain 'g' and resid 40 through 43 Processing sheet with id= 66, first strand: chain 'g' and resid 45 through 48 removed outlier: 3.906A pdb=" N MET g 48 " --> pdb=" O HIS g 26 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS g 26 " --> pdb=" O MET g 48 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET g 69 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'n' and resid 40 through 43 Processing sheet with id= 68, first strand: chain 'n' and resid 45 through 48 removed outlier: 4.076A pdb=" N MET n 48 " --> pdb=" O HIS n 26 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N HIS n 26 " --> pdb=" O MET n 48 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG n 25 " --> pdb=" O LEU n 21 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU n 71 " --> pdb=" O SER n 18 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'M' and resid 225 through 228 removed outlier: 4.169A pdb=" N CYS M 225 " --> pdb=" O LEU M 518 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR M 515 " --> pdb=" O SER M 511 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER M 511 " --> pdb=" O THR M 515 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU M 506 " --> pdb=" O SER M 501 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY M 497 " --> pdb=" O CYS M 510 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'M' and resid 236 through 240 removed outlier: 5.645A pdb=" N MET M 245 " --> pdb=" O SER M 240 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'M' and resid 278 through 282 removed outlier: 5.051A pdb=" N ALA M 278 " --> pdb=" O CYS M 299 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASN M 295 " --> pdb=" O HIS M 282 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU M 296 " --> pdb=" O TRP M 308 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA M 300 " --> pdb=" O SER M 304 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER M 304 " --> pdb=" O ALA M 300 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL M 305 " --> pdb=" O ILE M 319 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'M' and resid 328 through 332 removed outlier: 4.695A pdb=" N ARG M 328 " --> pdb=" O THR M 341 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE M 337 " --> pdb=" O HIS M 332 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ARG M 336 " --> pdb=" O LEU M 352 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER M 346 " --> pdb=" O CYS M 342 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU M 349 " --> pdb=" O ILE M 358 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU M 356 " --> pdb=" O ASP M 351 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'M' and resid 370 through 374 removed outlier: 3.506A pdb=" N ASP M 370 " --> pdb=" O GLY M 383 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU M 379 " --> pdb=" O HIS M 374 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE M 388 " --> pdb=" O GLY M 384 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY M 389 " --> pdb=" O LEU M 403 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'M' and resid 411 through 416 removed outlier: 3.532A pdb=" N SER M 416 " --> pdb=" O HIS M 421 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N HIS M 421 " --> pdb=" O SER M 416 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER M 426 " --> pdb=" O THR M 430 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR M 430 " --> pdb=" O SER M 426 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'M' and resid 453 through 457 removed outlier: 3.688A pdb=" N ALA M 469 " --> pdb=" O THR M 473 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR M 473 " --> pdb=" O ALA M 469 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS M 486 " --> pdb=" O ILE M 476 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'N' and resid 630 through 633 removed outlier: 3.529A pdb=" N VAL N 633 " --> pdb=" O VAL N 545 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL N 545 " --> pdb=" O VAL N 633 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR N 546 " --> pdb=" O VAL N 582 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL N 582 " --> pdb=" O TYR N 546 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN N 580 " --> pdb=" O VAL N 548 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU N 645 " --> pdb=" O LEU N 569 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY N 571 " --> pdb=" O GLU N 645 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS N 647 " --> pdb=" O GLY N 571 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL N 573 " --> pdb=" O LYS N 647 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'N' and resid 542 through 545 removed outlier: 3.917A pdb=" N TRP N 634 " --> pdb=" O VAL N 545 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.483A pdb=" N GLN O 34 " --> pdb=" O THR O 105 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'O' and resid 52 through 58 Processing sheet with id= 80, first strand: chain 'h' and resid 40 through 43 Processing sheet with id= 81, first strand: chain 'h' and resid 45 through 49 removed outlier: 7.377A pdb=" N ARG h 16 " --> pdb=" O GLU h 83 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'j' and resid 89 through 97 removed outlier: 4.146A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL j 108 " --> pdb=" O ASN j 45 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'k' and resid 46 through 49 removed outlier: 3.590A pdb=" N ARG k 29 " --> pdb=" O THR k 47 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU k 26 " --> pdb=" O THR k 22 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'l' and resid 54 through 59 removed outlier: 6.500A pdb=" N MET l 54 " --> pdb=" O GLY l 81 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY l 81 " --> pdb=" O MET l 54 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'l' and resid 69 through 75 removed outlier: 3.619A pdb=" N SER l 70 " --> pdb=" O HIS l 65 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN l 40 " --> pdb=" O SER l 66 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'm' and resid 42 through 45 Processing sheet with id= 87, first strand: chain 'm' and resid 47 through 51 Processing sheet with id= 88, first strand: chain 'V' and resid 3 through 8 removed outlier: 6.742A pdb=" N LYS V 3 " --> pdb=" O ASP V 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP V 16 " --> pdb=" O LYS V 3 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'W' and resid 79 through 82 removed outlier: 3.849A pdb=" N ARG W 79 " --> pdb=" O GLU W 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR W 99 " --> pdb=" O LEU W 51 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU W 51 " --> pdb=" O TYR W 99 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'X' and resid 41 through 46 Processing sheet with id= 91, first strand: chain 'o' and resid 39 through 43 removed outlier: 3.515A pdb=" N LEU o 40 " --> pdb=" O LEU o 72 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'o' and resid 61 through 68 removed outlier: 3.618A pdb=" N ARG o 65 " --> pdb=" O GLU o 47 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N CYS o 45 " --> pdb=" O LEU o 67 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP o 44 " --> pdb=" O THR o 30 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR o 30 " --> pdb=" O ASP o 44 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARG o 25 " --> pdb=" O LEU o 21 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'p' and resid 30 through 33 removed outlier: 4.739A pdb=" N ASN p 37 " --> pdb=" O ASP p 33 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N MET p 36 " --> pdb=" O GLY p 62 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY p 62 " --> pdb=" O MET p 36 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'p' and resid 52 through 55 Processing sheet with id= 95, first strand: chain 'q' and resid 63 through 67 removed outlier: 5.999A pdb=" N CYS q 63 " --> pdb=" O GLY q 103 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY q 103 " --> pdb=" O CYS q 63 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'q' and resid 89 through 96 removed outlier: 3.708A pdb=" N VAL q 90 " --> pdb=" O GLU q 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU q 76 " --> pdb=" O VAL q 90 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS q 92 " --> pdb=" O TRP q 74 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG q 94 " --> pdb=" O GLU q 72 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU q 72 " --> pdb=" O ARG q 94 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS q 50 " --> pdb=" O CYS q 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL q 108 " --> pdb=" O ASN q 45 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'r' and resid 41 through 44 Processing sheet with id= 98, first strand: chain 'r' and resid 54 through 59 removed outlier: 4.836A pdb=" N ARG r 54 " --> pdb=" O TYR r 50 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN r 45 " --> pdb=" O LYS r 31 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS r 31 " --> pdb=" O ASN r 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU r 21 " --> pdb=" O PHE r 70 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE r 70 " --> pdb=" O GLU r 21 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 's' and resid 69 through 75 removed outlier: 5.278A pdb=" N ALA s 61 " --> pdb=" O LEU s 74 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN s 40 " --> pdb=" O SER s 66 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N MET s 41 " --> pdb=" O LEU s 35 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU s 35 " --> pdb=" O MET s 41 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE s 43 " --> pdb=" O VAL s 33 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG s 30 " --> pdb=" O VAL s 90 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU s 86 " --> pdb=" O TRP s 34 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 't' and resid 47 through 50 removed outlier: 3.781A pdb=" N TYR t 71 " --> pdb=" O LYS t 22 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'u' and resid 15 through 21 removed outlier: 4.285A pdb=" N LYS u 15 " --> pdb=" O LEU u 31 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL u 27 " --> pdb=" O LEU u 19 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG u 25 " --> pdb=" O LEU u 21 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS u 26 " --> pdb=" O MET u 48 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'u' and resid 39 through 43 Processing sheet with id=103, first strand: chain 'U' and resid 133 through 136 removed outlier: 4.690A pdb=" N LYS U 141 " --> pdb=" O CYS U 136 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'U' and resid 163 through 167 removed outlier: 3.906A pdb=" N LYS U 171 " --> pdb=" O ASN U 166 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'U' and resid 381 through 387 removed outlier: 6.150A pdb=" N SER U 352 " --> pdb=" O THR U 444 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN U 436 " --> pdb=" O LEU U 360 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'U' and resid 390 through 394 removed outlier: 3.705A pdb=" N ALA U 501 " --> pdb=" O ILE U 551 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE U 500 " --> pdb=" O LEU U 519 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS U 525 " --> pdb=" O HIS U 520 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP U 526 " --> pdb=" O ILE U 537 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN U 533 " --> pdb=" O GLN U 530 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'U' and resid 457 through 460 removed outlier: 4.021A pdb=" N PHE U 463 " --> pdb=" O ASN U 460 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Q' and resid 686 through 689 removed outlier: 8.180A pdb=" N ARG Q 686 " --> pdb=" O ASN Q 707 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN Q 700 " --> pdb=" O ILE Q 718 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN Q 712 " --> pdb=" O ASP Q 706 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU Q 763 " --> pdb=" O ILE Q 719 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG Q 755 " --> pdb=" O VAL Q 766 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Q' and resid 928 through 935 removed outlier: 3.965A pdb=" N PHE Q 929 " --> pdb=" O MET Q 946 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ARG Q 940 " --> pdb=" O ASP Q 935 " (cutoff:3.500A) 4406 hydrogen bonds defined for protein. 12996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 279 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 209 stacking parallelities Total time for adding SS restraints: 72.31 Time building geometry restraints manager: 39.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 16020 1.31 - 1.44: 29137 1.44 - 1.57: 57568 1.57 - 1.70: 813 1.70 - 1.83: 822 Bond restraints: 104360 Sorted by residual: bond pdb=" CBS M7M J 0 " pdb=" OBR M7M J 0 " ideal model delta sigma weight residual 1.302 1.536 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" CBS M7M J 0 " pdb=" CBY M7M J 0 " ideal model delta sigma weight residual 1.538 1.322 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" P A J 1 " pdb=" O5' A J 1 " ideal model delta sigma weight residual 1.593 1.494 0.099 1.50e-02 4.44e+03 4.35e+01 bond pdb=" CG LYS m 30 " pdb=" CD LYS m 30 " ideal model delta sigma weight residual 1.520 1.359 0.161 3.00e-02 1.11e+03 2.88e+01 bond pdb=" CD LYS m 30 " pdb=" CE LYS m 30 " ideal model delta sigma weight residual 1.520 1.372 0.148 3.00e-02 1.11e+03 2.44e+01 ... (remaining 104355 not shown) Histogram of bond angle deviations from ideal: 91.48 - 100.03: 55 100.03 - 108.59: 9788 108.59 - 117.14: 67535 117.14 - 125.70: 62622 125.70 - 134.25: 2876 Bond angle restraints: 142876 Sorted by residual: angle pdb=" C3' A P 64 " pdb=" O3' A P 64 " pdb=" P C P 65 " ideal model delta sigma weight residual 120.20 106.30 13.90 1.50e+00 4.44e-01 8.58e+01 angle pdb=" C3' U K 65 " pdb=" O3' U K 65 " pdb=" P G K 66 " ideal model delta sigma weight residual 120.20 106.87 13.33 1.50e+00 4.44e-01 7.89e+01 angle pdb=" C3' C P 62 " pdb=" O3' C P 62 " pdb=" P G P 63 " ideal model delta sigma weight residual 120.20 106.90 13.30 1.50e+00 4.44e-01 7.86e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P C B 68 " ideal model delta sigma weight residual 120.20 107.23 12.97 1.50e+00 4.44e-01 7.48e+01 angle pdb=" C3' A B 66 " pdb=" O3' A B 66 " pdb=" P A B 67 " ideal model delta sigma weight residual 120.20 107.44 12.76 1.50e+00 4.44e-01 7.23e+01 ... (remaining 142871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 61768 35.69 - 71.39: 2185 71.39 - 107.08: 213 107.08 - 142.77: 13 142.77 - 178.46: 5 Dihedral angle restraints: 64184 sinusoidal: 30541 harmonic: 33643 Sorted by residual: dihedral pdb=" O4' U P 101 " pdb=" C1' U P 101 " pdb=" N1 U P 101 " pdb=" C2 U P 101 " ideal model delta sinusoidal sigma weight residual 200.00 50.96 149.04 1 1.50e+01 4.44e-03 7.93e+01 dihedral pdb=" O4' U P 97 " pdb=" C1' U P 97 " pdb=" N1 U P 97 " pdb=" C2 U P 97 " ideal model delta sinusoidal sigma weight residual 232.00 53.54 178.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C J 42 " pdb=" C1' C J 42 " pdb=" N1 C J 42 " pdb=" C2 C J 42 " ideal model delta sinusoidal sigma weight residual -128.00 49.20 -177.20 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 64181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.998: 16150 0.998 - 1.996: 0 1.996 - 2.994: 0 2.994 - 3.992: 0 3.992 - 4.990: 2 Chirality restraints: 16152 Sorted by residual: chirality pdb=" C2 IHP C3000 " pdb=" C1 IHP C3000 " pdb=" C3 IHP C3000 " pdb=" O12 IHP C3000 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.99 2.00e-01 2.50e+01 6.23e+02 chirality pdb=" C3 IHP C3000 " pdb=" C2 IHP C3000 " pdb=" C4 IHP C3000 " pdb=" O13 IHP C3000 " both_signs ideal model delta sigma weight residual False -2.34 2.50 -4.84 2.00e-01 2.50e+01 5.84e+02 chirality pdb=" CB VAL m 75 " pdb=" CA VAL m 75 " pdb=" CG1 VAL m 75 " pdb=" CG2 VAL m 75 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 16149 not shown) Planarity restraints: 16855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 559 " -0.049 2.00e-02 2.50e+03 5.21e-02 4.74e+01 pdb=" CG PHE I 559 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE I 559 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE I 559 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE I 559 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE I 559 " -0.053 2.00e-02 2.50e+03 pdb=" CZ PHE I 559 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 430 " 0.088 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO E 431 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO E 431 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO E 431 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE t 10 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C PHE t 10 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE t 10 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU t 11 " 0.025 2.00e-02 2.50e+03 ... (remaining 16852 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 853 2.55 - 3.14: 81851 3.14 - 3.73: 169125 3.73 - 4.31: 230285 4.31 - 4.90: 368596 Nonbonded interactions: 850710 Sorted by model distance: nonbonded pdb=" O1B GTP D1500 " pdb="MG MG D1501 " model vdw 1.966 2.170 nonbonded pdb=" O1G GTP D1500 " pdb="MG MG D1501 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 143 " pdb="MG MG D1501 " model vdw 2.099 2.170 nonbonded pdb=" OD1 ASP E1227 " pdb=" N VAL E1228 " model vdw 2.106 2.520 nonbonded pdb=" O GLU D 776 " pdb=" OH TYR D 817 " model vdw 2.196 2.440 ... (remaining 850705 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 8 through 88) selection = (chain 'h' and (resid 8 through 50 or resid 61 through 88)) } ncs_group { reference = chain 'b' selection = chain 'i' selection = (chain 'p' and resid 2 through 82) } ncs_group { reference = (chain 'c' and resid 10 through 114) selection = (chain 'q' and resid 10 through 114) } ncs_group { reference = (chain 'd' and resid 3 through 83) selection = (chain 'k' and resid 3 through 83) selection = (chain 'r' and resid 3 through 83) } ncs_group { reference = (chain 'e' and resid 14 through 89) selection = chain 'l' selection = (chain 's' and resid 14 through 89) } ncs_group { reference = (chain 'f' and resid 4 through 75) selection = chain 'm' selection = (chain 't' and resid 4 through 75) } ncs_group { reference = (chain 'g' and resid 4 through 76) selection = (chain 'n' and resid 4 through 76) selection = chain 'u' } 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=0.06 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: 10.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 30.360 Check model and map are aligned: 1.180 Set scattering table: 0.810 Process input model: 332.170 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 381.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 : 0.006 0.234 104360 Z= 0.385 Angle : 0.846 15.498 142876 Z= 0.480 Chirality : 0.078 4.990 16152 Planarity : 0.006 0.128 16855 Dihedral : 17.263 178.464 42376 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 0.57 % Allowed : 12.47 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.08), residues: 11376 helix: 0.91 (0.08), residues: 4707 sheet: -0.34 (0.12), residues: 1779 loop : -0.97 (0.08), residues: 4890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP G 157 HIS 0.014 0.001 HIS p 39 PHE 0.106 0.002 PHE I 559 TYR 0.034 0.002 TYR f 50 ARG 0.044 0.001 ARG h 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1072 time to evaluate : 8.885 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: C 1410 ASP cc_start: 0.8100 (p0) cc_final: 0.7853 (p0) REVERT: C 1599 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6521 (mt0) REVERT: C 1659 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6955 (mppt) REVERT: E 84 MET cc_start: 0.2817 (mmt) cc_final: 0.2310 (tpt) REVERT: E 455 PHE cc_start: 0.3892 (t80) cc_final: 0.3660 (t80) REVERT: E 1367 MET cc_start: 0.7015 (ttp) cc_final: 0.6339 (ttp) REVERT: E 1846 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5812 (pt) REVERT: E 2114 MET cc_start: 0.1055 (ptt) cc_final: -0.0550 (mtt) REVERT: F 246 GLU cc_start: 0.2992 (pp20) cc_final: 0.2757 (pm20) REVERT: F 353 MET cc_start: 0.0815 (ptt) cc_final: 0.0435 (ttm) REVERT: G 679 MET cc_start: 0.5823 (tpt) cc_final: 0.5584 (tpt) REVERT: I 517 MET cc_start: 0.5018 (mmm) cc_final: 0.4564 (ptm) REVERT: I 557 MET cc_start: 0.5281 (ttm) cc_final: 0.4953 (ttp) REVERT: a 28 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.4463 (mt) REVERT: g 75 ARG cc_start: 0.6869 (mmm160) cc_final: 0.5737 (mmp-170) REVERT: g 76 VAL cc_start: 0.5121 (m) cc_final: 0.4898 (p) REVERT: L 346 PRO cc_start: 0.1522 (Cg_endo) cc_final: 0.0813 (Cg_exo) REVERT: L 378 MET cc_start: 0.5506 (tpt) cc_final: 0.3602 (tpt) REVERT: M 522 GLU cc_start: 0.3849 (tt0) cc_final: 0.3261 (tp30) REVERT: N 457 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.5511 (mt0) REVERT: N 465 ARG cc_start: 0.6600 (ptt90) cc_final: 0.6030 (ptt180) REVERT: h 80 MET cc_start: 0.2761 (mmp) cc_final: 0.1239 (ttm) REVERT: k 76 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5053 (ttp) REVERT: k 82 MET cc_start: 0.7514 (ttt) cc_final: 0.7174 (ptp) REVERT: l 41 MET cc_start: -0.1182 (ptt) cc_final: -0.1473 (mtm) REVERT: l 74 LEU cc_start: 0.1697 (OUTLIER) cc_final: 0.1339 (tp) REVERT: m 27 MET cc_start: -0.3097 (pmm) cc_final: -0.3299 (mpp) REVERT: m 40 MET cc_start: -0.0679 (ppp) cc_final: -0.1278 (tmm) REVERT: n 48 MET cc_start: 0.3107 (OUTLIER) cc_final: 0.2806 (mmt) REVERT: n 59 MET cc_start: 0.6744 (ptt) cc_final: 0.6460 (tpt) REVERT: V 1 MET cc_start: 0.1519 (tmm) cc_final: -0.0226 (mmp) REVERT: V 40 MET cc_start: 0.4226 (pmm) cc_final: 0.3506 (tpt) REVERT: V 42 ARG cc_start: 0.2164 (mtt90) cc_final: 0.1915 (mmt90) REVERT: V 80 ARG cc_start: 0.1003 (ptt90) cc_final: 0.0580 (tmm160) REVERT: W 35 MET cc_start: 0.7714 (mtm) cc_final: 0.7410 (mpp) REVERT: Y 66 MET cc_start: -0.1973 (mmm) cc_final: -0.2352 (tpp) REVERT: Y 249 MET cc_start: 0.7421 (mmp) cc_final: 0.6299 (mmm) REVERT: o 17 MET cc_start: 0.2675 (tpp) cc_final: 0.2140 (mtm) REVERT: p 1 MET cc_start: 0.3747 (pmm) cc_final: 0.3049 (mtt) REVERT: p 36 MET cc_start: 0.3276 (ppp) cc_final: 0.2596 (tpt) REVERT: p 65 ILE cc_start: 0.3583 (OUTLIER) cc_final: 0.3214 (mp) REVERT: q 17 GLN cc_start: 0.5773 (tm-30) cc_final: 0.4752 (tp40) REVERT: q 20 GLU cc_start: 0.3349 (OUTLIER) cc_final: 0.2988 (mm-30) REVERT: q 99 MET cc_start: 0.0919 (tpt) cc_final: 0.0713 (mmt) REVERT: r 72 ILE cc_start: 0.8043 (mp) cc_final: 0.7722 (mp) REVERT: u 13 MET cc_start: 0.2340 (tpp) cc_final: 0.1104 (tpt) REVERT: S 715 GLU cc_start: 0.5634 (mt-10) cc_final: 0.5391 (pm20) outliers start: 58 outliers final: 9 residues processed: 1115 average time/residue: 1.0769 time to fit residues: 2040.3652 Evaluate side-chains 616 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 598 time to evaluate : 8.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1659 LYS Chi-restraints excluded: chain E residue 460 GLN Chi-restraints excluded: chain E residue 631 LEU Chi-restraints excluded: chain E residue 1846 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain N residue 452 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain k residue 76 MET Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain q residue 20 GLU Chi-restraints excluded: chain U residue 339 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 989 optimal weight: 8.9990 chunk 888 optimal weight: 5.9990 chunk 492 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 599 optimal weight: 7.9990 chunk 474 optimal weight: 5.9990 chunk 918 optimal weight: 0.7980 chunk 355 optimal weight: 20.0000 chunk 558 optimal weight: 0.8980 chunk 683 optimal weight: 2.9990 chunk 1064 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 HIS ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1217 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1363 GLN C1400 ASN C1520 ASN ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1737 ASN ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2154 HIS D 548 ASN E 121 GLN ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 885 GLN ** E1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1158 HIS E1447 ASN ** E1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 776 ASN ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 511 GLN I 591 ASN I 672 ASN ** b 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 ASN L 111 HIS ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 GLN O 114 GLN O 121 GLN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 ASN i 26 HIS j 34 GLN j 41 GLN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 59 GLN Y 158 GLN ** Y 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 GLN ** s 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 88 GLN U 233 ASN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 407 GLN ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 104360 Z= 0.322 Angle : 0.664 16.489 142876 Z= 0.339 Chirality : 0.044 0.678 16152 Planarity : 0.005 0.084 16855 Dihedral : 15.469 175.239 18839 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 1.80 % Allowed : 14.07 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.08), residues: 11376 helix: 1.06 (0.07), residues: 4812 sheet: -0.20 (0.12), residues: 1758 loop : -0.91 (0.08), residues: 4806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 434 HIS 0.013 0.001 HIS F 282 PHE 0.031 0.002 PHE C1719 TYR 0.033 0.002 TYR G 882 ARG 0.009 0.001 ARG F 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 646 time to evaluate : 8.594 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: C 684 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: C 1407 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7676 (p0) REVERT: C 1410 ASP cc_start: 0.8201 (p0) cc_final: 0.7997 (p0) REVERT: C 1561 PHE cc_start: 0.7167 (m-80) cc_final: 0.6841 (m-80) REVERT: C 1599 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7235 (mm-40) REVERT: C 1602 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6279 (p0) REVERT: E 78 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6673 (mmm160) REVERT: E 97 MET cc_start: 0.3637 (tmm) cc_final: 0.2967 (tmm) REVERT: E 1126 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8093 (mpp) REVERT: E 1367 MET cc_start: 0.7240 (ttp) cc_final: 0.6529 (ttp) REVERT: F 353 MET cc_start: 0.0492 (ptt) cc_final: -0.0203 (ttt) REVERT: G 679 MET cc_start: 0.6226 (tpt) cc_final: 0.5953 (tpt) REVERT: I 557 MET cc_start: 0.6421 (ttm) cc_final: 0.5929 (ttm) REVERT: I 672 ASN cc_start: 0.1695 (OUTLIER) cc_final: 0.1148 (t0) REVERT: c 19 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6488 (tpt170) REVERT: f 47 THR cc_start: 0.4947 (OUTLIER) cc_final: 0.4628 (t) REVERT: f 55 LEU cc_start: 0.6337 (mm) cc_final: 0.6017 (mt) REVERT: g 75 ARG cc_start: 0.7332 (mmm160) cc_final: 0.5788 (mmp-170) REVERT: R 115 MET cc_start: 0.3953 (ptt) cc_final: 0.3181 (tpt) REVERT: h 9 MET cc_start: -0.1455 (ttm) cc_final: -0.2142 (mtt) REVERT: h 48 PHE cc_start: 0.1005 (OUTLIER) cc_final: 0.0726 (m-10) REVERT: h 80 MET cc_start: 0.2420 (OUTLIER) cc_final: 0.1310 (ttt) REVERT: i 72 ASP cc_start: 0.4258 (OUTLIER) cc_final: 0.3759 (p0) REVERT: k 82 MET cc_start: 0.7518 (ttt) cc_final: 0.7183 (ptp) REVERT: m 40 MET cc_start: -0.0910 (ppp) cc_final: -0.1678 (tmm) REVERT: n 48 MET cc_start: 0.2184 (pmm) cc_final: 0.1938 (mpp) REVERT: n 59 MET cc_start: 0.6872 (ptt) cc_final: 0.6556 (tpt) REVERT: V 40 MET cc_start: 0.4752 (pmm) cc_final: 0.3844 (tpt) REVERT: V 42 ARG cc_start: 0.2412 (mtt90) cc_final: 0.1937 (mmt90) REVERT: V 80 ARG cc_start: 0.0308 (ptt90) cc_final: -0.0058 (tmm160) REVERT: X 1 MET cc_start: 0.2171 (mmt) cc_final: 0.1802 (mmt) REVERT: X 109 ARG cc_start: 0.6073 (mmm160) cc_final: 0.5828 (mmm-85) REVERT: Y 39 ASP cc_start: 0.4320 (OUTLIER) cc_final: 0.3953 (t0) REVERT: Y 181 ILE cc_start: 0.0061 (OUTLIER) cc_final: -0.0252 (mm) REVERT: Y 249 MET cc_start: 0.7127 (mmp) cc_final: 0.6722 (mmm) REVERT: o 48 PHE cc_start: 0.7031 (m-80) cc_final: 0.6818 (m-10) REVERT: p 8 MET cc_start: 0.6730 (mmm) cc_final: 0.6321 (mmm) REVERT: p 68 PHE cc_start: 0.5815 (t80) cc_final: 0.4901 (t80) REVERT: q 17 GLN cc_start: 0.5484 (tm-30) cc_final: 0.4687 (tp40) REVERT: r 14 GLU cc_start: 0.4085 (OUTLIER) cc_final: 0.3744 (mm-30) REVERT: s 47 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3361 (mp) REVERT: t 27 MET cc_start: 0.3599 (tpt) cc_final: 0.2379 (ttt) REVERT: t 50 TYR cc_start: 0.6532 (m-10) cc_final: 0.5908 (m-10) REVERT: u 13 MET cc_start: 0.1248 (tpp) cc_final: 0.0335 (tpt) REVERT: Q 914 ARG cc_start: 0.5818 (mtt90) cc_final: 0.5470 (ttt-90) outliers start: 183 outliers final: 62 residues processed: 793 average time/residue: 0.8996 time to fit residues: 1243.6232 Evaluate side-chains 643 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 567 time to evaluate : 9.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1400 ASN Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1602 ASP Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 1126 MET Chi-restraints excluded: chain E residue 1173 THR Chi-restraints excluded: chain E residue 1406 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain G residue 324 LYS Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 672 ASN Chi-restraints excluded: chain a residue 18 ARG Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain c residue 19 ARG Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 309 HIS Chi-restraints excluded: chain N residue 452 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain R residue 79 HIS Chi-restraints excluded: chain h residue 48 PHE Chi-restraints excluded: chain h residue 80 MET Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain S residue 710 ILE Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 591 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 885 optimal weight: 50.0000 chunk 724 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 1066 optimal weight: 0.9990 chunk 1151 optimal weight: 3.9990 chunk 949 optimal weight: 5.9990 chunk 1057 optimal weight: 0.9980 chunk 363 optimal weight: 0.0870 chunk 855 optimal weight: 10.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 573 GLN C 960 ASN C1217 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1737 ASN ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1875 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 702 GLN E 771 ASN ** E1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1447 ASN E1898 HIS ** E2058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 GLN ** a 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 HIS ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 ASN R 103 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 GLN Y 231 HIS ** s 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 88 GLN ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 233 ASN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 104360 Z= 0.198 Angle : 0.576 12.277 142876 Z= 0.293 Chirality : 0.041 0.198 16152 Planarity : 0.004 0.069 16855 Dihedral : 15.234 175.154 18807 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 14.90 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.08), residues: 11376 helix: 1.31 (0.08), residues: 4811 sheet: -0.21 (0.12), residues: 1800 loop : -0.81 (0.09), residues: 4765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 312 HIS 0.012 0.001 HIS F 282 PHE 0.036 0.001 PHE C1379 TYR 0.027 0.001 TYR E1295 ARG 0.010 0.000 ARG E1843 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 608 time to evaluate : 8.850 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: C 684 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: C 756 TYR cc_start: 0.7948 (t80) cc_final: 0.7710 (t80) REVERT: C 1407 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7628 (p0) REVERT: C 1561 PHE cc_start: 0.7262 (m-80) cc_final: 0.6955 (m-80) REVERT: E 78 ARG cc_start: 0.6878 (mmm160) cc_final: 0.6566 (mmm160) REVERT: E 97 MET cc_start: 0.3455 (tmm) cc_final: 0.3081 (tmm) REVERT: E 992 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.7101 (t80) REVERT: E 1367 MET cc_start: 0.7321 (ttp) cc_final: 0.7023 (ttp) REVERT: E 1829 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (tp) REVERT: E 1954 TRP cc_start: 0.3057 (m100) cc_final: 0.2307 (m100) REVERT: F 353 MET cc_start: 0.0569 (ptt) cc_final: -0.0161 (ttt) REVERT: G 679 MET cc_start: 0.6267 (tpt) cc_final: 0.5706 (tpt) REVERT: H 139 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7102 (pt) REVERT: I 557 MET cc_start: 0.6471 (ttm) cc_final: 0.5945 (ttm) REVERT: b 26 HIS cc_start: 0.3839 (OUTLIER) cc_final: 0.3382 (m170) REVERT: b 39 HIS cc_start: 0.4512 (OUTLIER) cc_final: 0.4288 (m-70) REVERT: c 19 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6413 (tpt170) REVERT: c 25 ASN cc_start: 0.5785 (OUTLIER) cc_final: 0.5575 (p0) REVERT: c 93 ASP cc_start: 0.5655 (OUTLIER) cc_final: 0.5398 (m-30) REVERT: e 82 ASP cc_start: 0.6424 (OUTLIER) cc_final: 0.6088 (p0) REVERT: f 55 LEU cc_start: 0.6233 (mm) cc_final: 0.5954 (mt) REVERT: g 75 ARG cc_start: 0.7148 (mmm160) cc_final: 0.6715 (tpp-160) REVERT: N 457 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.5956 (tt0) REVERT: R 115 MET cc_start: 0.3798 (ptt) cc_final: 0.2984 (tpt) REVERT: h 9 MET cc_start: -0.1481 (ttm) cc_final: -0.2168 (mtt) REVERT: h 48 PHE cc_start: 0.1158 (OUTLIER) cc_final: 0.0937 (m-10) REVERT: h 80 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.1438 (ttt) REVERT: i 45 MET cc_start: -0.3102 (tpt) cc_final: -0.3492 (mmm) REVERT: i 72 ASP cc_start: 0.4317 (OUTLIER) cc_final: 0.3830 (p0) REVERT: j 99 MET cc_start: -0.0404 (ptm) cc_final: -0.1355 (pmm) REVERT: k 76 MET cc_start: 0.5778 (pmm) cc_final: 0.5065 (ttp) REVERT: k 82 MET cc_start: 0.7435 (ttt) cc_final: 0.7089 (ptp) REVERT: m 40 MET cc_start: -0.0888 (ppp) cc_final: -0.1673 (tmm) REVERT: n 48 MET cc_start: 0.2556 (OUTLIER) cc_final: 0.2289 (mpp) REVERT: V 40 MET cc_start: 0.4527 (pmm) cc_final: 0.3460 (tpt) REVERT: V 42 ARG cc_start: 0.2481 (mtt90) cc_final: 0.1992 (mmt90) REVERT: W 35 MET cc_start: 0.7338 (mtm) cc_final: 0.7007 (mpp) REVERT: W 71 PHE cc_start: 0.5404 (OUTLIER) cc_final: 0.4736 (t80) REVERT: W 86 LEU cc_start: 0.3171 (OUTLIER) cc_final: 0.2916 (pp) REVERT: Y 39 ASP cc_start: 0.4322 (OUTLIER) cc_final: 0.3956 (t0) REVERT: Y 66 MET cc_start: 0.0435 (tpp) cc_final: -0.0153 (mmm) REVERT: p 36 MET cc_start: 0.2089 (ppp) cc_final: 0.1268 (tpt) REVERT: p 68 PHE cc_start: 0.5520 (t80) cc_final: 0.5160 (t80) REVERT: q 17 GLN cc_start: 0.5548 (tm-30) cc_final: 0.4765 (tp40) REVERT: q 65 MET cc_start: 0.6262 (mmp) cc_final: 0.5944 (mmp) REVERT: r 14 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.4020 (mm-30) REVERT: r 29 ARG cc_start: 0.7269 (mmt90) cc_final: 0.7016 (tpt170) REVERT: s 47 ILE cc_start: 0.4504 (OUTLIER) cc_final: 0.3538 (mp) REVERT: s 79 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7287 (tp) REVERT: t 27 MET cc_start: 0.3721 (tpt) cc_final: 0.2765 (ttt) REVERT: t 50 TYR cc_start: 0.6607 (m-10) cc_final: 0.5813 (m-10) REVERT: u 13 MET cc_start: 0.1150 (tpp) cc_final: 0.0497 (tpt) REVERT: u 38 MET cc_start: 0.6053 (ppp) cc_final: 0.5715 (ppp) REVERT: S 741 MET cc_start: -0.0681 (ptt) cc_final: -0.1389 (ptm) REVERT: U 264 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8010 (mtt90) REVERT: Q 897 MET cc_start: 0.0337 (tpp) cc_final: -0.0130 (tpp) outliers start: 199 outliers final: 75 residues processed: 774 average time/residue: 0.9109 time to fit residues: 1237.3911 Evaluate side-chains 658 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 560 time to evaluate : 8.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1999 VAL Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 953 PHE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1259 PHE Chi-restraints excluded: chain E residue 1518 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1829 ILE Chi-restraints excluded: chain E residue 1849 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2036 VAL Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain H residue 139 ILE Chi-restraints excluded: chain I residue 472 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 19 ARG Chi-restraints excluded: chain c residue 25 ASN Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 82 ASP Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain N residue 452 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 48 PHE Chi-restraints excluded: chain h residue 80 MET Chi-restraints excluded: chain i residue 36 MET Chi-restraints excluded: chain i residue 40 LEU Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain Z residue 287 GLU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 546 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 1053 optimal weight: 30.0000 chunk 801 optimal weight: 5.9990 chunk 553 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 508 optimal weight: 30.0000 chunk 715 optimal weight: 3.9990 chunk 1070 optimal weight: 50.0000 chunk 1132 optimal weight: 3.9990 chunk 559 optimal weight: 0.9980 chunk 1014 optimal weight: 0.9990 chunk 305 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1188 ASN C1217 GLN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1944 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1069 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 HIS I 248 HIS a 76 ASN b 26 HIS b 54 GLN ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 62 HIS t 67 ASN U 233 ASN U 241 GLN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 380 GLN ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 104360 Z= 0.243 Angle : 0.565 12.977 142876 Z= 0.287 Chirality : 0.041 0.203 16152 Planarity : 0.004 0.061 16855 Dihedral : 15.115 174.468 18807 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 15.63 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.08), residues: 11376 helix: 1.40 (0.08), residues: 4816 sheet: -0.21 (0.12), residues: 1811 loop : -0.80 (0.09), residues: 4749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 262 HIS 0.022 0.001 HIS b 26 PHE 0.032 0.001 PHE H 102 TYR 0.020 0.001 TYR G 882 ARG 0.009 0.000 ARG g 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 577 time to evaluate : 8.953 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: C 756 TYR cc_start: 0.7928 (t80) cc_final: 0.7684 (t80) REVERT: C 1407 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7747 (p0) REVERT: C 1561 PHE cc_start: 0.7269 (m-80) cc_final: 0.6954 (m-80) REVERT: C 1599 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6620 (mt0) REVERT: E 78 ARG cc_start: 0.6793 (mmm160) cc_final: 0.6433 (mmm160) REVERT: E 97 MET cc_start: 0.3324 (tmm) cc_final: 0.3036 (tmm) REVERT: E 641 MET cc_start: 0.7338 (mmm) cc_final: 0.6987 (mmm) REVERT: E 992 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7056 (t80) REVERT: E 1367 MET cc_start: 0.7335 (ttp) cc_final: 0.6988 (ttp) REVERT: E 1829 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7943 (mm) REVERT: E 1943 MET cc_start: 0.3685 (tpp) cc_final: 0.2914 (ttm) REVERT: F 353 MET cc_start: 0.0605 (ptt) cc_final: -0.0217 (ttt) REVERT: G 485 LYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5739 (mtpt) REVERT: G 679 MET cc_start: 0.6249 (tpt) cc_final: 0.5629 (ttt) REVERT: I 557 MET cc_start: 0.6460 (ttm) cc_final: 0.5808 (ttm) REVERT: b 26 HIS cc_start: 0.3993 (OUTLIER) cc_final: 0.3703 (m170) REVERT: c 25 ASN cc_start: 0.5808 (OUTLIER) cc_final: 0.5539 (p0) REVERT: c 93 ASP cc_start: 0.5672 (OUTLIER) cc_final: 0.5338 (m-30) REVERT: c 96 ILE cc_start: 0.6036 (mp) cc_final: 0.5833 (mm) REVERT: f 55 LEU cc_start: 0.6162 (mm) cc_final: 0.5883 (mt) REVERT: g 75 ARG cc_start: 0.7195 (mmm160) cc_final: 0.6757 (tpp-160) REVERT: N 457 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.5977 (tt0) REVERT: R 115 MET cc_start: 0.3977 (ptt) cc_final: 0.3129 (tpt) REVERT: h 9 MET cc_start: -0.0989 (ttm) cc_final: -0.1816 (mtt) REVERT: h 48 PHE cc_start: 0.1095 (OUTLIER) cc_final: 0.0873 (m-10) REVERT: h 80 MET cc_start: 0.2847 (OUTLIER) cc_final: 0.1762 (ttt) REVERT: i 45 MET cc_start: -0.2689 (tpt) cc_final: -0.2927 (mmm) REVERT: i 72 ASP cc_start: 0.4415 (OUTLIER) cc_final: 0.3924 (p0) REVERT: k 76 MET cc_start: 0.5760 (pmm) cc_final: 0.4967 (ttp) REVERT: k 82 MET cc_start: 0.7384 (ttt) cc_final: 0.6995 (ptp) REVERT: m 40 MET cc_start: -0.0865 (ppp) cc_final: -0.1684 (tmm) REVERT: n 48 MET cc_start: 0.2641 (OUTLIER) cc_final: 0.2363 (mpp) REVERT: V 40 MET cc_start: 0.4567 (pmm) cc_final: 0.3742 (tpt) REVERT: V 42 ARG cc_start: 0.1969 (mtt90) cc_final: 0.1597 (mmt90) REVERT: W 35 MET cc_start: 0.7379 (mtm) cc_final: 0.6944 (mpp) REVERT: W 71 PHE cc_start: 0.5517 (OUTLIER) cc_final: 0.4870 (t80) REVERT: X 1 MET cc_start: 0.1635 (mmt) cc_final: 0.1010 (mmt) REVERT: X 81 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5256 (pt0) REVERT: Y 39 ASP cc_start: 0.4368 (OUTLIER) cc_final: 0.4027 (t0) REVERT: Y 66 MET cc_start: 0.0708 (tpp) cc_final: 0.0153 (mmp) REVERT: Y 181 ILE cc_start: 0.0143 (OUTLIER) cc_final: -0.0198 (mm) REVERT: p 36 MET cc_start: 0.2462 (ppp) cc_final: 0.1697 (tpt) REVERT: p 68 PHE cc_start: 0.5357 (t80) cc_final: 0.5123 (t80) REVERT: q 65 MET cc_start: 0.6256 (mmp) cc_final: 0.5878 (mmp) REVERT: s 47 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.3507 (mp) REVERT: s 79 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7092 (tp) REVERT: t 27 MET cc_start: 0.3986 (tpt) cc_final: 0.2859 (ttt) REVERT: t 50 TYR cc_start: 0.6727 (m-10) cc_final: 0.6087 (m-10) REVERT: u 13 MET cc_start: 0.1206 (tpp) cc_final: 0.0740 (tpt) REVERT: u 18 SER cc_start: -0.2550 (OUTLIER) cc_final: -0.3294 (m) REVERT: u 38 MET cc_start: 0.5860 (ppp) cc_final: 0.5531 (ppp) REVERT: u 59 MET cc_start: 0.3297 (tpt) cc_final: 0.2653 (ttt) REVERT: S 741 MET cc_start: -0.0537 (ptt) cc_final: -0.1220 (ptm) REVERT: U 264 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8023 (mtt90) REVERT: Q 697 VAL cc_start: 0.0719 (OUTLIER) cc_final: 0.0483 (p) REVERT: Q 727 LYS cc_start: 0.3844 (pttt) cc_final: 0.3546 (tppt) REVERT: Q 930 MET cc_start: 0.4396 (ppp) cc_final: 0.2886 (ptt) outliers start: 208 outliers final: 99 residues processed: 752 average time/residue: 0.8956 time to fit residues: 1186.5033 Evaluate side-chains 673 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 553 time to evaluate : 8.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1819 LEU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 1999 VAL Chi-restraints excluded: chain C residue 2100 THR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1173 THR Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1829 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2036 VAL Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 26 HIS Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 25 ASN Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 48 PHE Chi-restraints excluded: chain h residue 80 MET Chi-restraints excluded: chain i residue 36 MET Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain r residue 9 VAL Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain s residue 79 LEU Chi-restraints excluded: chain u residue 18 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain U residue 546 GLU Chi-restraints excluded: chain Q residue 697 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 943 optimal weight: 30.0000 chunk 643 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 843 optimal weight: 8.9990 chunk 467 optimal weight: 30.0000 chunk 966 optimal weight: 8.9990 chunk 783 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 578 optimal weight: 1.9990 chunk 1016 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 712 HIS ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1026 ASN C1172 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1428 HIS ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1998 ASN D 140 HIS E 407 GLN ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 621 HIS E 771 ASN ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 GLN ** E1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1191 GLN ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2058 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 734 GLN ** G 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 569 HIS I 672 ASN ** b 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 ASN ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN R 27 GLN R 103 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 231 HIS Z 353 GLN ** q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 233 ASN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 ASN ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 104360 Z= 0.536 Angle : 0.709 15.093 142876 Z= 0.361 Chirality : 0.046 0.266 16152 Planarity : 0.005 0.059 16855 Dihedral : 15.223 171.957 18806 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 3.00 % Allowed : 15.98 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.11 (0.08), residues: 11376 helix: 1.01 (0.07), residues: 4818 sheet: -0.44 (0.12), residues: 1842 loop : -1.01 (0.09), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 293 HIS 0.056 0.002 HIS b 26 PHE 0.028 0.002 PHE I 559 TYR 0.027 0.002 TYR C 453 ARG 0.015 0.001 ARG c 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 586 time to evaluate : 8.888 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: C 25 MET cc_start: -0.2541 (mtt) cc_final: -0.3190 (tmm) REVERT: C 258 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.7875 (t80) REVERT: C 1140 MET cc_start: 0.9250 (ttt) cc_final: 0.8954 (ttt) REVERT: C 1407 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (p0) REVERT: C 1474 MET cc_start: 0.8497 (tpp) cc_final: 0.8272 (ttm) REVERT: C 1914 MET cc_start: 0.5529 (mmm) cc_final: 0.4741 (tpt) REVERT: E 78 ARG cc_start: 0.6852 (mmm160) cc_final: 0.6515 (mmm160) REVERT: E 97 MET cc_start: 0.3137 (tmm) cc_final: 0.2924 (tmm) REVERT: E 114 GLU cc_start: 0.7012 (pp20) cc_final: 0.6722 (tm-30) REVERT: E 992 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7300 (t80) REVERT: E 1081 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7687 (ttm) REVERT: E 1829 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7876 (mm) REVERT: E 1902 MET cc_start: 0.0826 (OUTLIER) cc_final: -0.1239 (ppp) REVERT: E 1943 MET cc_start: 0.3888 (tpp) cc_final: 0.2878 (ttt) REVERT: F 262 TRP cc_start: -0.1092 (OUTLIER) cc_final: -0.1311 (m-10) REVERT: F 353 MET cc_start: 0.0391 (ptt) cc_final: -0.0521 (ttt) REVERT: G 240 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7989 (mtt) REVERT: G 338 MET cc_start: 0.5878 (ppp) cc_final: 0.5544 (ppp) REVERT: G 485 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5576 (mtpt) REVERT: G 679 MET cc_start: 0.6194 (tpt) cc_final: 0.5588 (ttt) REVERT: I 557 MET cc_start: 0.6833 (ttm) cc_final: 0.6251 (ttm) REVERT: g 75 ARG cc_start: 0.6972 (mmm160) cc_final: 0.6445 (tpp-160) REVERT: L 378 MET cc_start: 0.6720 (ttm) cc_final: 0.5536 (ttm) REVERT: M 478 THR cc_start: 0.5089 (OUTLIER) cc_final: 0.4722 (t) REVERT: N 457 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5728 (mt0) REVERT: N 597 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6054 (tp) REVERT: R 115 MET cc_start: 0.3945 (ptt) cc_final: 0.3202 (tpt) REVERT: h 9 MET cc_start: -0.0553 (ttm) cc_final: -0.1184 (mtt) REVERT: h 80 MET cc_start: 0.2867 (OUTLIER) cc_final: 0.1927 (ttt) REVERT: i 72 ASP cc_start: 0.4871 (OUTLIER) cc_final: 0.4470 (p0) REVERT: k 76 MET cc_start: 0.5777 (pmm) cc_final: 0.5093 (ttt) REVERT: k 82 MET cc_start: 0.7295 (ttt) cc_final: 0.6993 (ptp) REVERT: m 40 MET cc_start: -0.0841 (ppp) cc_final: -0.1667 (tmm) REVERT: n 48 MET cc_start: 0.2227 (OUTLIER) cc_final: 0.2008 (mpp) REVERT: V 40 MET cc_start: 0.4514 (pmm) cc_final: 0.3732 (tpt) REVERT: V 42 ARG cc_start: 0.2111 (mtt90) cc_final: 0.1574 (mmt90) REVERT: W 35 MET cc_start: 0.7438 (mtm) cc_final: 0.7075 (mpp) REVERT: W 71 PHE cc_start: 0.5341 (OUTLIER) cc_final: 0.4729 (t80) REVERT: W 97 ILE cc_start: 0.0970 (OUTLIER) cc_final: 0.0755 (tt) REVERT: X 81 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5326 (pt0) REVERT: Y 66 MET cc_start: 0.0830 (tpp) cc_final: 0.0403 (mmp) REVERT: p 36 MET cc_start: 0.2763 (ppp) cc_final: 0.1900 (tpt) REVERT: p 68 PHE cc_start: 0.5645 (t80) cc_final: 0.5390 (t80) REVERT: s 47 ILE cc_start: 0.4547 (OUTLIER) cc_final: 0.3726 (mp) REVERT: t 27 MET cc_start: 0.4086 (tpt) cc_final: 0.2956 (ttt) REVERT: t 50 TYR cc_start: 0.6605 (m-10) cc_final: 0.5993 (m-10) REVERT: u 13 MET cc_start: 0.1162 (tpp) cc_final: 0.0638 (tpt) REVERT: u 18 SER cc_start: -0.2348 (OUTLIER) cc_final: -0.3157 (m) REVERT: u 59 MET cc_start: 0.2519 (tpt) cc_final: 0.2153 (ttt) REVERT: S 741 MET cc_start: -0.0203 (ptt) cc_final: -0.0860 (ptm) REVERT: U 245 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8651 (t0) REVERT: U 264 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8258 (mtt90) outliers start: 305 outliers final: 167 residues processed: 854 average time/residue: 0.8874 time to fit residues: 1340.5951 Evaluate side-chains 725 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 536 time to evaluate : 8.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 515 TYR Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1181 ASP Chi-restraints excluded: chain C residue 1213 VAL Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1385 VAL Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1438 VAL Chi-restraints excluded: chain C residue 1448 LEU Chi-restraints excluded: chain C residue 1472 THR Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1574 ILE Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1747 ILE Chi-restraints excluded: chain C residue 1819 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 889 THR Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 947 VAL Chi-restraints excluded: chain D residue 953 PHE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1173 THR Chi-restraints excluded: chain E residue 1240 LEU Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1406 VAL Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1829 ILE Chi-restraints excluded: chain E residue 1831 LEU Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1902 MET Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 262 TRP Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 480 LEU Chi-restraints excluded: chain I residue 541 SER Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain d residue 82 MET Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 69 VAL Chi-restraints excluded: chain g residue 46 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 80 MET Chi-restraints excluded: chain i residue 36 MET Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 169 VAL Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain Y residue 231 HIS Chi-restraints excluded: chain Y residue 239 GLU Chi-restraints excluded: chain Y residue 245 ILE Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 25 VAL Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain u residue 18 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 245 ASN Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 521 HIS Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 543 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 381 optimal weight: 20.0000 chunk 1020 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 665 optimal weight: 1.9990 chunk 279 optimal weight: 0.0770 chunk 1133 optimal weight: 3.9990 chunk 941 optimal weight: 30.0000 chunk 525 optimal weight: 40.0000 chunk 94 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 chunk 595 optimal weight: 40.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN C 712 HIS ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1527 ASN ** C1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1064 GLN ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 GLN I 248 HIS ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 HIS b 64 ASN ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 ASN ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 54 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 233 ASN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 104360 Z= 0.302 Angle : 0.595 13.622 142876 Z= 0.303 Chirality : 0.042 0.237 16152 Planarity : 0.004 0.061 16855 Dihedral : 15.131 173.112 18806 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.34 % Allowed : 16.88 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.08 (0.08), residues: 11376 helix: 1.22 (0.07), residues: 4812 sheet: -0.41 (0.12), residues: 1872 loop : -0.93 (0.09), residues: 4692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E1954 HIS 0.022 0.001 HIS Y 231 PHE 0.025 0.002 PHE C1779 TYR 0.019 0.001 TYR U 179 ARG 0.005 0.000 ARG I 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 558 time to evaluate : 8.949 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: C 25 MET cc_start: -0.2666 (mtt) cc_final: -0.3231 (tmm) REVERT: C 696 MET cc_start: 0.7280 (tpt) cc_final: 0.6999 (tpp) REVERT: C 756 TYR cc_start: 0.7983 (t80) cc_final: 0.7661 (t80) REVERT: C 1407 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7777 (p0) REVERT: C 1914 MET cc_start: 0.5235 (mmm) cc_final: 0.4915 (tpt) REVERT: E 78 ARG cc_start: 0.6708 (mmm160) cc_final: 0.6346 (mmm160) REVERT: E 992 TYR cc_start: 0.7621 (t80) cc_final: 0.7243 (t80) REVERT: E 1081 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7657 (ttm) REVERT: E 1367 MET cc_start: 0.7035 (ttp) cc_final: 0.6799 (ttp) REVERT: E 1736 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: E 1943 MET cc_start: 0.3483 (tpp) cc_final: 0.2729 (ttt) REVERT: E 2118 GLN cc_start: 0.3496 (OUTLIER) cc_final: 0.3284 (tt0) REVERT: F 353 MET cc_start: 0.0336 (ptt) cc_final: -0.0588 (ttt) REVERT: G 240 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: G 485 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5792 (mtpt) REVERT: G 679 MET cc_start: 0.6635 (tpt) cc_final: 0.6201 (tpt) REVERT: I 557 MET cc_start: 0.6703 (ttm) cc_final: 0.6124 (ttm) REVERT: f 55 LEU cc_start: 0.6229 (mm) cc_final: 0.5943 (mt) REVERT: g 75 ARG cc_start: 0.7075 (mmm160) cc_final: 0.6464 (tpp-160) REVERT: M 478 THR cc_start: 0.5024 (OUTLIER) cc_final: 0.4711 (t) REVERT: N 457 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5745 (mt0) REVERT: N 597 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6094 (tp) REVERT: O 26 VAL cc_start: 0.7965 (t) cc_final: 0.7762 (t) REVERT: R 115 MET cc_start: 0.4106 (ptt) cc_final: 0.3326 (tpt) REVERT: h 9 MET cc_start: -0.0496 (ttm) cc_final: -0.1100 (mtt) REVERT: h 80 MET cc_start: 0.3001 (OUTLIER) cc_final: 0.2107 (ttt) REVERT: i 72 ASP cc_start: 0.5073 (OUTLIER) cc_final: 0.4650 (p0) REVERT: k 82 MET cc_start: 0.6963 (ttt) cc_final: 0.6672 (ptp) REVERT: m 40 MET cc_start: -0.0535 (ppp) cc_final: -0.1363 (tmm) REVERT: n 48 MET cc_start: 0.2484 (OUTLIER) cc_final: 0.2185 (mpp) REVERT: V 40 MET cc_start: 0.4393 (pmm) cc_final: 0.3628 (tpt) REVERT: V 42 ARG cc_start: 0.2322 (mtt90) cc_final: 0.1802 (mmt90) REVERT: W 35 MET cc_start: 0.7556 (mtm) cc_final: 0.7059 (mpp) REVERT: W 71 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.4763 (t80) REVERT: W 86 LEU cc_start: 0.3058 (OUTLIER) cc_final: 0.2835 (pp) REVERT: X 81 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5326 (pt0) REVERT: Y 66 MET cc_start: 0.0747 (tpp) cc_final: 0.0416 (mmp) REVERT: p 36 MET cc_start: 0.2733 (ppp) cc_final: 0.1917 (tpt) REVERT: p 68 PHE cc_start: 0.5757 (t80) cc_final: 0.5540 (t80) REVERT: s 47 ILE cc_start: 0.4464 (OUTLIER) cc_final: 0.3599 (mp) REVERT: s 78 MET cc_start: 0.4514 (tmm) cc_final: 0.4135 (tmm) REVERT: t 27 MET cc_start: 0.4044 (tpt) cc_final: 0.2954 (ttt) REVERT: t 50 TYR cc_start: 0.6594 (m-10) cc_final: 0.6049 (m-10) REVERT: u 13 MET cc_start: 0.1313 (tpp) cc_final: 0.0782 (tpt) REVERT: u 18 SER cc_start: -0.2485 (OUTLIER) cc_final: -0.3290 (m) REVERT: u 59 MET cc_start: 0.2469 (tpt) cc_final: 0.2248 (ttt) REVERT: S 741 MET cc_start: -0.0483 (ptt) cc_final: -0.1120 (ptm) REVERT: U 264 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8150 (mtt90) REVERT: Q 897 MET cc_start: 0.0466 (tpp) cc_final: 0.0092 (tpp) outliers start: 238 outliers final: 150 residues processed: 754 average time/residue: 0.8896 time to fit residues: 1184.4816 Evaluate side-chains 711 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 543 time to evaluate : 9.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1568 THR Chi-restraints excluded: chain C residue 1574 ILE Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1747 ILE Chi-restraints excluded: chain C residue 1819 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 871 THR Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1295 TYR Chi-restraints excluded: chain E residue 1315 SER Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1736 PHE Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2036 VAL Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain E residue 2118 GLN Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain G residue 663 ARG Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 646 MET Chi-restraints excluded: chain I residue 669 ILE Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 80 MET Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 36 MET Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 42 ARG Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain Y residue 245 ILE Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 18 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain Q residue 700 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 1093 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 646 optimal weight: 1.9990 chunk 828 optimal weight: 6.9990 chunk 641 optimal weight: 7.9990 chunk 954 optimal weight: 9.9990 chunk 633 optimal weight: 8.9990 chunk 1129 optimal weight: 1.9990 chunk 706 optimal weight: 4.9990 chunk 688 optimal weight: 9.9990 chunk 521 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 HIS C 712 HIS ** C1018 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1527 ASN ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1710 ASN ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** C1823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1113 ASN ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1727 HIS E1730 HIS ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 GLN G 888 HIS ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 660 HIS ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 16 GLN U 233 ASN ** U 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 104360 Z= 0.413 Angle : 0.642 15.892 142876 Z= 0.326 Chirality : 0.043 0.235 16152 Planarity : 0.005 0.058 16855 Dihedral : 15.112 172.994 18806 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 2.64 % Allowed : 17.22 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.04 (0.08), residues: 11376 helix: 1.09 (0.07), residues: 4839 sheet: -0.46 (0.12), residues: 1889 loop : -0.98 (0.09), residues: 4648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP e 34 HIS 0.018 0.001 HIS E1877 PHE 0.029 0.002 PHE C1442 TYR 0.020 0.002 TYR C1671 ARG 0.015 0.001 ARG c 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 555 time to evaluate : 9.022 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: C 25 MET cc_start: -0.2365 (mtt) cc_final: -0.2848 (tmm) REVERT: C 258 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7794 (t80) REVERT: C 756 TYR cc_start: 0.8004 (t80) cc_final: 0.7692 (t80) REVERT: C 976 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7805 (tpt) REVERT: C 1407 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7793 (p0) REVERT: E 78 ARG cc_start: 0.6804 (mmm160) cc_final: 0.6437 (mmm160) REVERT: E 97 MET cc_start: 0.5188 (tmm) cc_final: 0.4112 (ttp) REVERT: E 992 TYR cc_start: 0.7711 (t80) cc_final: 0.7339 (t80) REVERT: E 1081 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7712 (ttm) REVERT: E 1367 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6785 (ttp) REVERT: E 1736 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: E 1943 MET cc_start: 0.3308 (tpp) cc_final: 0.2709 (ttt) REVERT: E 2118 GLN cc_start: 0.3738 (OUTLIER) cc_final: 0.3108 (tt0) REVERT: F 353 MET cc_start: 0.0408 (ptt) cc_final: -0.0533 (ttt) REVERT: G 240 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: G 485 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5841 (mtpt) REVERT: G 679 MET cc_start: 0.6223 (tpt) cc_final: 0.5751 (ttt) REVERT: I 557 MET cc_start: 0.6841 (ttm) cc_final: 0.6243 (ttm) REVERT: f 55 LEU cc_start: 0.6288 (mm) cc_final: 0.6003 (mt) REVERT: g 75 ARG cc_start: 0.6786 (mmm160) cc_final: 0.6229 (tpp-160) REVERT: L 212 MET cc_start: 0.6622 (tpp) cc_final: 0.6291 (mtp) REVERT: M 478 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4883 (t) REVERT: N 457 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.5865 (mt0) REVERT: N 597 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6127 (tp) REVERT: O 26 VAL cc_start: 0.7857 (t) cc_final: 0.7641 (t) REVERT: R 115 MET cc_start: 0.4175 (ptt) cc_final: 0.3377 (tpt) REVERT: i 72 ASP cc_start: 0.5186 (OUTLIER) cc_final: 0.4797 (p0) REVERT: k 76 MET cc_start: 0.5764 (pmm) cc_final: 0.5116 (ttp) REVERT: k 82 MET cc_start: 0.6953 (ttt) cc_final: 0.6558 (mtt) REVERT: m 40 MET cc_start: -0.0504 (ppp) cc_final: -0.1293 (tmm) REVERT: n 48 MET cc_start: 0.1925 (OUTLIER) cc_final: 0.1680 (mpp) REVERT: n 71 GLU cc_start: 0.3989 (tp30) cc_final: 0.3773 (tt0) REVERT: V 40 MET cc_start: 0.4369 (pmm) cc_final: 0.3612 (tpt) REVERT: W 35 MET cc_start: 0.7581 (mtm) cc_final: 0.7097 (mpp) REVERT: W 71 PHE cc_start: 0.5098 (OUTLIER) cc_final: 0.4716 (t80) REVERT: X 81 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.5117 (pt0) REVERT: Y 66 MET cc_start: 0.0961 (tpp) cc_final: 0.0240 (mmp) REVERT: r 76 MET cc_start: 0.1269 (tpt) cc_final: 0.0289 (ppp) REVERT: s 47 ILE cc_start: 0.4567 (OUTLIER) cc_final: 0.3765 (mp) REVERT: s 78 MET cc_start: 0.4600 (tmm) cc_final: 0.4263 (tmm) REVERT: t 27 MET cc_start: 0.4156 (tpt) cc_final: 0.3175 (ttt) REVERT: t 50 TYR cc_start: 0.6467 (m-10) cc_final: 0.5894 (m-10) REVERT: u 13 MET cc_start: 0.1167 (tpp) cc_final: 0.0677 (tpt) REVERT: u 38 MET cc_start: 0.5703 (ppp) cc_final: 0.5405 (ppp) REVERT: u 69 MET cc_start: 0.5414 (tpp) cc_final: 0.4852 (tpp) REVERT: S 741 MET cc_start: -0.0135 (ptt) cc_final: -0.0792 (ptm) REVERT: U 245 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8627 (t0) REVERT: U 264 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8223 (mtt90) REVERT: Q 930 MET cc_start: 0.4492 (ppp) cc_final: 0.3060 (ptp) outliers start: 269 outliers final: 186 residues processed: 782 average time/residue: 0.8832 time to fit residues: 1221.7241 Evaluate side-chains 742 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 537 time to evaluate : 8.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 978 GLU Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1223 GLU Chi-restraints excluded: chain C residue 1244 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1385 VAL Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1438 VAL Chi-restraints excluded: chain C residue 1448 LEU Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1515 TRP Chi-restraints excluded: chain C residue 1568 THR Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1747 ILE Chi-restraints excluded: chain C residue 1787 ARG Chi-restraints excluded: chain C residue 1819 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 302 CYS Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 698 ILE Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 871 THR Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 1041 LEU Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1173 THR Chi-restraints excluded: chain E residue 1240 LEU Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1284 VAL Chi-restraints excluded: chain E residue 1295 TYR Chi-restraints excluded: chain E residue 1367 MET Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1736 PHE Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2036 VAL Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain E residue 2118 GLN Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain G residue 663 ARG Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 541 SER Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 606 THR Chi-restraints excluded: chain I residue 646 MET Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain c residue 105 SER Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 37 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 385 GLU Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 181 ILE Chi-restraints excluded: chain Y residue 225 TYR Chi-restraints excluded: chain Y residue 245 ILE Chi-restraints excluded: chain Z residue 287 GLU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain s residue 33 VAL Chi-restraints excluded: chain s residue 47 ILE Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 244 SER Chi-restraints excluded: chain U residue 245 ASN Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain Q residue 700 ASN Chi-restraints excluded: chain Q residue 847 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 698 optimal weight: 0.8980 chunk 451 optimal weight: 3.9990 chunk 674 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 218 optimal weight: 0.2980 chunk 718 optimal weight: 5.9990 chunk 769 optimal weight: 20.0000 chunk 558 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 887 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 712 HIS C1018 ASN C1023 ASN C1188 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1527 ASN ** C1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1710 ASN ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS C1823 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 873 HIS ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1730 HIS E1749 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN X 59 GLN u 28 GLN U 233 ASN U 372 GLN ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 104360 Z= 0.200 Angle : 0.567 19.035 142876 Z= 0.286 Chirality : 0.041 0.247 16152 Planarity : 0.004 0.057 16855 Dihedral : 15.020 174.455 18806 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 1.93 % Allowed : 18.16 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.24 (0.08), residues: 11376 helix: 1.37 (0.08), residues: 4826 sheet: -0.38 (0.12), residues: 1878 loop : -0.85 (0.09), residues: 4672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP l 34 HIS 0.015 0.001 HIS F 282 PHE 0.024 0.001 PHE I 767 TYR 0.032 0.001 TYR I 748 ARG 0.005 0.000 ARG c 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 563 time to evaluate : 11.080 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: C 25 MET cc_start: -0.2642 (mtt) cc_final: -0.2951 (tmm) REVERT: C 61 MET cc_start: 0.7726 (ppp) cc_final: 0.7400 (ptm) REVERT: C 696 MET cc_start: 0.7108 (tpt) cc_final: 0.6893 (tpp) REVERT: C 756 TYR cc_start: 0.7939 (t80) cc_final: 0.7661 (t80) REVERT: C 1407 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7824 (p0) REVERT: C 1599 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6662 (mt0) REVERT: C 2334 TYR cc_start: 0.7595 (m-80) cc_final: 0.7323 (m-80) REVERT: E 78 ARG cc_start: 0.6714 (mmm160) cc_final: 0.6337 (mmm160) REVERT: E 992 TYR cc_start: 0.7584 (t80) cc_final: 0.7270 (t80) REVERT: E 1081 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: E 1736 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: E 1943 MET cc_start: 0.3190 (tpp) cc_final: 0.2709 (ttt) REVERT: E 2118 GLN cc_start: 0.3846 (OUTLIER) cc_final: 0.3077 (tt0) REVERT: F 353 MET cc_start: 0.0422 (ptt) cc_final: -0.0525 (ttt) REVERT: G 338 MET cc_start: 0.5739 (ppp) cc_final: 0.5240 (ppp) REVERT: G 485 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6031 (mtpt) REVERT: G 679 MET cc_start: 0.6287 (tpt) cc_final: 0.5784 (ttt) REVERT: G 724 MET cc_start: 0.5029 (tmm) cc_final: 0.4704 (tmm) REVERT: I 557 MET cc_start: 0.6578 (ttm) cc_final: 0.6095 (ttm) REVERT: c 93 ASP cc_start: 0.5871 (OUTLIER) cc_final: 0.5663 (t0) REVERT: f 55 LEU cc_start: 0.6021 (mm) cc_final: 0.5784 (mt) REVERT: g 75 ARG cc_start: 0.6942 (mmm160) cc_final: 0.5920 (mmm160) REVERT: N 597 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6065 (tp) REVERT: O 26 VAL cc_start: 0.7811 (t) cc_final: 0.7594 (t) REVERT: R 115 MET cc_start: 0.4077 (ptt) cc_final: 0.3313 (tpt) REVERT: h 80 MET cc_start: 0.0054 (mmt) cc_final: -0.0655 (mtt) REVERT: i 72 ASP cc_start: 0.4977 (OUTLIER) cc_final: 0.4616 (p0) REVERT: k 76 MET cc_start: 0.5793 (pmm) cc_final: 0.5109 (ttp) REVERT: k 82 MET cc_start: 0.6951 (ttt) cc_final: 0.6499 (mtt) REVERT: m 40 MET cc_start: -0.0450 (ppp) cc_final: -0.1267 (tmm) REVERT: n 48 MET cc_start: 0.2069 (OUTLIER) cc_final: 0.1817 (mpp) REVERT: n 71 GLU cc_start: 0.3970 (tp30) cc_final: 0.3741 (tt0) REVERT: V 24 HIS cc_start: 0.3187 (t70) cc_final: 0.1689 (m-70) REVERT: V 40 MET cc_start: 0.4317 (pmm) cc_final: 0.3565 (tpt) REVERT: W 35 MET cc_start: 0.7604 (mtm) cc_final: 0.7155 (mpp) REVERT: W 71 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.4814 (t80) REVERT: W 86 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2842 (pp) REVERT: W 106 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4950 (tp) REVERT: X 81 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5009 (pt0) REVERT: Y 66 MET cc_start: 0.1017 (tpp) cc_final: 0.0206 (mmp) REVERT: Y 249 MET cc_start: 0.6895 (mmm) cc_final: 0.6382 (mmp) REVERT: p 8 MET cc_start: 0.6752 (mmm) cc_final: 0.6500 (mmm) REVERT: r 76 MET cc_start: 0.1211 (tpt) cc_final: 0.0125 (ppp) REVERT: s 78 MET cc_start: 0.4212 (tmm) cc_final: 0.3928 (tmm) REVERT: t 27 MET cc_start: 0.4130 (tpt) cc_final: 0.3119 (ttt) REVERT: t 50 TYR cc_start: 0.6559 (m-10) cc_final: 0.6024 (m-10) REVERT: u 13 MET cc_start: 0.1346 (tpp) cc_final: 0.0827 (tpt) REVERT: u 69 MET cc_start: 0.5742 (tpp) cc_final: 0.5167 (tpp) REVERT: S 741 MET cc_start: 0.0045 (ptt) cc_final: -0.0591 (ptm) REVERT: U 264 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8196 (mtt90) REVERT: Q 897 MET cc_start: 0.0366 (tpp) cc_final: -0.0051 (tpp) REVERT: Q 930 MET cc_start: 0.4582 (ppp) cc_final: 0.3077 (ptp) outliers start: 196 outliers final: 138 residues processed: 720 average time/residue: 0.9052 time to fit residues: 1145.9428 Evaluate side-chains 690 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 538 time to evaluate : 8.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1438 VAL Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1515 TRP Chi-restraints excluded: chain C residue 1568 THR Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2100 THR Chi-restraints excluded: chain C residue 2217 SER Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 953 PHE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 698 ILE Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 871 THR Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 1041 LEU Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1240 LEU Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1736 PHE Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2036 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2090 VAL Chi-restraints excluded: chain E residue 2118 GLN Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain G residue 663 ARG Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 472 ILE Chi-restraints excluded: chain I residue 541 SER Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 669 ILE Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 287 GLU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain s residue 15 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 244 SER Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain Q residue 700 ASN Chi-restraints excluded: chain Q residue 847 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 1027 optimal weight: 3.9990 chunk 1082 optimal weight: 10.0000 chunk 987 optimal weight: 20.0000 chunk 1052 optimal weight: 30.0000 chunk 1081 optimal weight: 7.9990 chunk 633 optimal weight: 0.9980 chunk 458 optimal weight: 5.9990 chunk 826 optimal weight: 50.0000 chunk 323 optimal weight: 0.0060 chunk 951 optimal weight: 9.9990 chunk 995 optimal weight: 9.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 712 HIS C1018 ASN C1188 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1388 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 HIS ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 GLN ** q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 233 ASN ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 104360 Z= 0.387 Angle : 0.630 20.571 142876 Z= 0.318 Chirality : 0.043 0.250 16152 Planarity : 0.005 0.054 16855 Dihedral : 15.021 174.393 18804 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 2.04 % Allowed : 18.18 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.08 (0.08), residues: 11376 helix: 1.24 (0.08), residues: 4840 sheet: -0.47 (0.11), residues: 1918 loop : -0.94 (0.09), residues: 4618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C1827 HIS 0.014 0.001 HIS F 282 PHE 0.055 0.002 PHE C1379 TYR 0.038 0.002 TYR F 310 ARG 0.006 0.000 ARG I 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 546 time to evaluate : 9.157 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: C 696 MET cc_start: 0.7116 (tpt) cc_final: 0.6900 (tpp) REVERT: C 756 TYR cc_start: 0.8023 (t80) cc_final: 0.7736 (t80) REVERT: C 976 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7761 (tpt) REVERT: C 1407 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7777 (p0) REVERT: C 2334 TYR cc_start: 0.7741 (m-80) cc_final: 0.7453 (m-80) REVERT: E 78 ARG cc_start: 0.6690 (mmm160) cc_final: 0.6347 (mmm160) REVERT: E 992 TYR cc_start: 0.7684 (t80) cc_final: 0.7367 (t80) REVERT: E 1081 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7709 (ttm) REVERT: E 1367 MET cc_start: 0.7012 (ttp) cc_final: 0.6704 (ttp) REVERT: E 1736 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: E 1943 MET cc_start: 0.3247 (tpp) cc_final: 0.2765 (ttt) REVERT: E 2118 GLN cc_start: 0.3822 (OUTLIER) cc_final: 0.3117 (tt0) REVERT: F 353 MET cc_start: 0.0465 (ptt) cc_final: -0.0516 (ttt) REVERT: G 240 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: G 338 MET cc_start: 0.5952 (ppp) cc_final: 0.5559 (ppp) REVERT: G 485 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5953 (mtpt) REVERT: G 679 MET cc_start: 0.6229 (tpt) cc_final: 0.5649 (ttt) REVERT: G 724 MET cc_start: 0.5153 (tmm) cc_final: 0.4439 (tmm) REVERT: I 557 MET cc_start: 0.6849 (ttm) cc_final: 0.6323 (ttm) REVERT: c 73 MET cc_start: 0.4612 (pmm) cc_final: 0.4412 (pmm) REVERT: c 93 ASP cc_start: 0.5875 (OUTLIER) cc_final: 0.5672 (t0) REVERT: f 55 LEU cc_start: 0.6125 (mm) cc_final: 0.5907 (mt) REVERT: g 75 ARG cc_start: 0.6803 (mmm160) cc_final: 0.6243 (tpp-160) REVERT: N 457 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.5965 (mt0) REVERT: N 597 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6107 (tp) REVERT: O 26 VAL cc_start: 0.7850 (t) cc_final: 0.7629 (t) REVERT: R 115 MET cc_start: 0.4372 (ptt) cc_final: 0.3437 (tpt) REVERT: i 72 ASP cc_start: 0.5229 (OUTLIER) cc_final: 0.4853 (p0) REVERT: k 76 MET cc_start: 0.5791 (pmm) cc_final: 0.5129 (ttp) REVERT: k 82 MET cc_start: 0.6989 (ttt) cc_final: 0.6607 (mtt) REVERT: m 40 MET cc_start: -0.0508 (ppp) cc_final: -0.1284 (tmm) REVERT: n 48 MET cc_start: 0.1929 (OUTLIER) cc_final: 0.1693 (mpp) REVERT: n 69 MET cc_start: 0.1155 (mmm) cc_final: 0.0746 (tmm) REVERT: V 24 HIS cc_start: 0.3181 (t70) cc_final: 0.1697 (m-70) REVERT: V 40 MET cc_start: 0.4294 (pmm) cc_final: 0.3448 (tpt) REVERT: W 35 MET cc_start: 0.7677 (mtm) cc_final: 0.7201 (mpp) REVERT: W 71 PHE cc_start: 0.5337 (OUTLIER) cc_final: 0.4990 (t80) REVERT: W 106 ILE cc_start: 0.5208 (OUTLIER) cc_final: 0.4921 (tp) REVERT: X 81 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5015 (pt0) REVERT: Y 66 MET cc_start: 0.1106 (tpp) cc_final: 0.0256 (mmp) REVERT: Y 117 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6696 (pp30) REVERT: p 8 MET cc_start: 0.6811 (mmm) cc_final: 0.6609 (mmm) REVERT: r 76 MET cc_start: 0.0846 (tpt) cc_final: 0.0135 (ppp) REVERT: s 78 MET cc_start: 0.4373 (tmm) cc_final: 0.4021 (tmm) REVERT: t 27 MET cc_start: 0.4179 (tpt) cc_final: 0.3167 (ttt) REVERT: t 50 TYR cc_start: 0.6626 (m-10) cc_final: 0.6098 (m-10) REVERT: u 13 MET cc_start: 0.1253 (tpp) cc_final: 0.0751 (tpt) REVERT: u 69 MET cc_start: 0.5773 (tpp) cc_final: 0.5195 (tpp) REVERT: U 264 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8194 (mtt90) REVERT: Q 897 MET cc_start: 0.0575 (tpp) cc_final: 0.0139 (tpp) REVERT: Q 930 MET cc_start: 0.4847 (ppp) cc_final: 0.3503 (ptp) outliers start: 208 outliers final: 163 residues processed: 718 average time/residue: 0.8915 time to fit residues: 1129.9471 Evaluate side-chains 712 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 532 time to evaluate : 9.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1223 GLU Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1385 VAL Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1438 VAL Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1515 TRP Chi-restraints excluded: chain C residue 1568 THR Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1819 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2100 THR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2217 SER Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 598 SER Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 953 PHE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 698 ILE Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 871 THR Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 1041 LEU Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1240 LEU Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1736 PHE Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2118 GLN Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 480 LEU Chi-restraints excluded: chain I residue 541 SER Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 669 ILE Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 25 LEU Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 47 THR Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 378 MET Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain h residue 19 CYS Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 287 GLU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 58 LEU Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 244 SER Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 320 VAL Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain U residue 543 THR Chi-restraints excluded: chain Q residue 700 ASN Chi-restraints excluded: chain Q residue 847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 1048 optimal weight: 8.9990 chunk 691 optimal weight: 9.9990 chunk 1113 optimal weight: 0.6980 chunk 679 optimal weight: 6.9990 chunk 528 optimal weight: 30.0000 chunk 773 optimal weight: 20.0000 chunk 1167 optimal weight: 0.0170 chunk 1074 optimal weight: 30.0000 chunk 929 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 718 optimal weight: 0.5980 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1188 ASN ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 GLN ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 GLN ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 ASN Y 117 GLN ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 104360 Z= 0.229 Angle : 0.585 21.433 142876 Z= 0.294 Chirality : 0.041 0.257 16152 Planarity : 0.004 0.056 16855 Dihedral : 14.965 174.981 18804 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 1.80 % Allowed : 18.51 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.22 (0.08), residues: 11376 helix: 1.37 (0.08), residues: 4832 sheet: -0.41 (0.12), residues: 1880 loop : -0.86 (0.09), residues: 4664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C1827 HIS 0.013 0.001 HIS F 282 PHE 0.043 0.001 PHE C1379 TYR 0.031 0.001 TYR F 310 ARG 0.006 0.000 ARG C1310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22752 Ramachandran restraints generated. 11376 Oldfield, 0 Emsley, 11376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 549 time to evaluate : 8.843 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: C 696 MET cc_start: 0.7125 (tpt) cc_final: 0.6867 (tpp) REVERT: C 756 TYR cc_start: 0.7937 (t80) cc_final: 0.7663 (t80) REVERT: C 1407 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7749 (p0) REVERT: C 2247 ASN cc_start: 0.7744 (t0) cc_final: 0.7481 (t0) REVERT: C 2334 TYR cc_start: 0.7716 (m-80) cc_final: 0.7466 (m-80) REVERT: E 78 ARG cc_start: 0.6713 (mmm160) cc_final: 0.6359 (mmm160) REVERT: E 992 TYR cc_start: 0.7630 (t80) cc_final: 0.7331 (t80) REVERT: E 1081 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7621 (ttm) REVERT: E 1367 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6642 (ttp) REVERT: E 1521 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7039 (m) REVERT: E 1736 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7586 (m-80) REVERT: E 1902 MET cc_start: 0.0884 (mpp) cc_final: -0.1051 (ppp) REVERT: E 1943 MET cc_start: 0.3403 (tpp) cc_final: 0.2721 (ttt) REVERT: E 2093 ASP cc_start: 0.5759 (OUTLIER) cc_final: 0.5236 (t70) REVERT: E 2118 GLN cc_start: 0.3785 (OUTLIER) cc_final: 0.2952 (tt0) REVERT: G 240 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7902 (mtt) REVERT: G 338 MET cc_start: 0.5879 (ppp) cc_final: 0.5498 (ppp) REVERT: G 679 MET cc_start: 0.6309 (tpt) cc_final: 0.5773 (ttt) REVERT: G 724 MET cc_start: 0.4964 (tmm) cc_final: 0.4482 (tmm) REVERT: I 557 MET cc_start: 0.6618 (ttm) cc_final: 0.6122 (ttm) REVERT: e 25 LEU cc_start: 0.5545 (pp) cc_final: 0.5158 (pp) REVERT: f 55 LEU cc_start: 0.6060 (mm) cc_final: 0.5777 (mt) REVERT: g 75 ARG cc_start: 0.7018 (mmm160) cc_final: 0.6042 (mmm160) REVERT: N 597 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6059 (tp) REVERT: O 26 VAL cc_start: 0.7801 (t) cc_final: 0.7576 (t) REVERT: R 115 MET cc_start: 0.4447 (ptt) cc_final: 0.3492 (tpt) REVERT: h 17 MET cc_start: -0.4972 (ttm) cc_final: -0.5202 (tmm) REVERT: h 80 MET cc_start: -0.0283 (mmt) cc_final: -0.0822 (tpp) REVERT: i 72 ASP cc_start: 0.5050 (OUTLIER) cc_final: 0.4715 (p0) REVERT: k 76 MET cc_start: 0.5817 (pmm) cc_final: 0.5179 (ttp) REVERT: k 82 MET cc_start: 0.7075 (ttt) cc_final: 0.6672 (mtt) REVERT: m 40 MET cc_start: -0.0475 (ppp) cc_final: -0.1272 (tmm) REVERT: n 48 MET cc_start: 0.2012 (OUTLIER) cc_final: 0.1725 (mpp) REVERT: V 24 HIS cc_start: 0.3131 (t70) cc_final: 0.1689 (m-70) REVERT: V 40 MET cc_start: 0.4471 (pmm) cc_final: 0.3607 (tpt) REVERT: W 35 MET cc_start: 0.7643 (mtm) cc_final: 0.7200 (mpp) REVERT: W 71 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4935 (t80) REVERT: W 86 LEU cc_start: 0.3035 (OUTLIER) cc_final: 0.2823 (pp) REVERT: W 106 ILE cc_start: 0.5192 (OUTLIER) cc_final: 0.4912 (tp) REVERT: X 81 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.4954 (pt0) REVERT: Y 66 MET cc_start: 0.1139 (tpp) cc_final: 0.0310 (mmp) REVERT: Y 117 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6536 (pp30) REVERT: r 76 MET cc_start: 0.0838 (tpt) cc_final: 0.0262 (ppp) REVERT: s 78 MET cc_start: 0.4165 (tmm) cc_final: 0.3826 (tmm) REVERT: t 27 MET cc_start: 0.4154 (tpt) cc_final: 0.3157 (ttt) REVERT: t 50 TYR cc_start: 0.6592 (m-10) cc_final: 0.5963 (m-10) REVERT: u 13 MET cc_start: 0.1448 (tpp) cc_final: 0.0949 (tpt) REVERT: u 38 MET cc_start: 0.5559 (ppp) cc_final: 0.5244 (ppp) REVERT: u 44 GLU cc_start: 0.7351 (pm20) cc_final: 0.6908 (pm20) REVERT: u 69 MET cc_start: 0.5904 (tpp) cc_final: 0.5343 (tpp) REVERT: u 73 LEU cc_start: -0.0919 (mp) cc_final: -0.1399 (mp) REVERT: U 264 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8163 (mtt90) REVERT: Q 897 MET cc_start: 0.0426 (tpp) cc_final: 0.0071 (tpp) REVERT: Q 930 MET cc_start: 0.4835 (ppp) cc_final: 0.3498 (ptp) outliers start: 183 outliers final: 147 residues processed: 701 average time/residue: 0.8978 time to fit residues: 1107.7195 Evaluate side-chains 701 residues out of total 10239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 537 time to evaluate : 8.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 495 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 871 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 964 ASP Chi-restraints excluded: chain C residue 1021 ASP Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1076 ASP Chi-restraints excluded: chain C residue 1089 CYS Chi-restraints excluded: chain C residue 1220 VAL Chi-restraints excluded: chain C residue 1223 GLU Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1271 MET Chi-restraints excluded: chain C residue 1351 THR Chi-restraints excluded: chain C residue 1385 VAL Chi-restraints excluded: chain C residue 1407 ASP Chi-restraints excluded: chain C residue 1438 VAL Chi-restraints excluded: chain C residue 1489 LEU Chi-restraints excluded: chain C residue 1515 TRP Chi-restraints excluded: chain C residue 1568 THR Chi-restraints excluded: chain C residue 1581 LEU Chi-restraints excluded: chain C residue 1614 ILE Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1975 GLU Chi-restraints excluded: chain C residue 1991 TYR Chi-restraints excluded: chain C residue 2100 THR Chi-restraints excluded: chain C residue 2157 VAL Chi-restraints excluded: chain C residue 2217 SER Chi-restraints excluded: chain C residue 2262 LEU Chi-restraints excluded: chain C residue 2333 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 566 THR Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 780 CYS Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 953 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 698 ILE Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 871 THR Chi-restraints excluded: chain E residue 914 LYS Chi-restraints excluded: chain E residue 1041 LEU Chi-restraints excluded: chain E residue 1081 MET Chi-restraints excluded: chain E residue 1135 LEU Chi-restraints excluded: chain E residue 1240 LEU Chi-restraints excluded: chain E residue 1367 MET Chi-restraints excluded: chain E residue 1453 VAL Chi-restraints excluded: chain E residue 1521 VAL Chi-restraints excluded: chain E residue 1665 ASP Chi-restraints excluded: chain E residue 1685 LEU Chi-restraints excluded: chain E residue 1736 PHE Chi-restraints excluded: chain E residue 1776 ILE Chi-restraints excluded: chain E residue 1884 PHE Chi-restraints excluded: chain E residue 1920 ILE Chi-restraints excluded: chain E residue 2067 VAL Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2093 ASP Chi-restraints excluded: chain E residue 2118 GLN Chi-restraints excluded: chain F residue 93 TRP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 HIS Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 240 MET Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 344 ASP Chi-restraints excluded: chain G residue 400 VAL Chi-restraints excluded: chain G residue 804 LEU Chi-restraints excluded: chain H residue 55 MET Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 480 LEU Chi-restraints excluded: chain I residue 541 SER Chi-restraints excluded: chain I residue 597 HIS Chi-restraints excluded: chain I residue 655 LEU Chi-restraints excluded: chain I residue 669 ILE Chi-restraints excluded: chain I residue 671 VAL Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain a residue 40 LEU Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 40 THR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain e residue 26 GLN Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 87 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 311 ASP Chi-restraints excluded: chain N residue 457 GLN Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain O residue 17 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain h residue 46 ASP Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 46 THR Chi-restraints excluded: chain i residue 72 ASP Chi-restraints excluded: chain j residue 65 MET Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain k residue 27 VAL Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 77 ILE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain W residue 67 LEU Chi-restraints excluded: chain W residue 71 PHE Chi-restraints excluded: chain W residue 86 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 128 LEU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 81 GLU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 117 GLN Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 287 GLU Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain U residue 114 SER Chi-restraints excluded: chain U residue 177 ASP Chi-restraints excluded: chain U residue 178 ASN Chi-restraints excluded: chain U residue 196 THR Chi-restraints excluded: chain U residue 230 ILE Chi-restraints excluded: chain U residue 234 ASP Chi-restraints excluded: chain U residue 264 ARG Chi-restraints excluded: chain U residue 303 VAL Chi-restraints excluded: chain U residue 320 VAL Chi-restraints excluded: chain U residue 339 LYS Chi-restraints excluded: chain U residue 389 MET Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 410 ILE Chi-restraints excluded: chain U residue 523 THR Chi-restraints excluded: chain Q residue 700 ASN Chi-restraints excluded: chain Q residue 847 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1172 random chunks: chunk 570 optimal weight: 20.0000 chunk 738 optimal weight: 5.9990 chunk 990 optimal weight: 50.0000 chunk 284 optimal weight: 0.6980 chunk 857 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 931 optimal weight: 30.0000 chunk 389 optimal weight: 0.7980 chunk 956 optimal weight: 0.0060 chunk 117 optimal weight: 0.9980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 HIS ** D 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN ** E 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 GLN ** I 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 GLN ** Q 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.138446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.106351 restraints weight = 353887.428| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 4.20 r_work: 0.3588 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 104360 Z= 0.180 Angle : 0.567 21.421 142876 Z= 0.284 Chirality : 0.040 0.332 16152 Planarity : 0.004 0.054 16855 Dihedral : 14.876 175.181 18804 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 1.73 % Allowed : 18.68 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.08), residues: 11376 helix: 1.48 (0.08), residues: 4835 sheet: -0.31 (0.12), residues: 1881 loop : -0.81 (0.09), residues: 4660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C1827 HIS 0.012 0.001 HIS F 282 PHE 0.039 0.001 PHE C1379 TYR 0.028 0.001 TYR F 310 ARG 0.007 0.000 ARG e 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23835.65 seconds wall clock time: 420 minutes 27.23 seconds (25227.23 seconds total)