Starting phenix.real_space_refine on Sat Mar 2 11:51:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgh_25882/03_2024/7tgh_25882_updated.pdb" } resolution = 2.6 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= 1.092 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 Fe 38 7.16 5 Zn 3 6.06 5 P 114 5.49 5 S 614 5.16 5 C 99645 2.51 5 N 25065 2.21 5 O 27887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 126": "OD1" <-> "OD2" Residue "2 GLU 155": "OE1" <-> "OE2" Residue "2B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 44": "OE1" <-> "OE2" Residue "3 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A GLU 285": "OE1" <-> "OE2" Residue "3A ASP 357": "OD1" <-> "OD2" Residue "3B ASP 360": "OD1" <-> "OD2" Residue "3B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D GLU 131": "OE1" <-> "OE2" Residue "3D TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E ASP 46": "OD1" <-> "OD2" Residue "3E GLU 84": "OE1" <-> "OE2" Residue "3F ASP 53": "OD1" <-> "OD2" Residue "3F GLU 70": "OE1" <-> "OE2" Residue "3G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3H ASP 119": "OD1" <-> "OD2" Residue "3I ASP 45": "OD1" <-> "OD2" Residue "3I GLU 57": "OE1" <-> "OE2" Residue "3b TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3d TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3e GLU 125": "OE1" <-> "OE2" Residue "3f ASP 19": "OD1" <-> "OD2" Residue "3h GLU 55": "OE1" <-> "OE2" Residue "3h TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3i GLU 99": "OE1" <-> "OE2" Residue "4 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4L GLU 34": "OE1" <-> "OE2" Residue "4L TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 283": "OE1" <-> "OE2" Residue "5 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 420": "OE1" <-> "OE2" Residue "5 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B ASP 59": "OD1" <-> "OD2" Residue "6 GLU 79": "OE1" <-> "OE2" Residue "6 GLU 160": "OE1" <-> "OE2" Residue "6 GLU 184": "OE1" <-> "OE2" Residue "6 ASP 222": "OD1" <-> "OD2" Residue "A6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ASP 106": "OD1" <-> "OD2" Residue "AL PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM GLU 81": "OE1" <-> "OE2" Residue "B7 GLU 9": "OE1" <-> "OE2" Residue "C1 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ASP 229": "OD1" <-> "OD2" Residue "C2 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ASP 36": "OD1" <-> "OD2" Residue "C2 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TD ASP 12": "OD1" <-> "OD2" Residue "TD PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TD PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TD PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FX ASP 36": "OD1" <-> "OD2" Residue "FX GLU 85": "OE1" <-> "OE2" Residue "T2 PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T1 GLU 148": "OE1" <-> "OE2" Residue "T1 PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X1 ASP 27": "OD1" <-> "OD2" Residue "X1 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T6 ASP 77": "OD1" <-> "OD2" Residue "T6 ASP 111": "OD1" <-> "OD2" Residue "T5 GLU 64": "OE1" <-> "OE2" Residue "T5 ASP 147": "OD1" <-> "OD2" Residue "R PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 ASP 337": "OD1" <-> "OD2" Residue "S1 TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 GLU 52": "OE1" <-> "OE2" Residue "S3 PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ASP 120": "OD1" <-> "OD2" Residue "S8 ASP 65": "OD1" <-> "OD2" Residue "S8 ASP 68": "OD1" <-> "OD2" Residue "S8 GLU 104": "OE1" <-> "OE2" Residue "S8 ASP 169": "OD1" <-> "OD2" Residue "B9 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B9 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A8 GLU 127": "OE1" <-> "OE2" Residue "V2 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 ASP 101": "OD1" <-> "OD2" Residue "V2 GLU 226": "OE1" <-> "OE2" Residue "BM ASP 196": "OD1" <-> "OD2" Residue "AN ASP 230": "OD1" <-> "OD2" Residue "T4 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T4 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T4 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T3 TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T3 TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T3 PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P1 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA GLU 109": "OE1" <-> "OE2" Residue "TA ASP 123": "OD1" <-> "OD2" Residue "S5 PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S5 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P2 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P2 ASP 156": "OD1" <-> "OD2" Residue "T9 GLU 43": "OE1" <-> "OE2" Residue "T9 PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153366 Number of models: 1 Model: "" Number of chains: 146 Chain: "1" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2313 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain: "1B" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 516 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "2" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 3065 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 353} Chain: "2B" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1483 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain: "3" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1017 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "3A" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3511 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Chain: "3B" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3826 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 16, 'TRANS': 462} Chain: "3C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3590 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 413} Chain: "3D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2488 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "3E" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1846 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "3F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 703 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "3G" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2595 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "3H" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1098 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "3I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "3J" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 501 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "3M" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 150 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "3a" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3495 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 10, 'TRANS': 440} Chain breaks: 1 Chain: "3b" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3815 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 16, 'TRANS': 461} Chain: "3c" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3589 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 413} Chain: "3d" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2403 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 269} Chain: "3e" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 882 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "3f" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "3g" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2682 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 14, 'TRANS': 302} Chain breaks: 1 Chain: "3h" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1046 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "3i" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 948 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "3j" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 443 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 5, 'TRANS': 45} Chain: "3l" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 124 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "3m" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 121 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "4" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4170 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 493} Chain: "4L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 957 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "5" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4844 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 575} Chain: "5B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 888 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "6" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "A2" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 765 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "A5" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "A6" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1421 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain: "A7" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2339 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 264} Chain: "A9" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2718 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "AB" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 926 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain: "AC" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "AL" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1612 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "AM" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1349 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "B7" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "B8" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1408 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain: "BL" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1045 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'TRANS': 208} Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 627 Unresolved non-hydrogen dihedrals: 209 Planarities with less than four sites: {'UNK:plan-1': 209} Unresolved non-hydrogen planarities: 209 Chain: "C1" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1769 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 217} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C2" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1624 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 213} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C3" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2804 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 326} Chain: "TD" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 608 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "J1" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2146 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain breaks: 2 Chain: "FX" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1162 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "T2" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2117 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain: "T1" Number of atoms: 3884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3884 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain: "A1" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 799 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "X1" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1227 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "T6" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 903 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "T5" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1088 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S1" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5394 Classifications: {'peptide': 687} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 654} Chain: "S2" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3599 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "S3" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1681 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain: "S4" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1463 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "S6" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "S7" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1286 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 152} Chain: "S8" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1812 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 201} Chain: "B9" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1579 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "TX" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1206 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 138} Chain: "A8" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "TB" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 801 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "V1" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3410 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 417} Chain: "V2" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1858 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B6" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 596 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 61} Chain: "BM" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1163 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "C4" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 842 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "AN" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1879 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "B4" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 898 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "T4" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1408 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 1 Chain: "T8" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1064 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "B2" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 955 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "T3" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2442 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P1" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1896 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "B3" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 594 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "TA" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 854 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "S5" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 693 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "TC" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 781 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "P2" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1414 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain: "A3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1065 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "T9" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "TE" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 413 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T7" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1187 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "1" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "2B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 79 Chain: "3B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "3C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'CDL': 1, 'HEM': 2, 'PC1': 3, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 26 Chain: "3D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "3E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 116 Unusual residues: {'3PE': 1, 'FES': 1, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "3F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' ZN': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "3G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "3H" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'CDL': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 28 Chain: "3I" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 186 Unusual residues: {'CDL': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 122 Chain: "3J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "3b" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Chain: "3c" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 275 Unusual residues: {'CDL': 2, 'HEM': 2, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 119 Chain: "3d" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3g" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "3i" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "3j" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "4" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "5" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 405 Unusual residues: {'3PE': 2, 'CDL': 2, 'PC1': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "5B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'3PE': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "6" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "A9" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {' ZN': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AB" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "AL" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "AM" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 Chain: "B8" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PE': 1, 'ADP': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "TD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "J1" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "FX" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T1" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Chain: "A1" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "X1" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B6" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "BM" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C4" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 181 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "AN" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 87 Chain: "B4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 63 Chain: "T4" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "T8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B2" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "P1" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "TA" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "TC" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "P2" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 82 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "A3" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "T7" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23087 SG CYS3E 197 128.129 136.201 39.274 1.00121.68 S ATOM 23122 SG CYS3E 202 131.723 136.997 38.491 1.00121.05 S ATOM 23231 SG CYS3E 216 130.596 139.402 37.500 1.00122.97 S ATOM 23087 SG CYS3E 197 128.129 136.201 39.274 1.00121.68 S ATOM 90233 SG CYSFX 81 97.127 145.383 154.254 1.00 38.32 S ATOM 90408 SG CYSFX 104 98.622 142.912 156.647 1.00 40.19 S ATOM 90426 SG CYSFX 107 93.876 139.761 155.638 1.00 41.84 S ATOM 90738 SG CYSFX 145 92.959 142.258 153.217 1.00 43.48 S ATOM A024B SG CYSS1 138 90.566 88.526 248.133 1.00 25.00 S ATOM A022M SG CYSS1 129 97.187 90.272 248.745 1.00 22.01 S ATOM A0237 SG CYSS1 132 94.965 84.206 247.865 1.00 21.73 S ATOM A02DO SG CYSS1 180 82.661 83.290 254.044 1.00 25.63 S ATOM A02D0 SG CYSS1 177 87.688 81.094 257.325 1.00 23.15 S ATOM A02EC SG CYSS1 183 83.488 77.348 254.584 1.00 25.61 S ATOM A02ND SG CYSS1 227 86.933 81.039 250.886 1.00 24.69 S ATOM A01OX SG CYSS1 65 77.652 87.801 256.156 1.00 26.61 S ATOM A01RB SG CYSS1 76 80.143 90.290 256.313 1.00 29.87 S ATOM A01S0 SG CYSS1 79 75.527 94.075 255.729 1.00 30.90 S ATOM A01UT SG CYSS1 93 73.629 90.777 255.535 1.00 31.63 S ATOM A0B63 SG CYSS6 87 110.776 82.592 256.676 1.00 32.44 S ATOM A0BBZ SG CYSS6 115 108.318 81.311 254.058 1.00 27.37 S ATOM A0BCQ SG CYSS6 118 111.877 81.074 253.725 1.00 27.14 S ATOM A0BZM SG CYSS7 96 112.475 102.468 219.346 1.00 22.56 S ATOM A0BLK SG CYSS7 32 118.547 103.865 220.353 1.00 27.36 S ATOM A0BLE SG CYSS7 31 114.531 108.209 222.040 1.00 30.94 S ATOM A0C61 SG CYSS7 126 114.006 102.617 224.673 1.00 23.53 S ATOM A0DFU SG CYSS8 181 111.515 94.328 234.988 1.00 20.21 S ATOM A0DF9 SG CYSS8 178 109.829 99.961 232.439 1.00 22.45 S ATOM A0DEJ SG CYSS8 175 113.822 95.976 228.968 1.00 20.43 S ATOM A0D83 SG CYSS8 146 107.594 94.503 229.811 1.00 20.34 S ATOM A0DGN SG CYSS8 185 110.299 90.197 242.151 1.00 19.96 S ATOM A0D7D SG CYSS8 142 107.624 89.355 236.423 1.00 20.47 S ATOM A0D67 SG CYSS8 136 109.515 84.482 239.645 1.00 21.69 S ATOM A0D6Q SG CYSS8 139 104.628 88.342 241.861 1.00 20.37 S ATOM A0JHA SG CYSV1 383 80.235 90.440 266.189 1.00 29.72 S ATOM A0JGR SG CYSV1 380 79.922 84.603 269.462 1.00 31.90 S ATOM A0JHU SG CYSV1 386 83.702 90.053 270.800 1.00 29.96 S ATOM A0JQP SG CYSV1 426 77.230 89.782 272.066 1.00 33.09 S ATOM A0KNO SG CYSV2 125 88.400 83.089 289.620 1.00 53.50 S ATOM A0KOJ SG CYSV2 130 88.711 84.633 292.934 1.00 55.57 S ATOM A0KWD SG CYSV2 166 83.622 85.335 288.638 1.00 52.46 S ATOM A0KX0 SG CYSV2 170 83.500 87.127 291.667 1.00 57.05 S Time building chain proxies: 57.14, per 1000 atoms: 0.37 Number of scatterers: 153366 At special positions: 0 Unit cell: (219.605, 236.305, 326.485, 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 3 29.99 Fe 38 26.01 S 614 16.00 P 114 15.00 O 27887 8.00 N 25065 7.00 C 99645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS3F 28 " - pdb=" SG CYS3F 72 " distance=2.03 Simple disulfide: pdb=" SG CYS3F 32 " - pdb=" SG CYS3F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS3f 32 " - pdb=" SG CYS3f 68 " distance=2.03 Simple disulfide: pdb=" SG CYS3f 42 " - pdb=" SG CYS3f 58 " distance=2.02 Simple disulfide: pdb=" SG CYSB7 35 " - pdb=" SG CYSB7 75 " distance=2.03 Simple disulfide: pdb=" SG CYSC2 31 " - pdb=" SG CYSC2 39 " distance=2.04 Simple disulfide: pdb=" SG CYST6 58 " - pdb=" SG CYST6 93 " distance=2.03 Simple disulfide: pdb=" SG CYST6 68 " - pdb=" SG CYST6 82 " distance=2.03 Simple disulfide: pdb=" SG CYSS2 231 " - pdb=" SG CYSS2 244 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 125 " - pdb=" SG CYSA8 159 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 135 " - pdb=" SG CYSA8 149 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 170 " - pdb=" SG CYSA8 201 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 180 " - pdb=" SG CYSA8 191 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 15 " - pdb=" SG CYSS5 46 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 25 " - pdb=" SG CYSS5 36 " distance=2.03 Simple disulfide: pdb=" SG CYSA3 123 " - pdb=" SG CYSA3 130 " distance=2.03 Simple disulfide: pdb=" SG CYST9 35 " - pdb=" SG CYST9 78 " distance=2.03 Simple disulfide: pdb=" SG CYST9 45 " - pdb=" SG CYST9 68 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 45.96 Conformation dependent library (CDL) restraints added in 18.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES3E 301 " pdb="FE2 FES3E 301 " - pdb=" NE2 HIS3E 199 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 197 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 216 " pdb="FE1 FES3E 301 " - pdb=" SG CYS3E 202 " pdb=" FESFX 201 " pdb="FE2 FESFX 201 " - pdb=" SG CYSFX 107 " pdb="FE1 FESFX 201 " - pdb=" SG CYSFX 104 " pdb="FE1 FESFX 201 " - pdb=" SG CYSFX 81 " pdb="FE2 FESFX 201 " - pdb=" SG CYSFX 145 " pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 76 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 79 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 93 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 65 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 170 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 166 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 125 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 130 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 125 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 132 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 138 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 129 " pdb=" SF4S1 802 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 183 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 177 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 227 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 180 " pdb=" SF4S7 201 " pdb="FE1 SF4S7 201 " - pdb=" SG CYSS7 96 " pdb="FE4 SF4S7 201 " - pdb=" SG CYSS7 126 " pdb="FE2 SF4S7 201 " - pdb=" SG CYSS7 32 " pdb="FE3 SF4S7 201 " - pdb=" SG CYSS7 31 " pdb=" SF4S8 301 " pdb="FE4 SF4S8 301 " - pdb=" SG CYSS8 146 " pdb="FE3 SF4S8 301 " - pdb=" SG CYSS8 175 " pdb="FE1 SF4S8 301 " - pdb=" SG CYSS8 181 " pdb="FE2 SF4S8 301 " - pdb=" SG CYSS8 178 " pdb=" SF4S8 302 " pdb="FE4 SF4S8 302 " - pdb=" SG CYSS8 139 " pdb="FE2 SF4S8 302 " - pdb=" SG CYSS8 142 " pdb="FE3 SF4S8 302 " - pdb=" SG CYSS8 136 " pdb="FE1 SF4S8 302 " - pdb=" SG CYSS8 185 " pdb=" SF4V1 500 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 386 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 380 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 426 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 383 " Number of angles added : 93 Zn2+ tetrahedral coordination pdb=" ZN3F 101 " pdb="ZN ZN3F 101 " - pdb=" NE2 HISAN 12 " pdb="ZN ZN3F 101 " - pdb=" ND1 HIS3F 27 " pdb=" ZNA9 402 " pdb="ZN ZNA9 402 " - pdb=" NE2 HISA9 177 " pdb="ZN ZNA9 402 " - pdb=" NE2 HISA9 181 " pdb=" ZNS6 201 " pdb="ZN ZNS6 201 " - pdb=" NE2 HISS6 97 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 118 " pdb="ZN ZNS6 201 " - pdb=" SG CYSS6 115 " Number of angles added : 3 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 34650 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: 710 helices and 70 sheets defined 58.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 69.20 Creating SS restraints... Processing helix chain '1' and resid 1 through 52 Proline residue: 1 7 - end of helix removed outlier: 3.575A pdb=" N VAL 1 10 " --> pdb=" O ALA 1 6 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASN 1 11 " --> pdb=" O PRO 1 7 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE 1 12 " --> pdb=" O LEU 1 8 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER 1 14 " --> pdb=" O VAL 1 10 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU 1 15 " --> pdb=" O ASN 1 11 " (cutoff:3.500A) Proline residue: 1 16 - end of helix Processing helix chain '1' and resid 65 through 78 removed outlier: 5.904A pdb=" N GLY 1 78 " --> pdb=" O LEU 1 74 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 108 Proline residue: 1 94 - end of helix removed outlier: 3.740A pdb=" N THR 1 103 " --> pdb=" O ALA 1 99 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE 1 104 " --> pdb=" O ILE 1 100 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP 1 105 " --> pdb=" O CYS 1 101 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE 1 106 " --> pdb=" O TYR 1 102 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN 1 107 " --> pdb=" O THR 1 103 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER 1 108 " --> pdb=" O PHE 1 104 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 145 removed outlier: 4.203A pdb=" N LYS 1 145 " --> pdb=" O GLY 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 146 through 175 Processing helix chain '1' and resid 182 through 191 removed outlier: 4.637A pdb=" N PHE 1 186 " --> pdb=" O CYS 1 182 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL 1 187 " --> pdb=" O PHE 1 183 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE 1 188 " --> pdb=" O SER 1 184 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR 1 189 " --> pdb=" O VAL 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 194 through 200 removed outlier: 4.326A pdb=" N ILE 1 198 " --> pdb=" O TRP 1 194 " (cutoff:3.500A) Processing helix chain '1' and resid 202 through 215 Processing helix chain '1' and resid 238 through 263 removed outlier: 3.526A pdb=" N ALA 1 242 " --> pdb=" O GLY 1 238 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 275 removed outlier: 4.797A pdb=" N TYR 1 274 " --> pdb=" O PRO 1 270 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 1 275 " --> pdb=" O ASN 1 271 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 270 through 275' Processing helix chain '1B' and resid 1 through 24 removed outlier: 4.531A pdb=" N VAL1B 5 " --> pdb=" O MET1B 1 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA1B 17 " --> pdb=" O PHE1B 13 " (cutoff:3.500A) Processing helix chain '1B' and resid 28 through 59 removed outlier: 5.777A pdb=" N ILE1B 41 " --> pdb=" O TRP1B 37 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TYR1B 42 " --> pdb=" O LYS1B 38 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 33 removed outlier: 4.169A pdb=" N TYR 2 10 " --> pdb=" O LEU 2 6 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE 2 12 " --> pdb=" O SER 2 8 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU 2 14 " --> pdb=" O TYR 2 10 " (cutoff:3.500A) Proline residue: 2 15 - end of helix removed outlier: 3.829A pdb=" N ILE 2 32 " --> pdb=" O PHE 2 28 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN 2 33 " --> pdb=" O LYS 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 77 Processing helix chain '2' and resid 92 through 120 removed outlier: 4.245A pdb=" N LYS 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE 2 119 " --> pdb=" O LYS 2 115 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU 2 120 " --> pdb=" O HIS 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 144 removed outlier: 3.684A pdb=" N PHE 2 128 " --> pdb=" O SER 2 124 " (cutoff:3.500A) Proline residue: 2 139 - end of helix removed outlier: 3.559A pdb=" N SER 2 144 " --> pdb=" O MET 2 140 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 168 removed outlier: 3.887A pdb=" N SER 2 168 " --> pdb=" O LYS 2 164 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 218 Processing helix chain '2' and resid 222 through 237 Processing helix chain '2' and resid 241 through 261 removed outlier: 3.519A pdb=" N LEU 2 245 " --> pdb=" O ASN 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 266 through 276 removed outlier: 3.789A pdb=" N ILE 2 270 " --> pdb=" O GLN 2 266 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU 2 271 " --> pdb=" O LEU 2 267 " (cutoff:3.500A) Processing helix chain '2' and resid 277 through 302 removed outlier: 4.258A pdb=" N PHE 2 293 " --> pdb=" O PHE 2 289 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU 2 294 " --> pdb=" O LEU 2 290 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE 2 300 " --> pdb=" O PHE 2 296 " (cutoff:3.500A) Processing helix chain '2' and resid 304 through 309 removed outlier: 3.993A pdb=" N ASN 2 308 " --> pdb=" O LEU 2 304 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASN 2 309 " --> pdb=" O SER 2 305 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 304 through 309' Processing helix chain '2' and resid 310 through 330 removed outlier: 4.144A pdb=" N ILE 2 314 " --> pdb=" O PHE 2 310 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER 2 328 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE 2 329 " --> pdb=" O TYR 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 335 through 360 removed outlier: 3.620A pdb=" N PHE 2 360 " --> pdb=" O ILE 2 356 " (cutoff:3.500A) Processing helix chain '2B' and resid 15 through 43 removed outlier: 3.634A pdb=" N SER2B 19 " --> pdb=" O SER2B 15 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR2B 42 " --> pdb=" O VAL2B 38 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN2B 43 " --> pdb=" O ILE2B 39 " (cutoff:3.500A) Processing helix chain '2B' and resid 52 through 58 removed outlier: 4.413A pdb=" N PHE2B 56 " --> pdb=" O GLN2B 52 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN2B 57 " --> pdb=" O PHE2B 53 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER2B 58 " --> pdb=" O LYS2B 54 " (cutoff:3.500A) No H-bonds generated for 'chain '2B' and resid 52 through 58' Processing helix chain '2B' and resid 59 through 75 Processing helix chain '2B' and resid 79 through 96 removed outlier: 4.231A pdb=" N THR2B 83 " --> pdb=" O LEU2B 79 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY2B 84 " --> pdb=" O LEU2B 80 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS2B 85 " --> pdb=" O GLY2B 81 " (cutoff:3.500A) Processing helix chain '2B' and resid 97 through 123 removed outlier: 4.641A pdb=" N ASN2B 118 " --> pdb=" O PHE2B 114 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU2B 119 " --> pdb=" O TYR2B 115 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG2B 120 " --> pdb=" O ILE2B 116 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE2B 121 " --> pdb=" O GLN2B 117 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL2B 123 " --> pdb=" O LEU2B 119 " (cutoff:3.500A) Processing helix chain '2B' and resid 141 through 162 removed outlier: 3.582A pdb=" N THR2B 145 " --> pdb=" O ASN2B 141 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE2B 159 " --> pdb=" O ASN2B 155 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU2B 160 " --> pdb=" O PHE2B 156 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE2B 161 " --> pdb=" O PHE2B 157 " (cutoff:3.500A) Processing helix chain '2B' and resid 163 through 178 removed outlier: 4.114A pdb=" N TYR2B 175 " --> pdb=" O TYR2B 171 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE2B 176 " --> pdb=" O ILE2B 172 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR2B 177 " --> pdb=" O SER2B 173 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE2B 178 " --> pdb=" O SER2B 174 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 29 removed outlier: 3.979A pdb=" N HIS 3 8 " --> pdb=" O ALA 3 4 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 3 28 " --> pdb=" O THR 3 24 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR 3 29 " --> pdb=" O TRP 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 85 removed outlier: 4.015A pdb=" N ALA 3 65 " --> pdb=" O PHE 3 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 3 70 " --> pdb=" O VAL 3 66 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL 3 73 " --> pdb=" O ILE 3 69 " (cutoff:3.500A) Proline residue: 3 80 - end of helix Processing helix chain '3' and resid 89 through 114 Processing helix chain '3A' and resid 23 through 32 Processing helix chain '3A' and resid 38 through 46 removed outlier: 3.673A pdb=" N ALA3A 46 " --> pdb=" O LYS3A 42 " (cutoff:3.500A) Processing helix chain '3A' and resid 98 through 103 removed outlier: 3.977A pdb=" N GLU3A 102 " --> pdb=" O GLY3A 98 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR3A 103 " --> pdb=" O THR3A 99 " (cutoff:3.500A) No H-bonds generated for 'chain '3A' and resid 98 through 103' Processing helix chain '3A' and resid 108 through 117 Processing helix chain '3A' and resid 125 through 137 Processing helix chain '3A' and resid 156 through 173 removed outlier: 3.522A pdb=" N ALA3A 160 " --> pdb=" O LEU3A 156 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR3A 161 " --> pdb=" O ALA3A 157 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP3A 162 " --> pdb=" O HIS3A 158 " (cutoff:3.500A) Processing helix chain '3A' and resid 176 through 198 removed outlier: 4.596A pdb=" N LYS3A 198 " --> pdb=" O GLU3A 194 " (cutoff:3.500A) Processing helix chain '3A' and resid 199 through 213 removed outlier: 4.091A pdb=" N PHE3A 203 " --> pdb=" O THR3A 199 " (cutoff:3.500A) Processing helix chain '3A' and resid 232 through 244 removed outlier: 3.605A pdb=" N GLU3A 242 " --> pdb=" O LYS3A 238 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN3A 243 " --> pdb=" O PHE3A 239 " (cutoff:3.500A) Processing helix chain '3A' and resid 245 through 250 removed outlier: 3.675A pdb=" N ILE3A 249 " --> pdb=" O THR3A 245 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE3A 250 " --> pdb=" O PRO3A 246 " (cutoff:3.500A) No H-bonds generated for 'chain '3A' and resid 245 through 250' Processing helix chain '3A' and resid 258 through 270 removed outlier: 3.756A pdb=" N PHE3A 262 " --> pdb=" O SER3A 258 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS3A 269 " --> pdb=" O LEU3A 265 " (cutoff:3.500A) Processing helix chain '3A' and resid 318 through 337 removed outlier: 5.340A pdb=" N LEU3A 334 " --> pdb=" O ASN3A 330 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS3A 335 " --> pdb=" O ASN3A 331 " (cutoff:3.500A) Processing helix chain '3A' and resid 371 through 389 Processing helix chain '3A' and resid 391 through 412 removed outlier: 4.528A pdb=" N ARG3A 412 " --> pdb=" O SER3A 408 " (cutoff:3.500A) Processing helix chain '3A' and resid 413 through 427 Processing helix chain '3A' and resid 431 through 442 removed outlier: 3.694A pdb=" N TYR3A 435 " --> pdb=" O GLN3A 431 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL3A 436 " --> pdb=" O HIS3A 432 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS3A 437 " --> pdb=" O THR3A 433 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL3A 442 " --> pdb=" O GLN3A 438 " (cutoff:3.500A) Processing helix chain '3A' and resid 443 through 457 removed outlier: 3.681A pdb=" N THR3A 456 " --> pdb=" O ALA3A 452 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER3A 457 " --> pdb=" O LYS3A 453 " (cutoff:3.500A) Processing helix chain '3A' and resid 473 through 482 Processing helix chain '3A' and resid 225 through 230 removed outlier: 3.929A pdb=" N VAL3A 228 " --> pdb=" O ARG3A 225 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS3A 229 " --> pdb=" O GLY3A 226 " (cutoff:3.500A) Processing helix chain '3B' and resid 55 through 60 removed outlier: 4.275A pdb=" N TYR3B 60 " --> pdb=" O THR3B 56 " (cutoff:3.500A) Processing helix chain '3B' and resid 95 through 100 removed outlier: 4.267A pdb=" N GLU3B 99 " --> pdb=" O GLY3B 95 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR3B 100 " --> pdb=" O THR3B 96 " (cutoff:3.500A) No H-bonds generated for 'chain '3B' and resid 95 through 100' Processing helix chain '3B' and resid 105 through 117 removed outlier: 3.571A pdb=" N PHE3B 109 " --> pdb=" O GLY3B 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN3B 111 " --> pdb=" O ALA3B 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG3B 112 " --> pdb=" O GLN3B 108 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU3B 115 " --> pdb=" O GLN3B 111 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG3B 116 " --> pdb=" O ARG3B 112 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY3B 117 " --> pdb=" O LEU3B 113 " (cutoff:3.500A) Processing helix chain '3B' and resid 122 through 134 Processing helix chain '3B' and resid 156 through 170 Processing helix chain '3B' and resid 174 through 196 removed outlier: 3.669A pdb=" N LYS3B 182 " --> pdb=" O VAL3B 178 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU3B 183 " --> pdb=" O GLU3B 179 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA3B 184 " --> pdb=" O ALA3B 180 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN3B 193 " --> pdb=" O ALA3B 189 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN3B 194 " --> pdb=" O LEU3B 190 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP3B 195 " --> pdb=" O SER3B 191 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN3B 196 " --> pdb=" O ALA3B 192 " (cutoff:3.500A) Processing helix chain '3B' and resid 197 through 210 removed outlier: 3.756A pdb=" N ARG3B 210 " --> pdb=" O PHE3B 206 " (cutoff:3.500A) Processing helix chain '3B' and resid 221 through 228 removed outlier: 3.731A pdb=" N HIS3B 226 " --> pdb=" O ARG3B 222 " (cutoff:3.500A) Processing helix chain '3B' and resid 229 through 241 Processing helix chain '3B' and resid 255 through 267 Processing helix chain '3B' and resid 317 through 329 removed outlier: 3.618A pdb=" N ARG3B 326 " --> pdb=" O ASN3B 322 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU3B 328 " --> pdb=" O PHE3B 324 " (cutoff:3.500A) Processing helix chain '3B' and resid 349 through 359 Proline residue: 3B 359 - end of helix Processing helix chain '3B' and resid 384 through 405 removed outlier: 4.136A pdb=" N GLY3B 388 " --> pdb=" O ASN3B 384 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN3B 389 " --> pdb=" O GLU3B 385 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN3B 390 " --> pdb=" O ILE3B 386 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER3B 395 " --> pdb=" O MET3B 391 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN3B 396 " --> pdb=" O LEU3B 392 " (cutoff:3.500A) Processing helix chain '3B' and resid 407 through 425 removed outlier: 3.994A pdb=" N GLU3B 425 " --> pdb=" O GLU3B 421 " (cutoff:3.500A) Processing helix chain '3B' and resid 427 through 442 Processing helix chain '3B' and resid 447 through 458 removed outlier: 4.090A pdb=" N LEU3B 458 " --> pdb=" O ARG3B 454 " (cutoff:3.500A) Processing helix chain '3B' and resid 459 through 471 Processing helix chain '3B' and resid 494 through 501 removed outlier: 4.491A pdb=" N THR3B 501 " --> pdb=" O ILE3B 497 " (cutoff:3.500A) Processing helix chain '3B' and resid 507 through 513 removed outlier: 4.004A pdb=" N ILE3B 512 " --> pdb=" O THR3B 508 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL3B 513 " --> pdb=" O HIS3B 509 " (cutoff:3.500A) Processing helix chain '3C' and resid 12 through 23 Processing helix chain '3C' and resid 29 through 56 removed outlier: 4.485A pdb=" N LEU3C 33 " --> pdb=" O ASP3C 29 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE3C 34 " --> pdb=" O ILE3C 30 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY3C 35 " --> pdb=" O ASN3C 31 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE3C 36 " --> pdb=" O SER3C 32 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER3C 55 " --> pdb=" O MET3C 51 " (cutoff:3.500A) Processing helix chain '3C' and resid 59 through 74 Proline residue: 3C 64 - end of helix removed outlier: 3.565A pdb=" N VAL3C 72 " --> pdb=" O GLU3C 68 " (cutoff:3.500A) Processing helix chain '3C' and resid 76 through 106 Processing helix chain '3C' and resid 109 through 138 removed outlier: 4.642A pdb=" N ALA3C 114 " --> pdb=" O TYR3C 110 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA3C 115 " --> pdb=" O GLU3C 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS3C 117 " --> pdb=" O GLU3C 113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER3C 118 " --> pdb=" O ALA3C 114 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY3C 119 " --> pdb=" O ALA3C 115 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS3C 138 " --> pdb=" O LEU3C 134 " (cutoff:3.500A) Processing helix chain '3C' and resid 139 through 158 removed outlier: 3.762A pdb=" N PHE3C 156 " --> pdb=" O LEU3C 152 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE3C 157 " --> pdb=" O TYR3C 153 " (cutoff:3.500A) Processing helix chain '3C' and resid 174 through 204 removed outlier: 3.763A pdb=" N MET3C 203 " --> pdb=" O HIS3C 199 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N HIS3C 204 " --> pdb=" O GLY3C 200 " (cutoff:3.500A) Processing helix chain '3C' and resid 224 through 249 removed outlier: 4.212A pdb=" N ASN3C 229 " --> pdb=" O GLU3C 225 " (cutoff:3.500A) Processing helix chain '3C' and resid 258 through 263 removed outlier: 4.427A pdb=" N TRP3C 262 " --> pdb=" O GLU3C 258 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY3C 263 " --> pdb=" O PHE3C 259 " (cutoff:3.500A) No H-bonds generated for 'chain '3C' and resid 258 through 263' Processing helix chain '3C' and resid 279 through 293 Proline residue: 3C 284 - end of helix Proline residue: 3C 293 - end of helix Processing helix chain '3C' and resid 294 through 312 removed outlier: 3.858A pdb=" N PHE3C 306 " --> pdb=" O LEU3C 302 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR3C 311 " --> pdb=" O PHE3C 307 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN3C 312 " --> pdb=" O ILE3C 308 " (cutoff:3.500A) Processing helix chain '3C' and resid 352 through 372 removed outlier: 4.249A pdb=" N TYR3C 372 " --> pdb=" O TYR3C 368 " (cutoff:3.500A) Processing helix chain '3C' and resid 378 through 383 removed outlier: 3.653A pdb=" N ASN3C 383 " --> pdb=" O TYR3C 379 " (cutoff:3.500A) Processing helix chain '3C' and resid 385 through 401 removed outlier: 3.585A pdb=" N LEU3C 389 " --> pdb=" O ASN3C 385 " (cutoff:3.500A) Processing helix chain '3C' and resid 407 through 426 removed outlier: 4.565A pdb=" N GLU3C 411 " --> pdb=" O PRO3C 407 " (cutoff:3.500A) Processing helix chain '3C' and resid 162 through 167 removed outlier: 4.600A pdb=" N TRP3C 166 " --> pdb=" O PHE3C 163 " (cutoff:3.500A) Processing helix chain '3c' and resid 12 through 23 Processing helix chain '3c' and resid 29 through 56 removed outlier: 4.276A pdb=" N LEU3c 33 " --> pdb=" O ASP3c 29 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE3c 34 " --> pdb=" O ILE3c 30 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY3c 35 " --> pdb=" O ASN3c 31 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE3c 36 " --> pdb=" O SER3c 32 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER3c 55 " --> pdb=" O MET3c 51 " (cutoff:3.500A) Processing helix chain '3c' and resid 59 through 74 Proline residue: 3c 64 - end of helix removed outlier: 3.618A pdb=" N VAL3c 72 " --> pdb=" O GLU3c 68 " (cutoff:3.500A) Processing helix chain '3c' and resid 76 through 106 Processing helix chain '3c' and resid 109 through 138 removed outlier: 4.887A pdb=" N ALA3c 114 " --> pdb=" O TYR3c 110 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA3c 115 " --> pdb=" O GLU3c 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER3c 118 " --> pdb=" O ALA3c 114 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY3c 119 " --> pdb=" O ALA3c 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS3c 137 " --> pdb=" O GLY3c 133 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N CYS3c 138 " --> pdb=" O LEU3c 134 " (cutoff:3.500A) Processing helix chain '3c' and resid 139 through 158 Processing helix chain '3c' and resid 174 through 204 removed outlier: 3.529A pdb=" N ARG3c 180 " --> pdb=" O ASP3c 176 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N HIS3c 204 " --> pdb=" O GLY3c 200 " (cutoff:3.500A) Processing helix chain '3c' and resid 224 through 249 removed outlier: 4.590A pdb=" N ASN3c 229 " --> pdb=" O GLU3c 225 " (cutoff:3.500A) Processing helix chain '3c' and resid 258 through 263 removed outlier: 4.373A pdb=" N TRP3c 262 " --> pdb=" O GLU3c 258 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY3c 263 " --> pdb=" O PHE3c 259 " (cutoff:3.500A) No H-bonds generated for 'chain '3c' and resid 258 through 263' Processing helix chain '3c' and resid 279 through 293 Proline residue: 3c 284 - end of helix Proline residue: 3c 293 - end of helix Processing helix chain '3c' and resid 294 through 312 removed outlier: 6.061A pdb=" N GLY3c 298 " --> pdb=" O PHE3c 294 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU3c 299 " --> pdb=" O HIS3c 295 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN3c 312 " --> pdb=" O ILE3c 308 " (cutoff:3.500A) Processing helix chain '3c' and resid 352 through 372 removed outlier: 4.134A pdb=" N TYR3c 372 " --> pdb=" O TYR3c 368 " (cutoff:3.500A) Processing helix chain '3c' and resid 378 through 383 removed outlier: 3.961A pdb=" N ASN3c 383 " --> pdb=" O TYR3c 379 " (cutoff:3.500A) Processing helix chain '3c' and resid 385 through 401 removed outlier: 3.609A pdb=" N LEU3c 389 " --> pdb=" O ASN3c 385 " (cutoff:3.500A) Processing helix chain '3c' and resid 407 through 426 removed outlier: 4.426A pdb=" N GLU3c 411 " --> pdb=" O PRO3c 407 " (cutoff:3.500A) Processing helix chain '3c' and resid 162 through 167 removed outlier: 4.396A pdb=" N TRP3c 166 " --> pdb=" O PHE3c 163 " (cutoff:3.500A) Processing helix chain '3D' and resid 56 through 61 removed outlier: 3.628A pdb=" N SER3D 60 " --> pdb=" O TRP3D 56 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE3D 61 " --> pdb=" O PRO3D 57 " (cutoff:3.500A) No H-bonds generated for 'chain '3D' and resid 56 through 61' Processing helix chain '3D' and resid 66 through 80 Processing helix chain '3D' and resid 101 through 113 removed outlier: 4.517A pdb=" N PHE3D 112 " --> pdb=" O MET3D 108 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N THR3D 113 " --> pdb=" O VAL3D 109 " (cutoff:3.500A) Processing helix chain '3D' and resid 146 through 155 Processing helix chain '3D' and resid 161 through 166 removed outlier: 4.775A pdb=" N ILE3D 165 " --> pdb=" O ASP3D 161 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS3D 166 " --> pdb=" O PHE3D 162 " (cutoff:3.500A) No H-bonds generated for 'chain '3D' and resid 161 through 166' Processing helix chain '3D' and resid 171 through 181 removed outlier: 3.883A pdb=" N GLY3D 181 " --> pdb=" O ASN3D 177 " (cutoff:3.500A) Processing helix chain '3D' and resid 227 through 244 removed outlier: 5.478A pdb=" N ARG3D 244 " --> pdb=" O ASN3D 240 " (cutoff:3.500A) Processing helix chain '3D' and resid 249 through 285 Proline residue: 3D 269 - end of helix removed outlier: 3.593A pdb=" N SER3D 284 " --> pdb=" O ARG3D 280 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU3D 285 " --> pdb=" O ASN3D 281 " (cutoff:3.500A) Processing helix chain '3D' and resid 298 through 304 Processing helix chain '3D' and resid 309 through 314 Processing helix chain '3D' and resid 91 through 96 removed outlier: 3.511A pdb=" N TYR3D 94 " --> pdb=" O LYS3D 91 " (cutoff:3.500A) Processing helix chain '3E' and resid 25 through 36 removed outlier: 3.803A pdb=" N SER3E 35 " --> pdb=" O ASN3E 31 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS3E 36 " --> pdb=" O GLN3E 32 " (cutoff:3.500A) Processing helix chain '3E' and resid 72 through 77 Processing helix chain '3E' and resid 84 through 119 removed outlier: 4.543A pdb=" N ARG3E 88 " --> pdb=" O GLU3E 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU3E 118 " --> pdb=" O VAL3E 114 " (cutoff:3.500A) Processing helix chain '3E' and resid 158 through 165 removed outlier: 5.298A pdb=" N GLU3E 165 " --> pdb=" O GLU3E 161 " (cutoff:3.500A) Processing helix chain '3F' and resid 12 through 17 Processing helix chain '3F' and resid 20 through 33 Proline residue: 3F 30 - end of helix removed outlier: 3.683A pdb=" N LEU3F 33 " --> pdb=" O LYS3F 29 " (cutoff:3.500A) Processing helix chain '3F' and resid 34 through 50 removed outlier: 3.629A pdb=" N LEU3F 49 " --> pdb=" O LYS3F 45 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL3F 50 " --> pdb=" O LEU3F 46 " (cutoff:3.500A) Processing helix chain '3F' and resid 58 through 82 Proline residue: 3F 75 - end of helix removed outlier: 3.887A pdb=" N GLN3F 80 " --> pdb=" O GLN3F 76 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU3F 81 " --> pdb=" O ILE3F 77 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL3F 82 " --> pdb=" O ILE3F 78 " (cutoff:3.500A) Processing helix chain '3G' and resid 34 through 48 Processing helix chain '3G' and resid 50 through 60 Processing helix chain '3G' and resid 61 through 79 removed outlier: 3.744A pdb=" N TYR3G 68 " --> pdb=" O ALA3G 64 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG3G 69 " --> pdb=" O LYS3G 65 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP3G 70 " --> pdb=" O PHE3G 66 " (cutoff:3.500A) Processing helix chain '3G' and resid 81 through 86 removed outlier: 4.072A pdb=" N SER3G 85 " --> pdb=" O THR3G 81 " (cutoff:3.500A) Processing helix chain '3G' and resid 89 through 95 removed outlier: 4.610A pdb=" N ARG3G 95 " --> pdb=" O ARG3G 91 " (cutoff:3.500A) Processing helix chain '3G' and resid 96 through 106 Processing helix chain '3G' and resid 110 through 127 removed outlier: 4.511A pdb=" N VAL3G 125 " --> pdb=" O ARG3G 121 " (cutoff:3.500A) Processing helix chain '3G' and resid 135 through 145 removed outlier: 3.954A pdb=" N GLU3G 141 " --> pdb=" O TRP3G 137 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG3G 145 " --> pdb=" O GLU3G 141 " (cutoff:3.500A) Processing helix chain '3G' and resid 146 through 169 removed outlier: 3.743A pdb=" N THR3G 150 " --> pdb=" O GLN3G 146 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER3G 167 " --> pdb=" O ARG3G 163 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP3G 168 " --> pdb=" O GLU3G 164 " (cutoff:3.500A) Processing helix chain '3G' and resid 182 through 188 removed outlier: 3.948A pdb=" N PHE3G 187 " --> pdb=" O PRO3G 183 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN3G 188 " --> pdb=" O LEU3G 184 " (cutoff:3.500A) Processing helix chain '3G' and resid 194 through 201 removed outlier: 4.666A pdb=" N PHE3G 201 " --> pdb=" O ALA3G 197 " (cutoff:3.500A) Processing helix chain '3G' and resid 212 through 221 removed outlier: 3.784A pdb=" N ASN3G 220 " --> pdb=" O LYS3G 216 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY3G 221 " --> pdb=" O GLN3G 217 " (cutoff:3.500A) Processing helix chain '3G' and resid 231 through 250 Proline residue: 3G 250 - end of helix Processing helix chain '3G' and resid 261 through 274 removed outlier: 4.047A pdb=" N PHE3G 265 " --> pdb=" O ASP3G 261 " (cutoff:3.500A) Processing helix chain '3G' and resid 281 through 297 removed outlier: 3.953A pdb=" N ALA3G 296 " --> pdb=" O LEU3G 292 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA3G 297 " --> pdb=" O LYS3G 293 " (cutoff:3.500A) Processing helix chain '3G' and resid 315 through 320 Proline residue: 3G 320 - end of helix Processing helix chain '3H' and resid 32 through 37 removed outlier: 4.221A pdb=" N LEU3H 36 " --> pdb=" O LYS3H 32 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE3H 37 " --> pdb=" O GLN3H 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3H' and resid 32 through 37' Processing helix chain '3H' and resid 40 through 45 removed outlier: 3.889A pdb=" N SER3H 44 " --> pdb=" O SER3H 40 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL3H 45 " --> pdb=" O VAL3H 41 " (cutoff:3.500A) No H-bonds generated for 'chain '3H' and resid 40 through 45' Processing helix chain '3H' and resid 64 through 69 removed outlier: 4.028A pdb=" N GLN3H 68 " --> pdb=" O SER3H 64 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE3H 69 " --> pdb=" O PRO3H 65 " (cutoff:3.500A) No H-bonds generated for 'chain '3H' and resid 64 through 69' Processing helix chain '3H' and resid 95 through 127 removed outlier: 5.387A pdb=" N THR3H 99 " --> pdb=" O ARG3H 95 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N PHE3H 102 " --> pdb=" O ARG3H 98 " (cutoff:3.500A) Proline residue: 3H 103 - end of helix Processing helix chain '3H' and resid 78 through 94 removed outlier: 4.017A pdb=" N VAL3H 83 " --> pdb=" O GLY3H 78 " (cutoff:3.500A) Processing helix chain '3I' and resid 23 through 28 removed outlier: 3.865A pdb=" N VAL3I 27 " --> pdb=" O PRO3I 23 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N THR3I 28 " --> pdb=" O TYR3I 24 " (cutoff:3.500A) No H-bonds generated for 'chain '3I' and resid 23 through 28' Processing helix chain '3I' and resid 40 through 45 removed outlier: 3.774A pdb=" N ASP3I 45 " --> pdb=" O LYS3I 41 " (cutoff:3.500A) Processing helix chain '3I' and resid 46 through 63 removed outlier: 4.808A pdb=" N TYR3I 61 " --> pdb=" O GLU3I 57 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR3I 62 " --> pdb=" O ASN3I 58 " (cutoff:3.500A) Proline residue: 3I 63 - end of helix Processing helix chain '3I' and resid 64 through 94 Proline residue: 3I 84 - end of helix removed outlier: 3.544A pdb=" N ASN3I 93 " --> pdb=" O TYR3I 89 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA3I 94 " --> pdb=" O GLN3I 90 " (cutoff:3.500A) Processing helix chain '3I' and resid 97 through 115 Processing helix chain '3J' and resid 5 through 37 removed outlier: 3.960A pdb=" N TYR3J 24 " --> pdb=" O ARG3J 20 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY3J 25 " --> pdb=" O TYR3J 21 " (cutoff:3.500A) Proline residue: 3J 26 - end of helix Processing helix chain '3J' and resid 38 through 47 Processing helix chain '3a' and resid 24 through 32 Processing helix chain '3a' and resid 38 through 46 removed outlier: 3.615A pdb=" N LYS3a 42 " --> pdb=" O ALA3a 38 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL3a 43 " --> pdb=" O GLU3a 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR3a 44 " --> pdb=" O THR3a 40 " (cutoff:3.500A) Processing helix chain '3a' and resid 98 through 103 removed outlier: 3.987A pdb=" N GLU3a 102 " --> pdb=" O GLY3a 98 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N THR3a 103 " --> pdb=" O THR3a 99 " (cutoff:3.500A) No H-bonds generated for 'chain '3a' and resid 98 through 103' Processing helix chain '3a' and resid 108 through 117 Processing helix chain '3a' and resid 125 through 137 Processing helix chain '3a' and resid 156 through 173 removed outlier: 3.531A pdb=" N ALA3a 160 " --> pdb=" O LEU3a 156 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR3a 161 " --> pdb=" O ALA3a 157 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP3a 162 " --> pdb=" O HIS3a 158 " (cutoff:3.500A) Processing helix chain '3a' and resid 176 through 198 removed outlier: 4.122A pdb=" N LYS3a 198 " --> pdb=" O GLU3a 194 " (cutoff:3.500A) Processing helix chain '3a' and resid 199 through 212 removed outlier: 3.927A pdb=" N PHE3a 203 " --> pdb=" O THR3a 199 " (cutoff:3.500A) Processing helix chain '3a' and resid 224 through 229 removed outlier: 3.818A pdb=" N VAL3a 228 " --> pdb=" O LEU3a 224 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS3a 229 " --> pdb=" O ARG3a 225 " (cutoff:3.500A) No H-bonds generated for 'chain '3a' and resid 224 through 229' Processing helix chain '3a' and resid 232 through 244 removed outlier: 3.579A pdb=" N ASN3a 243 " --> pdb=" O PHE3a 239 " (cutoff:3.500A) Processing helix chain '3a' and resid 245 through 250 removed outlier: 3.601A pdb=" N ILE3a 249 " --> pdb=" O THR3a 245 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE3a 250 " --> pdb=" O PRO3a 246 " (cutoff:3.500A) No H-bonds generated for 'chain '3a' and resid 245 through 250' Processing helix chain '3a' and resid 258 through 270 removed outlier: 3.694A pdb=" N PHE3a 262 " --> pdb=" O SER3a 258 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS3a 269 " --> pdb=" O LEU3a 265 " (cutoff:3.500A) Processing helix chain '3a' and resid 318 through 337 removed outlier: 4.777A pdb=" N LEU3a 334 " --> pdb=" O ASN3a 330 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS3a 335 " --> pdb=" O ASN3a 331 " (cutoff:3.500A) Processing helix chain '3a' and resid 371 through 389 Processing helix chain '3a' and resid 391 through 412 removed outlier: 4.145A pdb=" N ARG3a 412 " --> pdb=" O SER3a 408 " (cutoff:3.500A) Processing helix chain '3a' and resid 413 through 427 Processing helix chain '3a' and resid 431 through 442 removed outlier: 3.777A pdb=" N TYR3a 435 " --> pdb=" O GLN3a 431 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N VAL3a 436 " --> pdb=" O HIS3a 432 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LYS3a 437 " --> pdb=" O THR3a 433 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL3a 442 " --> pdb=" O GLN3a 438 " (cutoff:3.500A) Processing helix chain '3a' and resid 443 through 457 removed outlier: 3.809A pdb=" N THR3a 456 " --> pdb=" O ALA3a 452 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER3a 457 " --> pdb=" O LYS3a 453 " (cutoff:3.500A) Processing helix chain '3a' and resid 473 through 481 Processing helix chain '3b' and resid 55 through 60 removed outlier: 3.551A pdb=" N GLN3b 59 " --> pdb=" O PRO3b 55 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR3b 60 " --> pdb=" O THR3b 56 " (cutoff:3.500A) No H-bonds generated for 'chain '3b' and resid 55 through 60' Processing helix chain '3b' and resid 95 through 100 removed outlier: 4.137A pdb=" N GLU3b 99 " --> pdb=" O GLY3b 95 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR3b 100 " --> pdb=" O THR3b 96 " (cutoff:3.500A) No H-bonds generated for 'chain '3b' and resid 95 through 100' Processing helix chain '3b' and resid 105 through 117 removed outlier: 4.272A pdb=" N PHE3b 109 " --> pdb=" O GLY3b 105 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU3b 115 " --> pdb=" O GLN3b 111 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG3b 116 " --> pdb=" O ARG3b 112 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY3b 117 " --> pdb=" O LEU3b 113 " (cutoff:3.500A) Processing helix chain '3b' and resid 122 through 134 Processing helix chain '3b' and resid 156 through 169 Processing helix chain '3b' and resid 174 through 196 removed outlier: 3.659A pdb=" N LYS3b 182 " --> pdb=" O VAL3b 178 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU3b 183 " --> pdb=" O GLU3b 179 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA3b 184 " --> pdb=" O ALA3b 180 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA3b 192 " --> pdb=" O ASN3b 188 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN3b 193 " --> pdb=" O ALA3b 189 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN3b 194 " --> pdb=" O LEU3b 190 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP3b 195 " --> pdb=" O SER3b 191 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN3b 196 " --> pdb=" O ALA3b 192 " (cutoff:3.500A) Processing helix chain '3b' and resid 197 through 210 removed outlier: 3.782A pdb=" N ARG3b 210 " --> pdb=" O PHE3b 206 " (cutoff:3.500A) Processing helix chain '3b' and resid 212 through 217 removed outlier: 4.516A pdb=" N GLN3b 216 " --> pdb=" O HIS3b 212 " (cutoff:3.500A) Proline residue: 3b 217 - end of helix No H-bonds generated for 'chain '3b' and resid 212 through 217' Processing helix chain '3b' and resid 221 through 228 removed outlier: 3.667A pdb=" N HIS3b 226 " --> pdb=" O ARG3b 222 " (cutoff:3.500A) Processing helix chain '3b' and resid 229 through 241 Processing helix chain '3b' and resid 242 through 247 removed outlier: 3.690A pdb=" N PHE3b 246 " --> pdb=" O VAL3b 242 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL3b 247 " --> pdb=" O GLY3b 243 " (cutoff:3.500A) No H-bonds generated for 'chain '3b' and resid 242 through 247' Processing helix chain '3b' and resid 255 through 267 Processing helix chain '3b' and resid 317 through 329 Processing helix chain '3b' and resid 349 through 359 Proline residue: 3b 359 - end of helix Processing helix chain '3b' and resid 384 through 405 removed outlier: 4.038A pdb=" N GLY3b 388 " --> pdb=" O ASN3b 384 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN3b 389 " --> pdb=" O GLU3b 385 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN3b 390 " --> pdb=" O ILE3b 386 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER3b 395 " --> pdb=" O MET3b 391 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN3b 396 " --> pdb=" O LEU3b 392 " (cutoff:3.500A) Processing helix chain '3b' and resid 407 through 425 removed outlier: 4.138A pdb=" N GLU3b 425 " --> pdb=" O GLU3b 421 " (cutoff:3.500A) Processing helix chain '3b' and resid 427 through 442 Processing helix chain '3b' and resid 447 through 458 removed outlier: 3.979A pdb=" N LEU3b 458 " --> pdb=" O ARG3b 454 " (cutoff:3.500A) Processing helix chain '3b' and resid 459 through 471 Processing helix chain '3b' and resid 494 through 503 removed outlier: 4.213A pdb=" N THR3b 501 " --> pdb=" O ILE3b 497 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU3b 502 " --> pdb=" O LYS3b 498 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLY3b 503 " --> pdb=" O ARG3b 499 " (cutoff:3.500A) Processing helix chain '3b' and resid 507 through 513 removed outlier: 3.829A pdb=" N ILE3b 512 " --> pdb=" O THR3b 508 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL3b 513 " --> pdb=" O HIS3b 509 " (cutoff:3.500A) Processing helix chain '3d' and resid 56 through 61 removed outlier: 3.592A pdb=" N SER3d 60 " --> pdb=" O TRP3d 56 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE3d 61 " --> pdb=" O PRO3d 57 " (cutoff:3.500A) No H-bonds generated for 'chain '3d' and resid 56 through 61' Processing helix chain '3d' and resid 66 through 80 Processing helix chain '3d' and resid 101 through 113 removed outlier: 4.263A pdb=" N PHE3d 112 " --> pdb=" O MET3d 108 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR3d 113 " --> pdb=" O VAL3d 109 " (cutoff:3.500A) Processing helix chain '3d' and resid 146 through 155 Processing helix chain '3d' and resid 171 through 181 removed outlier: 4.519A pdb=" N ILE3d 175 " --> pdb=" O GLY3d 171 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR3d 176 " --> pdb=" O ILE3d 172 " (cutoff:3.500A) Processing helix chain '3d' and resid 227 through 244 removed outlier: 3.675A pdb=" N GLN3d 243 " --> pdb=" O ILE3d 239 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG3d 244 " --> pdb=" O ASN3d 240 " (cutoff:3.500A) Processing helix chain '3d' and resid 249 through 285 Proline residue: 3d 269 - end of helix removed outlier: 5.486A pdb=" N LEU3d 285 " --> pdb=" O ASN3d 281 " (cutoff:3.500A) Processing helix chain '3d' and resid 298 through 304 removed outlier: 4.678A pdb=" N TYR3d 303 " --> pdb=" O ASN3d 299 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY3d 304 " --> pdb=" O HIS3d 300 " (cutoff:3.500A) Processing helix chain '3d' and resid 309 through 314 Processing helix chain '3d' and resid 44 through 49 removed outlier: 5.859A pdb=" N VAL3d 47 " --> pdb=" O VAL3d 44 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY3d 48 " --> pdb=" O THR3d 45 " (cutoff:3.500A) Processing helix chain '3d' and resid 91 through 96 removed outlier: 4.816A pdb=" N LEU3d 95 " --> pdb=" O TYR3d 92 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU3d 96 " --> pdb=" O ASP3d 93 " (cutoff:3.500A) Processing helix chain '3e' and resid 72 through 77 Processing helix chain '3e' and resid 84 through 120 removed outlier: 3.752A pdb=" N ARG3e 88 " --> pdb=" O GLU3e 84 " (cutoff:3.500A) Processing helix chain '3f' and resid 10 through 17 removed outlier: 3.847A pdb=" N ILE3f 14 " --> pdb=" O THR3f 10 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN3f 16 " --> pdb=" O SER3f 12 " (cutoff:3.500A) Processing helix chain '3f' and resid 20 through 33 Proline residue: 3f 30 - end of helix removed outlier: 3.886A pdb=" N LEU3f 33 " --> pdb=" O LYS3f 29 " (cutoff:3.500A) Processing helix chain '3f' and resid 34 through 50 removed outlier: 4.176A pdb=" N LEU3f 49 " --> pdb=" O LYS3f 45 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL3f 50 " --> pdb=" O LEU3f 46 " (cutoff:3.500A) Processing helix chain '3f' and resid 58 through 81 removed outlier: 3.749A pdb=" N LEU3f 62 " --> pdb=" O CYS3f 58 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS3f 72 " --> pdb=" O CYS3f 68 " (cutoff:3.500A) Proline residue: 3f 75 - end of helix removed outlier: 3.564A pdb=" N ILE3f 78 " --> pdb=" O GLN3f 74 " (cutoff:3.500A) Processing helix chain '3g' and resid 34 through 48 Processing helix chain '3g' and resid 50 through 60 removed outlier: 4.390A pdb=" N VAL3g 54 " --> pdb=" O GLY3g 50 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE3g 55 " --> pdb=" O PHE3g 51 " (cutoff:3.500A) Processing helix chain '3g' and resid 61 through 79 removed outlier: 3.754A pdb=" N TYR3g 68 " --> pdb=" O ALA3g 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG3g 69 " --> pdb=" O LYS3g 65 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP3g 70 " --> pdb=" O PHE3g 66 " (cutoff:3.500A) Processing helix chain '3g' and resid 81 through 87 removed outlier: 4.129A pdb=" N SER3g 85 " --> pdb=" O THR3g 81 " (cutoff:3.500A) Processing helix chain '3g' and resid 89 through 95 removed outlier: 4.502A pdb=" N ARG3g 95 " --> pdb=" O ARG3g 91 " (cutoff:3.500A) Processing helix chain '3g' and resid 96 through 106 Processing helix chain '3g' and resid 110 through 128 removed outlier: 4.962A pdb=" N MET3g 115 " --> pdb=" O THR3g 111 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL3g 125 " --> pdb=" O ARG3g 121 " (cutoff:3.500A) Processing helix chain '3g' and resid 135 through 145 removed outlier: 4.651A pdb=" N ARG3g 145 " --> pdb=" O GLU3g 141 " (cutoff:3.500A) Processing helix chain '3g' and resid 146 through 169 removed outlier: 3.797A pdb=" N THR3g 150 " --> pdb=" O GLN3g 146 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER3g 167 " --> pdb=" O ARG3g 163 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP3g 168 " --> pdb=" O GLU3g 164 " (cutoff:3.500A) Processing helix chain '3g' and resid 182 through 188 removed outlier: 4.781A pdb=" N GLN3g 188 " --> pdb=" O LEU3g 184 " (cutoff:3.500A) Processing helix chain '3g' and resid 194 through 201 removed outlier: 3.986A pdb=" N ARG3g 200 " --> pdb=" O GLU3g 196 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE3g 201 " --> pdb=" O ALA3g 197 " (cutoff:3.500A) Processing helix chain '3g' and resid 212 through 221 removed outlier: 3.825A pdb=" N ASN3g 220 " --> pdb=" O LYS3g 216 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY3g 221 " --> pdb=" O GLN3g 217 " (cutoff:3.500A) Processing helix chain '3g' and resid 231 through 250 removed outlier: 3.606A pdb=" N ALA3g 236 " --> pdb=" O ALA3g 232 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN3g 237 " --> pdb=" O ASP3g 233 " (cutoff:3.500A) Proline residue: 3g 250 - end of helix Processing helix chain '3g' and resid 261 through 273 Processing helix chain '3g' and resid 282 through 296 removed outlier: 3.681A pdb=" N ALA3g 296 " --> pdb=" O LEU3g 292 " (cutoff:3.500A) Processing helix chain '3g' and resid 315 through 320 removed outlier: 3.704A pdb=" N GLN3g 319 " --> pdb=" O PRO3g 315 " (cutoff:3.500A) Proline residue: 3g 320 - end of helix No H-bonds generated for 'chain '3g' and resid 315 through 320' Processing helix chain '3h' and resid 32 through 37 removed outlier: 4.208A pdb=" N LEU3h 36 " --> pdb=" O LYS3h 32 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE3h 37 " --> pdb=" O GLN3h 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3h' and resid 32 through 37' Processing helix chain '3h' and resid 40 through 45 removed outlier: 3.842A pdb=" N SER3h 44 " --> pdb=" O SER3h 40 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL3h 45 " --> pdb=" O VAL3h 41 " (cutoff:3.500A) No H-bonds generated for 'chain '3h' and resid 40 through 45' Processing helix chain '3h' and resid 64 through 69 removed outlier: 3.983A pdb=" N GLN3h 68 " --> pdb=" O SER3h 64 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE3h 69 " --> pdb=" O PRO3h 65 " (cutoff:3.500A) No H-bonds generated for 'chain '3h' and resid 64 through 69' Processing helix chain '3h' and resid 78 through 83 Processing helix chain '3h' and resid 95 through 124 removed outlier: 4.576A pdb=" N THR3h 99 " --> pdb=" O ARG3h 95 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE3h 102 " --> pdb=" O ARG3h 98 " (cutoff:3.500A) Proline residue: 3h 103 - end of helix Processing helix chain '3h' and resid 84 through 94 removed outlier: 3.552A pdb=" N VAL3h 91 " --> pdb=" O ARG3h 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP3h 92 " --> pdb=" O PHE3h 87 " (cutoff:3.500A) Processing helix chain '3i' and resid 23 through 28 removed outlier: 4.106A pdb=" N VAL3i 27 " --> pdb=" O PRO3i 23 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR3i 28 " --> pdb=" O TYR3i 24 " (cutoff:3.500A) No H-bonds generated for 'chain '3i' and resid 23 through 28' Processing helix chain '3i' and resid 40 through 45 removed outlier: 3.551A pdb=" N ALA3i 44 " --> pdb=" O GLY3i 40 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP3i 45 " --> pdb=" O LYS3i 41 " (cutoff:3.500A) No H-bonds generated for 'chain '3i' and resid 40 through 45' Processing helix chain '3i' and resid 46 through 63 removed outlier: 4.926A pdb=" N TYR3i 61 " --> pdb=" O GLU3i 57 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR3i 62 " --> pdb=" O ASN3i 58 " (cutoff:3.500A) Proline residue: 3i 63 - end of helix Processing helix chain '3i' and resid 64 through 94 Proline residue: 3i 84 - end of helix removed outlier: 3.549A pdb=" N ASN3i 93 " --> pdb=" O TYR3i 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA3i 94 " --> pdb=" O GLN3i 90 " (cutoff:3.500A) Processing helix chain '3i' and resid 97 through 112 Processing helix chain '3j' and resid 5 through 37 Proline residue: 3j 26 - end of helix Processing helix chain '3j' and resid 38 through 47 Processing helix chain '3l' and resid 15 through 37 Processing helix chain '4' and resid 3 through 37 removed outlier: 3.923A pdb=" N ILE 4 7 " --> pdb=" O ASN 4 3 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE 4 18 " --> pdb=" O ILE 4 14 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS 4 36 " --> pdb=" O PHE 4 32 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE 4 37 " --> pdb=" O TYR 4 33 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 89 removed outlier: 4.219A pdb=" N PHE 4 51 " --> pdb=" O SER 4 47 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP 4 88 " --> pdb=" O ASN 4 84 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE 4 89 " --> pdb=" O ILE 4 85 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 142 removed outlier: 4.170A pdb=" N ASP 4 138 " --> pdb=" O ILE 4 134 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR 4 139 " --> pdb=" O LEU 4 135 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG 4 140 " --> pdb=" O ALA 4 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU 4 141 " --> pdb=" O LEU 4 137 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR 4 142 " --> pdb=" O ASP 4 138 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 165 removed outlier: 4.859A pdb=" N PHE 4 150 " --> pdb=" O ILE 4 146 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER 4 151 " --> pdb=" O LYS 4 147 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE 4 152 " --> pdb=" O TYR 4 148 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR 4 153 " --> pdb=" O ILE 4 149 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 4 165 " --> pdb=" O VAL 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 189 removed outlier: 4.093A pdb=" N LEU 4 178 " --> pdb=" O CYS 4 174 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU 4 179 " --> pdb=" O TYR 4 175 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE 4 180 " --> pdb=" O GLU 4 176 " (cutoff:3.500A) Proline residue: 4 181 - end of helix Processing helix chain '4' and resid 194 through 225 removed outlier: 3.595A pdb=" N LEU 4 200 " --> pdb=" O ILE 4 196 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN 4 225 " --> pdb=" O ILE 4 221 " (cutoff:3.500A) Processing helix chain '4' and resid 228 through 236 removed outlier: 3.965A pdb=" N LEU 4 232 " --> pdb=" O GLU 4 228 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS 4 233 " --> pdb=" O PHE 4 229 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR 4 234 " --> pdb=" O ASN 4 230 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE 4 235 " --> pdb=" O ASP 4 231 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN 4 236 " --> pdb=" O LEU 4 232 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 228 through 236' Processing helix chain '4' and resid 238 through 258 removed outlier: 3.831A pdb=" N LYS 4 256 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) Proline residue: 4 258 - end of helix Processing helix chain '4' and resid 263 through 273 Processing helix chain '4' and resid 274 through 301 removed outlier: 5.023A pdb=" N VAL 4 286 " --> pdb=" O SER 4 282 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS 4 287 " --> pdb=" O GLY 4 283 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR 4 288 " --> pdb=" O PHE 4 284 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA 4 289 " --> pdb=" O LEU 4 285 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU 4 290 " --> pdb=" O VAL 4 286 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY 4 292 " --> pdb=" O THR 4 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE 4 300 " --> pdb=" O PHE 4 296 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE 4 301 " --> pdb=" O ASN 4 297 " (cutoff:3.500A) Processing helix chain '4' and resid 306 through 325 removed outlier: 3.522A pdb=" N LYS 4 323 " --> pdb=" O ASP 4 319 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET 4 324 " --> pdb=" O SER 4 320 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP 4 325 " --> pdb=" O SER 4 321 " (cutoff:3.500A) Processing helix chain '4' and resid 329 through 351 removed outlier: 3.541A pdb=" N ALA 4 348 " --> pdb=" O ILE 4 344 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE 4 349 " --> pdb=" O ILE 4 345 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N CYS 4 350 " --> pdb=" O TYR 4 346 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP 4 351 " --> pdb=" O LEU 4 347 " (cutoff:3.500A) Processing helix chain '4' and resid 355 through 386 removed outlier: 4.585A pdb=" N GLY 4 359 " --> pdb=" O CYS 4 355 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 4 360 " --> pdb=" O ALA 4 356 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA 4 365 " --> pdb=" O ILE 4 361 " (cutoff:3.500A) Processing helix chain '4' and resid 395 through 400 removed outlier: 4.338A pdb=" N ILE 4 399 " --> pdb=" O GLY 4 395 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR 4 400 " --> pdb=" O ILE 4 396 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 395 through 400' Processing helix chain '4' and resid 401 through 416 Processing helix chain '4' and resid 420 through 437 removed outlier: 3.595A pdb=" N ILE 4 424 " --> pdb=" O THR 4 420 " (cutoff:3.500A) Processing helix chain '4' and resid 438 through 465 removed outlier: 3.699A pdb=" N LEU 4 451 " --> pdb=" O VAL 4 447 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY 4 452 " --> pdb=" O ALA 4 448 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU 4 453 " --> pdb=" O ASN 4 449 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA 4 463 " --> pdb=" O SER 4 459 " (cutoff:3.500A) Processing helix chain '4' and resid 480 through 500 removed outlier: 4.364A pdb=" N TYR 4 499 " --> pdb=" O PHE 4 495 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE 4 500 " --> pdb=" O ILE 4 496 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 22 Processing helix chain '4L' and resid 25 through 52 Processing helix chain '4L' and resid 53 through 85 removed outlier: 4.720A pdb=" N LEU4L 57 " --> pdb=" O ASP4L 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER4L 58 " --> pdb=" O ILE4L 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN4L 83 " --> pdb=" O ILE4L 79 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN4L 85 " --> pdb=" O TYR4L 81 " (cutoff:3.500A) Processing helix chain '4L' and resid 89 through 94 removed outlier: 4.076A pdb=" N ASN4L 93 " --> pdb=" O ASN4L 89 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN4L 94 " --> pdb=" O THR4L 90 " (cutoff:3.500A) No H-bonds generated for 'chain '4L' and resid 89 through 94' Processing helix chain '5' and resid 164 through 171 Proline residue: 5 171 - end of helix Processing helix chain '5' and resid 172 through 191 Processing helix chain '5' and resid 195 through 222 removed outlier: 4.118A pdb=" N ASN 5 219 " --> pdb=" O LEU 5 215 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU 5 220 " --> pdb=" O TYR 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 276 removed outlier: 3.726A pdb=" N PHE 5 257 " --> pdb=" O THR 5 253 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU 5 260 " --> pdb=" O SER 5 256 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE 5 273 " --> pdb=" O TYR 5 269 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER 5 274 " --> pdb=" O ILE 5 270 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE 5 276 " --> pdb=" O THR 5 272 " (cutoff:3.500A) Processing helix chain '5' and resid 281 through 302 removed outlier: 3.722A pdb=" N SER 5 302 " --> pdb=" O LEU 5 298 " (cutoff:3.500A) Processing helix chain '5' and resid 304 through 325 removed outlier: 4.380A pdb=" N ASN 5 324 " --> pdb=" O PHE 5 320 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE 5 325 " --> pdb=" O PHE 5 321 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 361 removed outlier: 3.532A pdb=" N ALA 5 335 " --> pdb=" O GLY 5 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA 5 339 " --> pdb=" O ALA 5 335 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 378 removed outlier: 5.966A pdb=" N TYR 5 374 " --> pdb=" O ASN 5 370 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU 5 375 " --> pdb=" O ASN 5 371 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR 5 376 " --> pdb=" O GLN 5 372 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU 5 377 " --> pdb=" O ILE 5 373 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER 5 378 " --> pdb=" O TYR 5 374 " (cutoff:3.500A) Processing helix chain '5' and resid 389 through 407 Processing helix chain '5' and resid 412 through 419 Proline residue: 5 416 - end of helix removed outlier: 4.059A pdb=" N MET 5 419 " --> pdb=" O LEU 5 415 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 412 through 419' Processing helix chain '5' and resid 422 through 431 Processing helix chain '5' and resid 434 through 446 removed outlier: 4.352A pdb=" N GLY 5 438 " --> pdb=" O LEU 5 434 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE 5 439 " --> pdb=" O VAL 5 435 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 5 446 " --> pdb=" O LEU 5 442 " (cutoff:3.500A) Processing helix chain '5' and resid 447 through 453 removed outlier: 5.718A pdb=" N LYS 5 453 " --> pdb=" O PHE 5 449 " (cutoff:3.500A) Processing helix chain '5' and resid 454 through 477 Proline residue: 5 460 - end of helix removed outlier: 3.674A pdb=" N PHE 5 476 " --> pdb=" O LEU 5 472 " (cutoff:3.500A) Processing helix chain '5' and resid 479 through 502 removed outlier: 3.981A pdb=" N GLY 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) Processing helix chain '5' and resid 503 through 533 removed outlier: 3.837A pdb=" N VAL 5 507 " --> pdb=" O VAL 5 503 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE 5 508 " --> pdb=" O LEU 5 504 " (cutoff:3.500A) Processing helix chain '5' and resid 537 through 542 removed outlier: 4.296A pdb=" N MET 5 541 " --> pdb=" O ASP 5 537 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY 5 542 " --> pdb=" O PHE 5 538 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 537 through 542' Processing helix chain '5' and resid 544 through 549 Proline residue: 5 549 - end of helix Processing helix chain '5' and resid 550 through 563 Processing helix chain '5' and resid 568 through 581 removed outlier: 4.209A pdb=" N TYR 5 572 " --> pdb=" O THR 5 568 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE 5 573 " --> pdb=" O LEU 5 569 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 5 574 " --> pdb=" O GLY 5 570 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU 5 581 " --> pdb=" O LEU 5 577 " (cutoff:3.500A) Processing helix chain '5' and resid 587 through 614 removed outlier: 3.724A pdb=" N ALA 5 601 " --> pdb=" O LEU 5 597 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY 5 602 " --> pdb=" O GLY 5 598 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL 5 603 " --> pdb=" O ALA 5 599 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE 5 604 " --> pdb=" O ILE 5 600 " (cutoff:3.500A) Processing helix chain '5' and resid 621 through 630 removed outlier: 3.942A pdb=" N TYR 5 625 " --> pdb=" O LYS 5 621 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER 5 629 " --> pdb=" O TYR 5 625 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 5 630 " --> pdb=" O LEU 5 626 " (cutoff:3.500A) Processing helix chain '5' and resid 642 through 668 Processing helix chain '5' and resid 684 through 691 removed outlier: 4.221A pdb=" N TYR 5 688 " --> pdb=" O ASN 5 684 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 5 689 " --> pdb=" O ALA 5 685 " (cutoff:3.500A) Processing helix chain '5' and resid 693 through 716 removed outlier: 3.657A pdb=" N LEU 5 703 " --> pdb=" O ALA 5 699 " (cutoff:3.500A) Processing helix chain '5' and resid 724 through 748 Processing helix chain '5B' and resid 4 through 9 removed outlier: 4.379A pdb=" N LYS5B 8 " --> pdb=" O ASN5B 4 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N PHE5B 9 " --> pdb=" O LYS5B 5 " (cutoff:3.500A) No H-bonds generated for 'chain '5B' and resid 4 through 9' Processing helix chain '5B' and resid 10 through 18 removed outlier: 3.750A pdb=" N GLY5B 18 " --> pdb=" O PHE5B 14 " (cutoff:3.500A) Processing helix chain '5B' and resid 20 through 36 Processing helix chain '5B' and resid 54 through 70 removed outlier: 5.035A pdb=" N ILE5B 58 " --> pdb=" O THR5B 54 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE5B 68 " --> pdb=" O ASN5B 64 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN5B 69 " --> pdb=" O ASN5B 65 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE5B 70 " --> pdb=" O ASN5B 66 " (cutoff:3.500A) Processing helix chain '5B' and resid 74 through 99 Processing helix chain '5B' and resid 37 through 53 removed outlier: 3.636A pdb=" N GLU5B 46 " --> pdb=" O SER5B 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS5B 47 " --> pdb=" O ILE5B 42 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE5B 48 " --> pdb=" O PHE5B 43 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 28 removed outlier: 4.359A pdb=" N PHE 6 16 " --> pdb=" O ASN 6 12 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN 6 22 " --> pdb=" O SER 6 18 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU 6 23 " --> pdb=" O TYR 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 32 through 52 Processing helix chain '6' and resid 54 through 77 Processing helix chain '6' and resid 78 through 104 removed outlier: 3.547A pdb=" N THR 6 82 " --> pdb=" O LEU 6 78 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL 6 87 " --> pdb=" O GLY 6 83 " (cutoff:3.500A) Processing helix chain '6' and resid 114 through 121 Processing helix chain '6' and resid 122 through 133 Processing helix chain '6' and resid 151 through 156 removed outlier: 3.770A pdb=" N TYR 6 155 " --> pdb=" O PHE 6 151 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP 6 156 " --> pdb=" O ILE 6 152 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 151 through 156' Processing helix chain '6' and resid 157 through 164 removed outlier: 3.719A pdb=" N GLY 6 161 " --> pdb=" O ASP 6 157 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN 6 163 " --> pdb=" O TYR 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 170 through 178 Processing helix chain '6' and resid 181 through 221 removed outlier: 3.976A pdb=" N TYR 6 209 " --> pdb=" O SER 6 205 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR 6 210 " --> pdb=" O ASN 6 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE 6 211 " --> pdb=" O LYS 6 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL 6 212 " --> pdb=" O ASN 6 208 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS 6 213 " --> pdb=" O TYR 6 209 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN 6 214 " --> pdb=" O THR 6 210 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER 6 215 " --> pdb=" O ILE 6 211 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN 6 216 " --> pdb=" O VAL 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 237 through 244 removed outlier: 3.747A pdb=" N PHE 6 244 " --> pdb=" O ASN 6 240 " (cutoff:3.500A) Processing helix chain 'A2' and resid 2 through 8 removed outlier: 3.552A pdb=" N LYSA2 6 " --> pdb=" O SERA2 2 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEUA2 7 " --> pdb=" O SERA2 3 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILEA2 8 " --> pdb=" O TRPA2 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A2' and resid 2 through 8' Processing helix chain 'A2' and resid 23 through 36 removed outlier: 3.661A pdb=" N LEUA2 27 " --> pdb=" O SERA2 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLYA2 28 " --> pdb=" O GLNA2 24 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEUA2 29 " --> pdb=" O ARGA2 25 " (cutoff:3.500A) Processing helix chain 'A2' and resid 37 through 45 removed outlier: 3.644A pdb=" N GLNA2 43 " --> pdb=" O ASNA2 39 " (cutoff:3.500A) Proline residue: A2 45 - end of helix Processing helix chain 'A2' and resid 79 through 93 removed outlier: 3.580A pdb=" N GLNA2 93 " --> pdb=" O THRA2 89 " (cutoff:3.500A) Processing helix chain 'A5' and resid 48 through 53 removed outlier: 3.629A pdb=" N TYRA5 52 " --> pdb=" O ASNA5 48 " (cutoff:3.500A) Processing helix chain 'A5' and resid 73 through 93 removed outlier: 3.591A pdb=" N LYSA5 77 " --> pdb=" O META5 73 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLUA5 91 " --> pdb=" O HISA5 87 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILEA5 92 " --> pdb=" O LYSA5 88 " (cutoff:3.500A) Proline residue: A5 93 - end of helix Processing helix chain 'A5' and resid 96 through 117 removed outlier: 5.114A pdb=" N GLUA5 117 " --> pdb=" O THRA5 113 " (cutoff:3.500A) Processing helix chain 'A5' and resid 118 through 127 removed outlier: 4.190A pdb=" N PHEA5 126 " --> pdb=" O LEUA5 122 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLYA5 127 " --> pdb=" O GLUA5 123 " (cutoff:3.500A) Processing helix chain 'A5' and resid 130 through 148 removed outlier: 3.805A pdb=" N PHEA5 134 " --> pdb=" O SERA5 130 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLUA5 143 " --> pdb=" O GLYA5 139 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEUA5 144 " --> pdb=" O LYSA5 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VALA5 145 " --> pdb=" O GLUA5 141 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLUA5 146 " --> pdb=" O LEUA5 142 " (cutoff:3.500A) Processing helix chain 'A5' and resid 159 through 172 removed outlier: 3.504A pdb=" N GLNA5 163 " --> pdb=" O GLYA5 159 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SERA5 171 " --> pdb=" O ILEA5 167 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLNA5 172 " --> pdb=" O ARGA5 168 " (cutoff:3.500A) Processing helix chain 'A6' and resid 48 through 75 removed outlier: 3.599A pdb=" N ALAA6 52 " --> pdb=" O ASNA6 48 " (cutoff:3.500A) Proline residue: A6 68 - end of helix Processing helix chain 'A6' and resid 76 through 81 removed outlier: 3.937A pdb=" N PHEA6 80 " --> pdb=" O ILEA6 76 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THRA6 81 " --> pdb=" O GLYA6 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A6' and resid 76 through 81' Processing helix chain 'A6' and resid 82 through 98 removed outlier: 4.973A pdb=" N HISA6 98 " --> pdb=" O ARGA6 94 " (cutoff:3.500A) Processing helix chain 'A6' and resid 101 through 122 removed outlier: 3.558A pdb=" N HISA6 122 " --> pdb=" O GLUA6 118 " (cutoff:3.500A) Processing helix chain 'A6' and resid 125 through 134 removed outlier: 4.971A pdb=" N GLNA6 131 " --> pdb=" O THRA6 127 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYRA6 132 " --> pdb=" O ILEA6 128 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEUA6 133 " --> pdb=" O LEUA6 129 " (cutoff:3.500A) Processing helix chain 'A6' and resid 147 through 154 removed outlier: 3.632A pdb=" N GLYA6 154 " --> pdb=" O LYSA6 150 " (cutoff:3.500A) Processing helix chain 'A6' and resid 157 through 166 removed outlier: 4.600A pdb=" N GLYA6 166 " --> pdb=" O GLYA6 162 " (cutoff:3.500A) Processing helix chain 'A7' and resid 2 through 14 removed outlier: 3.956A pdb=" N GLUA7 6 " --> pdb=" O ARGA7 2 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASNA7 14 " --> pdb=" O GLUA7 10 " (cutoff:3.500A) Processing helix chain 'A7' and resid 41 through 46 removed outlier: 4.586A pdb=" N HISA7 45 " --> pdb=" O ASNA7 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLNA7 46 " --> pdb=" O ARGA7 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A7' and resid 41 through 46' Processing helix chain 'A7' and resid 83 through 92 removed outlier: 3.761A pdb=" N GLYA7 92 " --> pdb=" O LEUA7 88 " (cutoff:3.500A) Processing helix chain 'A7' and resid 101 through 116 Processing helix chain 'A7' and resid 140 through 162 removed outlier: 4.045A pdb=" N VALA7 144 " --> pdb=" O ASNA7 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAA7 145 " --> pdb=" O ARGA7 141 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLUA7 162 " --> pdb=" O VALA7 158 " (cutoff:3.500A) Processing helix chain 'A7' and resid 167 through 173 Processing helix chain 'A7' and resid 183 through 189 removed outlier: 3.808A pdb=" N ASPA7 187 " --> pdb=" O ASPA7 183 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASPA7 188 " --> pdb=" O META7 184 " (cutoff:3.500A) Proline residue: A7 189 - end of helix No H-bonds generated for 'chain 'A7' and resid 183 through 189' Processing helix chain 'A7' and resid 190 through 213 removed outlier: 3.663A pdb=" N LEUA7 212 " --> pdb=" O ARGA7 208 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLYA7 213 " --> pdb=" O ARGA7 209 " (cutoff:3.500A) Processing helix chain 'A7' and resid 221 through 226 removed outlier: 4.512A pdb=" N TRPA7 225 " --> pdb=" O ASPA7 221 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLNA7 226 " --> pdb=" O PROA7 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A7' and resid 221 through 226' Processing helix chain 'A7' and resid 233 through 245 Processing helix chain 'A7' and resid 252 through 260 removed outlier: 3.683A pdb=" N LEUA7 258 " --> pdb=" O LYSA7 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASNA7 259 " --> pdb=" O ALAA7 255 " (cutoff:3.500A) Processing helix chain 'A9' and resid 52 through 66 Proline residue: A9 56 - end of helix removed outlier: 4.667A pdb=" N ILEA9 65 " --> pdb=" O ALAA9 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLYA9 66 " --> pdb=" O LEUA9 62 " (cutoff:3.500A) Processing helix chain 'A9' and resid 80 through 91 removed outlier: 4.841A pdb=" N LEUA9 86 " --> pdb=" O TYRA9 82 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYSA9 87 " --> pdb=" O VALA9 83 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEUA9 88 " --> pdb=" O LYSA9 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYSA9 89 " --> pdb=" O GLUA9 85 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALAA9 90 " --> pdb=" O LEUA9 86 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLYA9 91 " --> pdb=" O LYSA9 87 " (cutoff:3.500A) Processing helix chain 'A9' and resid 105 through 114 removed outlier: 3.601A pdb=" N TYRA9 109 " --> pdb=" O ASPA9 105 " (cutoff:3.500A) Processing helix chain 'A9' and resid 131 through 154 removed outlier: 3.524A pdb=" N HISA9 141 " --> pdb=" O TYRA9 137 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VALA9 142 " --> pdb=" O ALAA9 138 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALAA9 143 " --> pdb=" O ASNA9 139 " (cutoff:3.500A) Proline residue: A9 154 - end of helix Processing helix chain 'A9' and resid 173 through 190 Processing helix chain 'A9' and resid 208 through 220 removed outlier: 3.541A pdb=" N TRPA9 212 " --> pdb=" O PHEA9 208 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYRA9 220 " --> pdb=" O ARGA9 216 " (cutoff:3.500A) Processing helix chain 'A9' and resid 237 through 252 removed outlier: 3.620A pdb=" N VALA9 241 " --> pdb=" O LEUA9 237 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAA9 242 " --> pdb=" O ILEA9 238 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLNA9 243 " --> pdb=" O ASNA9 239 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLNA9 252 " --> pdb=" O ALAA9 248 " (cutoff:3.500A) Processing helix chain 'A9' and resid 268 through 281 Processing helix chain 'A9' and resid 290 through 301 Processing helix chain 'A9' and resid 308 through 318 removed outlier: 3.880A pdb=" N VALA9 312 " --> pdb=" O ASNA9 308 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYSA9 316 " --> pdb=" O VALA9 312 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEUA9 317 " --> pdb=" O ILEA9 313 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASPA9 318 " --> pdb=" O LYSA9 314 " (cutoff:3.500A) Processing helix chain 'A9' and resid 327 through 332 removed outlier: 3.872A pdb=" N LEUA9 331 " --> pdb=" O THRA9 327 " (cutoff:3.500A) Processing helix chain 'A9' and resid 337 through 348 removed outlier: 3.770A pdb=" N GLUA9 343 " --> pdb=" O PROA9 339 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLNA9 344 " --> pdb=" O GLNA9 340 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHEA9 345 " --> pdb=" O GLYA9 341 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILEA9 346 " --> pdb=" O ALAA9 342 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASPA9 347 " --> pdb=" O GLUA9 343 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASPA9 348 " --> pdb=" O GLNA9 344 " (cutoff:3.500A) Processing helix chain 'A9' and resid 356 through 361 removed outlier: 4.002A pdb=" N LEUA9 360 " --> pdb=" O THRA9 356 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLUA9 361 " --> pdb=" O HISA9 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A9' and resid 356 through 361' Processing helix chain 'AB' and resid 59 through 75 removed outlier: 4.405A pdb=" N ASNAB 73 " --> pdb=" O LYSAB 69 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHEAB 74 " --> pdb=" O VALAB 70 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLUAB 75 " --> pdb=" O LEUAB 71 " (cutoff:3.500A) Processing helix chain 'AB' and resid 87 through 92 removed outlier: 3.525A pdb=" N GLYAB 92 " --> pdb=" O PHEAB 88 " (cutoff:3.500A) Processing helix chain 'AB' and resid 94 through 110 Processing helix chain 'AB' and resid 114 through 121 Processing helix chain 'AB' and resid 123 through 135 removed outlier: 3.772A pdb=" N VALAB 127 " --> pdb=" O ASNAB 123 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILEAB 135 " --> pdb=" O ILEAB 131 " (cutoff:3.500A) Processing helix chain 'AC' and resid 53 through 68 removed outlier: 3.809A pdb=" N HISAC 68 " --> pdb=" O LEUAC 64 " (cutoff:3.500A) Processing helix chain 'AC' and resid 82 through 87 Processing helix chain 'AC' and resid 89 through 105 Processing helix chain 'AC' and resid 109 through 117 removed outlier: 5.806A pdb=" N ARGAC 117 " --> pdb=" O LEUAC 113 " (cutoff:3.500A) Processing helix chain 'AC' and resid 118 through 129 removed outlier: 3.690A pdb=" N ALAAC 122 " --> pdb=" O THRAC 118 " (cutoff:3.500A) Processing helix chain 'AL' and resid 7 through 13 removed outlier: 4.239A pdb=" N LEUAL 12 " --> pdb=" O ILEAL 8 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THRAL 13 " --> pdb=" O ASNAL 9 " (cutoff:3.500A) Processing helix chain 'AL' and resid 14 through 23 Processing helix chain 'AL' and resid 24 through 36 removed outlier: 3.739A pdb=" N THRAL 28 " --> pdb=" O GLYAL 24 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLYAL 32 " --> pdb=" O THRAL 28 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HISAL 33 " --> pdb=" O TRPAL 29 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SERAL 36 " --> pdb=" O GLYAL 32 " (cutoff:3.500A) Processing helix chain 'AL' and resid 95 through 104 Processing helix chain 'AL' and resid 148 through 161 removed outlier: 4.064A pdb=" N PHEAL 152 " --> pdb=" O ASNAL 148 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SERAL 160 " --> pdb=" O GLNAL 156 " (cutoff:3.500A) Processing helix chain 'AL' and resid 188 through 193 removed outlier: 3.992A pdb=" N ILEAL 192 " --> pdb=" O ASPAL 188 " (cutoff:3.500A) Processing helix chain 'AM' and resid 31 through 39 Processing helix chain 'AM' and resid 47 through 90 Processing helix chain 'AM' and resid 91 through 117 Processing helix chain 'AM' and resid 120 through 129 removed outlier: 3.569A pdb=" N GLNAM 125 " --> pdb=" O GLUAM 121 " (cutoff:3.500A) Processing helix chain 'AM' and resid 157 through 167 removed outlier: 4.411A pdb=" N ARGAM 165 " --> pdb=" O VALAM 161 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRAM 166 " --> pdb=" O THRAM 162 " (cutoff:3.500A) Processing helix chain 'B7' and resid 17 through 25 Processing helix chain 'B7' and resid 27 through 34 removed outlier: 3.864A pdb=" N GLYB7 33 " --> pdb=" O ARGB7 29 " (cutoff:3.500A) Proline residue: B7 34 - end of helix Processing helix chain 'B7' and resid 35 through 50 Proline residue: B7 41 - end of helix Proline residue: B7 50 - end of helix Processing helix chain 'B7' and resid 52 through 59 Processing helix chain 'B7' and resid 66 through 85 removed outlier: 4.054A pdb=" N TYRB7 71 " --> pdb=" O LYSB7 67 " (cutoff:3.500A) Processing helix chain 'B7' and resid 86 through 96 removed outlier: 4.847A pdb=" N ASPB7 95 " --> pdb=" O ALAB7 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THRB7 96 " --> pdb=" O TYRB7 92 " (cutoff:3.500A) Processing helix chain 'B7' and resid 97 through 103 Processing helix chain 'B7' and resid 105 through 112 removed outlier: 4.179A pdb=" N SERB7 111 " --> pdb=" O THRB7 107 " (cutoff:3.500A) Processing helix chain 'B8' and resid 34 through 39 removed outlier: 5.002A pdb=" N ASNB8 38 " --> pdb=" O PROB8 34 " (cutoff:3.500A) Proline residue: B8 39 - end of helix No H-bonds generated for 'chain 'B8' and resid 34 through 39' Processing helix chain 'B8' and resid 77 through 103 removed outlier: 4.695A pdb=" N TYRB8 89 " --> pdb=" O SERB8 85 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRPB8 90 " --> pdb=" O GLNB8 86 " (cutoff:3.500A) Processing helix chain 'B8' and resid 116 through 121 removed outlier: 3.875A pdb=" N PHEB8 120 " --> pdb=" O ASPB8 116 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEUB8 121 " --> pdb=" O LEUB8 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 116 through 121' Processing helix chain 'B8' and resid 122 through 131 removed outlier: 3.712A pdb=" N TYRB8 128 " --> pdb=" O TYRB8 124 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARGB8 131 " --> pdb=" O GLNB8 127 " (cutoff:3.500A) Processing helix chain 'B8' and resid 160 through 195 removed outlier: 3.552A pdb=" N GLNB8 194 " --> pdb=" O LYSB8 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARGB8 195 " --> pdb=" O GLUB8 191 " (cutoff:3.500A) Processing helix chain 'BL' and resid 29 through 37 Processing helix chain 'BL' and resid 49 through 85 Processing helix chain 'BL' and resid 89 through 98 removed outlier: 4.897A pdb=" N LYSBL 97 " --> pdb=" O LYSBL 93 " (cutoff:3.500A) Processing helix chain 'BL' and resid 99 through 106 removed outlier: 4.003A pdb=" N SERBL 106 " --> pdb=" O ILEBL 102 " (cutoff:3.500A) Processing helix chain 'BL' and resid 120 through 140 Processing helix chain 'BL' and resid 152 through 173 removed outlier: 3.516A pdb=" N ALABL 157 " --> pdb=" O GLUBL 153 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERBL 158 " --> pdb=" O GLUBL 154 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYSBL 173 " --> pdb=" O LYSBL 169 " (cutoff:3.500A) Processing helix chain 'C1' and resid 188 through 214 removed outlier: 3.968A pdb=" N GLNC1 202 " --> pdb=" O HISC1 198 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEUC1 203 " --> pdb=" O ALAC1 199 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N HISC1 204 " --> pdb=" O LYSC1 200 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEUC1 205 " --> pdb=" O LYSC1 201 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYRC1 213 " --> pdb=" O HISC1 209 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEUC1 214 " --> pdb=" O ARGC1 210 " (cutoff:3.500A) Processing helix chain 'C1' and resid 218 through 223 removed outlier: 4.194A pdb=" N GLNC1 222 " --> pdb=" O SERC1 218 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYSC1 223 " --> pdb=" O ALAC1 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 218 through 223' Processing helix chain 'C1' and resid 226 through 232 Proline residue: C1 232 - end of helix Processing helix chain 'C1' and resid 245 through 250 removed outlier: 3.775A pdb=" N ARGC1 249 " --> pdb=" O GLYC1 245 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALAC1 250 " --> pdb=" O ASPC1 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 245 through 250' Processing helix chain 'C2' and resid 1 through 35 removed outlier: 3.615A pdb=" N GLNC2 5 " --> pdb=" O METC2 1 " (cutoff:3.500A) Processing helix chain 'C2' and resid 197 through 223 Processing helix chain 'C3' and resid 1 through 38 removed outlier: 3.550A pdb=" N GLUC3 11 " --> pdb=" O PHEC3 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYSC3 12 " --> pdb=" O ASPC3 8 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEUC3 18 " --> pdb=" O SERC3 14 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLYC3 19 " --> pdb=" O METC3 15 " (cutoff:3.500A) Proline residue: C3 20 - end of helix removed outlier: 3.563A pdb=" N ASNC3 35 " --> pdb=" O GLNC3 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEC3 36 " --> pdb=" O THRC3 32 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLNC3 37 " --> pdb=" O GLYC3 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLNC3 38 " --> pdb=" O LEUC3 34 " (cutoff:3.500A) Processing helix chain 'C3' and resid 195 through 221 removed outlier: 3.566A pdb=" N GLUC3 221 " --> pdb=" O ALAC3 217 " (cutoff:3.500A) Processing helix chain 'C3' and resid 223 through 240 Processing helix chain 'C3' and resid 241 through 254 Processing helix chain 'C3' and resid 258 through 266 removed outlier: 4.451A pdb=" N GLUC3 263 " --> pdb=" O GLYC3 259 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYRC3 264 " --> pdb=" O GLUC3 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILEC3 265 " --> pdb=" O GLUC3 261 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLUC3 266 " --> pdb=" O GLUC3 262 " (cutoff:3.500A) Processing helix chain 'C3' and resid 278 through 284 removed outlier: 3.989A pdb=" N PHEC3 282 " --> pdb=" O LEUC3 278 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYSC3 284 " --> pdb=" O SERC3 280 " (cutoff:3.500A) Processing helix chain 'C3' and resid 298 through 305 removed outlier: 4.541A pdb=" N TYRC3 304 " --> pdb=" O SERC3 300 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLNC3 305 " --> pdb=" O PHEC3 301 " (cutoff:3.500A) Processing helix chain 'C3' and resid 307 through 322 removed outlier: 3.711A pdb=" N TYRC3 311 " --> pdb=" O GLNC3 307 " (cutoff:3.500A) Proline residue: C3 322 - end of helix Processing helix chain 'C3' and resid 339 through 344 Processing helix chain 'TD' and resid 4 through 27 Proline residue: TD 19 - end of helix Proline residue: TD 27 - end of helix Processing helix chain 'TD' and resid 31 through 43 removed outlier: 3.567A pdb=" N ARGTD 43 " --> pdb=" O ARGTD 39 " (cutoff:3.500A) Processing helix chain 'TD' and resid 45 through 50 removed outlier: 4.232A pdb=" N VALTD 49 " --> pdb=" O ASPTD 45 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYSTD 50 " --> pdb=" O PHETD 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'TD' and resid 45 through 50' Processing helix chain 'TD' and resid 58 through 70 Processing helix chain 'J1' and resid 24 through 30 Processing helix chain 'J1' and resid 36 through 52 removed outlier: 3.937A pdb=" N LYSJ1 50 " --> pdb=" O LYSJ1 46 " (cutoff:3.500A) Processing helix chain 'J1' and resid 67 through 82 removed outlier: 4.278A pdb=" N VALJ1 82 " --> pdb=" O ALAJ1 78 " (cutoff:3.500A) Processing helix chain 'J1' and resid 83 through 94 removed outlier: 3.708A pdb=" N GLNJ1 94 " --> pdb=" O ASPJ1 90 " (cutoff:3.500A) Processing helix chain 'J1' and resid 130 through 147 removed outlier: 3.877A pdb=" N GLUJ1 134 " --> pdb=" O THRJ1 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYSJ1 145 " --> pdb=" O GLUJ1 141 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHEJ1 146 " --> pdb=" O GLUJ1 142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASNJ1 147 " --> pdb=" O ARGJ1 143 " (cutoff:3.500A) Processing helix chain 'J1' and resid 183 through 192 Processing helix chain 'J1' and resid 202 through 217 removed outlier: 3.842A pdb=" N ASNJ1 215 " --> pdb=" O ASNJ1 211 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASPJ1 216 " --> pdb=" O HISJ1 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGJ1 217 " --> pdb=" O GLNJ1 213 " (cutoff:3.500A) Processing helix chain 'J1' and resid 238 through 284 removed outlier: 5.271A pdb=" N VALJ1 258 " --> pdb=" O LEUJ1 254 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SERJ1 259 " --> pdb=" O THRJ1 255 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSJ1 278 " --> pdb=" O SERJ1 274 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLUJ1 279 " --> pdb=" O LEUJ1 275 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THRJ1 283 " --> pdb=" O GLUJ1 279 " (cutoff:3.500A) Processing helix chain 'FX' and resid 37 through 42 removed outlier: 3.698A pdb=" N LYSFX 41 " --> pdb=" O ARGFX 37 " (cutoff:3.500A) Processing helix chain 'FX' and resid 64 through 73 Processing helix chain 'FX' and resid 112 through 120 removed outlier: 3.554A pdb=" N GLYFX 120 " --> pdb=" O ARGFX 116 " (cutoff:3.500A) Processing helix chain 'FX' and resid 123 through 133 removed outlier: 3.706A pdb=" N SERFX 133 " --> pdb=" O ASNFX 129 " (cutoff:3.500A) Processing helix chain 'FX' and resid 143 through 148 removed outlier: 3.617A pdb=" N ILEFX 147 " --> pdb=" O LEUFX 143 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEUFX 148 " --> pdb=" O ALAFX 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'FX' and resid 143 through 148' Processing helix chain 'FX' and resid 167 through 172 removed outlier: 4.578A pdb=" N ASNFX 171 " --> pdb=" O VALFX 167 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N METFX 172 " --> pdb=" O TYRFX 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'FX' and resid 167 through 172' Processing helix chain 'T2' and resid 20 through 29 removed outlier: 4.015A pdb=" N ALAT2 24 " --> pdb=" O SERT2 20 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLNT2 25 " --> pdb=" O PROT2 21 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEUT2 26 " --> pdb=" O LEUT2 22 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILET2 28 " --> pdb=" O ALAT2 24 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASNT2 29 " --> pdb=" O GLNT2 25 " (cutoff:3.500A) Processing helix chain 'T2' and resid 45 through 64 removed outlier: 3.513A pdb=" N LEUT2 63 " --> pdb=" O GLYT2 59 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLYT2 64 " --> pdb=" O LEUT2 60 " (cutoff:3.500A) Processing helix chain 'T2' and resid 79 through 94 Processing helix chain 'T2' and resid 104 through 116 Processing helix chain 'T2' and resid 132 through 142 Proline residue: T2 142 - end of helix Processing helix chain 'T2' and resid 176 through 181 removed outlier: 3.788A pdb=" N ILET2 180 " --> pdb=" O LYST2 176 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N METT2 181 " --> pdb=" O PHET2 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'T2' and resid 176 through 181' Processing helix chain 'T2' and resid 211 through 227 Processing helix chain 'T2' and resid 242 through 249 Processing helix chain 'T2' and resid 250 through 256 Processing helix chain 'T2' and resid 267 through 279 removed outlier: 4.747A pdb=" N PHET2 277 " --> pdb=" O GLNT2 273 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYRT2 278 " --> pdb=" O THRT2 274 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASPT2 279 " --> pdb=" O ILET2 275 " (cutoff:3.500A) Processing helix chain 'T1' and resid 24 through 43 removed outlier: 4.372A pdb=" N LEUT1 29 " --> pdb=" O PROT1 25 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLNT1 30 " --> pdb=" O SERT1 26 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASNT1 43 " --> pdb=" O LYST1 39 " (cutoff:3.500A) Processing helix chain 'T1' and resid 53 through 60 removed outlier: 4.338A pdb=" N GLUT1 59 " --> pdb=" O LEUT1 55 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLYT1 60 " --> pdb=" O METT1 56 " (cutoff:3.500A) Processing helix chain 'T1' and resid 83 through 89 removed outlier: 3.792A pdb=" N ARGT1 89 " --> pdb=" O PHET1 85 " (cutoff:3.500A) Processing helix chain 'T1' and resid 95 through 113 removed outlier: 4.804A pdb=" N SERT1 113 " --> pdb=" O VALT1 109 " (cutoff:3.500A) Processing helix chain 'T1' and resid 114 through 120 Processing helix chain 'T1' and resid 132 through 151 Processing helix chain 'T1' and resid 168 through 175 removed outlier: 4.315A pdb=" N GLNT1 172 " --> pdb=" O ARGT1 168 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASPT1 173 " --> pdb=" O PHET1 169 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYRT1 174 " --> pdb=" O GLUT1 170 " (cutoff:3.500A) Processing helix chain 'T1' and resid 201 through 215 removed outlier: 4.309A pdb=" N GLYT1 205 " --> pdb=" O HIST1 201 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SERT1 215 " --> pdb=" O LEUT1 211 " (cutoff:3.500A) Processing helix chain 'T1' and resid 219 through 227 removed outlier: 4.941A pdb=" N SERT1 223 " --> pdb=" O ALAT1 219 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEUT1 224 " --> pdb=" O ASNT1 220 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VALT1 225 " --> pdb=" O VALT1 221 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THRT1 226 " --> pdb=" O LYST1 222 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALAT1 227 " --> pdb=" O SERT1 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'T1' and resid 219 through 227' Processing helix chain 'T1' and resid 235 through 258 Processing helix chain 'T1' and resid 274 through 295 Processing helix chain 'T1' and resid 302 through 307 removed outlier: 4.445A pdb=" N PHET1 306 " --> pdb=" O SERT1 302 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THRT1 307 " --> pdb=" O ARGT1 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'T1' and resid 302 through 307' Processing helix chain 'T1' and resid 314 through 329 removed outlier: 3.523A pdb=" N THRT1 328 " --> pdb=" O ALAT1 324 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LYST1 329 " --> pdb=" O VALT1 325 " (cutoff:3.500A) Processing helix chain 'T1' and resid 330 through 335 removed outlier: 3.782A pdb=" N LEUT1 334 " --> pdb=" O TYRT1 330 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLNT1 335 " --> pdb=" O LEUT1 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'T1' and resid 330 through 335' Processing helix chain 'T1' and resid 341 through 352 Processing helix chain 'T1' and resid 360 through 370 removed outlier: 4.345A pdb=" N SERT1 364 " --> pdb=" O GLYT1 360 " (cutoff:3.500A) Processing helix chain 'T1' and resid 380 through 391 Processing helix chain 'T1' and resid 395 through 402 Processing helix chain 'T1' and resid 415 through 430 removed outlier: 3.534A pdb=" N ASPT1 429 " --> pdb=" O ASPT1 425 " (cutoff:3.500A) Proline residue: T1 430 - end of helix Processing helix chain 'T1' and resid 431 through 448 removed outlier: 3.516A pdb=" N HIST1 435 " --> pdb=" O LYST1 431 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASNT1 442 " --> pdb=" O GLUT1 438 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VALT1 443 " --> pdb=" O ARGT1 439 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIST1 445 " --> pdb=" O GLNT1 441 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILET1 448 " --> pdb=" O VALT1 444 " (cutoff:3.500A) Processing helix chain 'T1' and resid 475 through 494 Processing helix chain 'A1' and resid 7 through 43 removed outlier: 3.703A pdb=" N ILEA1 13 " --> pdb=" O PROA1 9 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYSA1 15 " --> pdb=" O LYSA1 11 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THRA1 16 " --> pdb=" O THRA1 12 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THRA1 17 " --> pdb=" O ILEA1 13 " (cutoff:3.500A) Proline residue: A1 18 - end of helix Proline residue: A1 41 - end of helix Processing helix chain 'A1' and resid 53 through 69 removed outlier: 3.564A pdb=" N LYSA1 61 " --> pdb=" O ARGA1 57 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASPA1 63 " --> pdb=" O SERA1 59 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLUA1 64 " --> pdb=" O ARGA1 60 " (cutoff:3.500A) Processing helix chain 'A1' and resid 70 through 76 Processing helix chain 'X1' and resid 11 through 19 removed outlier: 4.436A pdb=" N ASNX1 15 " --> pdb=" O LEUX1 11 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEUX1 16 " --> pdb=" O GLYX1 12 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHEX1 17 " --> pdb=" O GLYX1 13 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYSX1 18 " --> pdb=" O LEUX1 14 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARGX1 19 " --> pdb=" O ASNX1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'X1' and resid 11 through 19' Processing helix chain 'X1' and resid 42 through 50 removed outlier: 3.571A pdb=" N PHEX1 50 " --> pdb=" O VALX1 46 " (cutoff:3.500A) Processing helix chain 'X1' and resid 51 through 76 removed outlier: 4.147A pdb=" N PHEX1 66 " --> pdb=" O ALAX1 62 " (cutoff:3.500A) Proline residue: X1 67 - end of helix removed outlier: 4.309A pdb=" N GLYX1 75 " --> pdb=" O TRPX1 71 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEUX1 76 " --> pdb=" O VALX1 72 " (cutoff:3.500A) Processing helix chain 'X1' and resid 80 through 113 Processing helix chain 'X1' and resid 134 through 141 removed outlier: 3.540A pdb=" N SERX1 141 " --> pdb=" O PHEX1 137 " (cutoff:3.500A) Processing helix chain 'X1' and resid 142 through 148 removed outlier: 4.314A pdb=" N LEUX1 146 " --> pdb=" O PHEX1 142 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILEX1 148 " --> pdb=" O LYSX1 144 " (cutoff:3.500A) Processing helix chain 'T6' and resid 39 through 47 removed outlier: 3.676A pdb=" N THRT6 46 " --> pdb=" O LEUT6 42 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYST6 47 " --> pdb=" O LEUT6 43 " (cutoff:3.500A) Processing helix chain 'T6' and resid 54 through 71 removed outlier: 3.828A pdb=" N ASPT6 70 " --> pdb=" O PHET6 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SERT6 71 " --> pdb=" O GLUT6 67 " (cutoff:3.500A) Processing helix chain 'T6' and resid 78 through 83 removed outlier: 4.466A pdb=" N CYST6 82 " --> pdb=" O ASNT6 78 " (cutoff:3.500A) Proline residue: T6 83 - end of helix No H-bonds generated for 'chain 'T6' and resid 78 through 83' Processing helix chain 'T6' and resid 84 through 93 Processing helix chain 'T6' and resid 94 through 115 removed outlier: 3.814A pdb=" N LEUT6 114 " --> pdb=" O LYST6 110 " (cutoff:3.500A) Processing helix chain 'T6' and resid 116 through 134 removed outlier: 4.069A pdb=" N TYRT6 132 " --> pdb=" O ASNT6 128 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLYT6 133 " --> pdb=" O LYST6 129 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILET6 134 " --> pdb=" O GLUT6 130 " (cutoff:3.500A) Processing helix chain 'T5' and resid 66 through 77 Processing helix chain 'T5' and resid 94 through 119 removed outlier: 3.812A pdb=" N TRPT5 98 " --> pdb=" O SERT5 94 " (cutoff:3.500A) Processing helix chain 'T5' and resid 125 through 146 removed outlier: 3.530A pdb=" N ILET5 129 " --> pdb=" O TRPT5 125 " (cutoff:3.500A) Proline residue: T5 133 - end of helix removed outlier: 3.581A pdb=" N ILET5 137 " --> pdb=" O PROT5 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILET5 138 " --> pdb=" O LEUT5 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SERT5 143 " --> pdb=" O SERT5 139 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLNT5 145 " --> pdb=" O GLYT5 141 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEUT5 146 " --> pdb=" O LYST5 142 " (cutoff:3.500A) Processing helix chain 'T5' and resid 155 through 164 removed outlier: 4.655A pdb=" N TYRT5 162 " --> pdb=" O GLNT5 158 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALAT5 163 " --> pdb=" O LYST5 159 " (cutoff:3.500A) Proline residue: T5 164 - end of helix Processing helix chain 'T5' and resid 165 through 191 Processing helix chain 'R' and resid 10 through 15 removed outlier: 4.226A pdb=" N PHE R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LYS R 15 " --> pdb=" O ASN R 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 10 through 15' Processing helix chain 'R' and resid 16 through 23 Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 41 through 75 Processing helix chain 'R' and resid 78 through 90 Proline residue: R 90 - end of helix Processing helix chain 'R' and resid 91 through 118 Proline residue: R 101 - end of helix removed outlier: 5.310A pdb=" N GLY R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'S1' and resid 49 through 58 Processing helix chain 'S1' and resid 107 through 126 removed outlier: 4.566A pdb=" N ASNS1 124 " --> pdb=" O PHES1 120 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HISS1 125 " --> pdb=" O LEUS1 121 " (cutoff:3.500A) Proline residue: S1 126 - end of helix Processing helix chain 'S1' and resid 138 through 147 Processing helix chain 'S1' and resid 173 through 178 removed outlier: 4.434A pdb=" N CYSS1 177 " --> pdb=" O SERS1 173 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILES1 178 " --> pdb=" O METS1 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 173 through 178' Processing helix chain 'S1' and resid 181 through 189 Processing helix chain 'S1' and resid 219 through 228 removed outlier: 4.216A pdb=" N VALS1 223 " --> pdb=" O LEUS1 219 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VALS1 224 " --> pdb=" O SERS1 220 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASPS1 225 " --> pdb=" O GLYS1 221 " (cutoff:3.500A) Proline residue: S1 228 - end of helix Processing helix chain 'S1' and resid 288 through 301 removed outlier: 4.962A pdb=" N PHES1 295 " --> pdb=" O THRS1 291 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASPS1 296 " --> pdb=" O ARGS1 292 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLYS1 297 " --> pdb=" O HISS1 293 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEUS1 298 " --> pdb=" O ALAS1 294 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYSS1 299 " --> pdb=" O PHES1 295 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARGS1 300 " --> pdb=" O ASPS1 296 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLNS1 301 " --> pdb=" O GLYS1 297 " (cutoff:3.500A) Processing helix chain 'S1' and resid 319 through 334 Processing helix chain 'S1' and resid 348 through 363 Processing helix chain 'S1' and resid 381 through 386 removed outlier: 4.463A pdb=" N TYRS1 385 " --> pdb=" O PHES1 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEUS1 386 " --> pdb=" O ARGS1 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 381 through 386' Processing helix chain 'S1' and resid 392 through 398 removed outlier: 3.645A pdb=" N ASPS1 396 " --> pdb=" O THRS1 392 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASPS1 398 " --> pdb=" O VALS1 394 " (cutoff:3.500A) Processing helix chain 'S1' and resid 406 through 411 Processing helix chain 'S1' and resid 412 through 425 removed outlier: 3.549A pdb=" N LYSS1 424 " --> pdb=" O LYSS1 420 " (cutoff:3.500A) Processing helix chain 'S1' and resid 448 through 457 Processing helix chain 'S1' and resid 459 through 469 removed outlier: 4.091A pdb=" N GLUS1 463 " --> pdb=" O HISS1 459 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYSS1 469 " --> pdb=" O LEUS1 465 " (cutoff:3.500A) Processing helix chain 'S1' and resid 476 through 482 removed outlier: 3.980A pdb=" N LEUS1 480 " --> pdb=" O GLYS1 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLUS1 481 " --> pdb=" O ALAS1 477 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARGS1 482 " --> pdb=" O SERS1 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 476 through 482' Processing helix chain 'S1' and resid 484 through 500 Processing helix chain 'S1' and resid 517 through 527 removed outlier: 3.514A pdb=" N ILES1 521 " --> pdb=" O GLUS1 517 " (cutoff:3.500A) Processing helix chain 'S1' and resid 550 through 555 removed outlier: 4.074A pdb=" N ILES1 554 " --> pdb=" O ARGS1 550 " (cutoff:3.500A) Proline residue: S1 555 - end of helix No H-bonds generated for 'chain 'S1' and resid 550 through 555' Processing helix chain 'S1' and resid 568 through 575 removed outlier: 5.899A pdb=" N TYRS1 572 " --> pdb=" O ASPS1 568 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYRS1 573 " --> pdb=" O GLUS1 569 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASPS1 575 " --> pdb=" O ALAS1 571 " (cutoff:3.500A) Processing helix chain 'S1' and resid 582 through 587 removed outlier: 3.784A pdb=" N LYSS1 586 " --> pdb=" O ALAS1 582 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASNS1 587 " --> pdb=" O TYRS1 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 582 through 587' Processing helix chain 'S1' and resid 612 through 625 Processing helix chain 'S1' and resid 632 through 644 Processing helix chain 'S1' and resid 645 through 650 removed outlier: 4.323A pdb=" N LYSS1 649 " --> pdb=" O PROS1 645 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYRS1 650 " --> pdb=" O HISS1 646 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 645 through 650' Processing helix chain 'S1' and resid 658 through 664 Processing helix chain 'S1' and resid 689 through 696 removed outlier: 3.543A pdb=" N SERS1 695 " --> pdb=" O ILES1 691 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VALS1 696 " --> pdb=" O SERS1 692 " (cutoff:3.500A) Processing helix chain 'S1' and resid 697 through 710 removed outlier: 5.240A pdb=" N HISS1 707 " --> pdb=" O THRS1 703 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLUS1 708 " --> pdb=" O ALAS1 704 " (cutoff:3.500A) Processing helix chain 'S2' and resid 4 through 10 removed outlier: 3.631A pdb=" N TRPS2 9 " --> pdb=" O ILES2 5 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYSS2 10 " --> pdb=" O PHES2 6 " (cutoff:3.500A) Processing helix chain 'S2' and resid 65 through 74 Proline residue: S2 74 - end of helix Processing helix chain 'S2' and resid 75 through 87 removed outlier: 3.580A pdb=" N METS2 79 " --> pdb=" O TYRS2 75 " (cutoff:3.500A) Proline residue: S2 80 - end of helix removed outlier: 3.746A pdb=" N ASPS2 83 " --> pdb=" O METS2 79 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASPS2 86 " --> pdb=" O PHES2 82 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYRS2 87 " --> pdb=" O ASPS2 83 " (cutoff:3.500A) Processing helix chain 'S2' and resid 89 through 106 removed outlier: 4.456A pdb=" N GLNS2 93 " --> pdb=" O SERS2 89 " (cutoff:3.500A) Processing helix chain 'S2' and resid 109 through 116 removed outlier: 3.538A pdb=" N THRS2 115 " --> pdb=" O SERS2 111 " (cutoff:3.500A) Processing helix chain 'S2' and resid 117 through 142 Processing helix chain 'S2' and resid 143 through 165 removed outlier: 5.089A pdb=" N VALS2 147 " --> pdb=" O SERS2 143 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHES2 148 " --> pdb=" O METS2 144 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRPS2 149 " --> pdb=" O SERS2 145 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAS2 150 " --> pdb=" O SERS2 146 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYSS2 156 " --> pdb=" O GLUS2 152 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEUS2 157 " --> pdb=" O GLUS2 153 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VALS2 164 " --> pdb=" O PHES2 160 " (cutoff:3.500A) Processing helix chain 'S2' and resid 180 through 185 removed outlier: 4.260A pdb=" N VALS2 184 " --> pdb=" O ASNS2 180 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N SERS2 185 " --> pdb=" O LEUS2 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 180 through 185' Processing helix chain 'S2' and resid 186 through 210 removed outlier: 3.565A pdb=" N GLUS2 190 " --> pdb=" O SERS2 186 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASPS2 191 " --> pdb=" O PHES2 187 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THRS2 201 " --> pdb=" O ARGS2 197 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VALS2 209 " --> pdb=" O GLUS2 205 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEUS2 210 " --> pdb=" O METS2 206 " (cutoff:3.500A) Processing helix chain 'S2' and resid 213 through 221 Processing helix chain 'S2' and resid 227 through 235 removed outlier: 3.997A pdb=" N GLYS2 235 " --> pdb=" O CYSS2 231 " (cutoff:3.500A) Processing helix chain 'S2' and resid 238 through 245 Processing helix chain 'S2' and resid 260 through 265 removed outlier: 3.772A pdb=" N LEUS2 264 " --> pdb=" O ASNS2 260 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASNS2 265 " --> pdb=" O TYRS2 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 260 through 265' Processing helix chain 'S2' and resid 275 through 302 Processing helix chain 'S2' and resid 321 through 327 removed outlier: 4.484A pdb=" N GLNS2 325 " --> pdb=" O ASNS2 321 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THRS2 326 " --> pdb=" O PHES2 322 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THRS2 327 " --> pdb=" O ASNS2 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 321 through 327' Processing helix chain 'S2' and resid 331 through 338 Processing helix chain 'S2' and resid 339 through 348 Processing helix chain 'S2' and resid 353 through 366 Processing helix chain 'S2' and resid 405 through 419 removed outlier: 4.056A pdb=" N HISS2 409 " --> pdb=" O SERS2 405 " (cutoff:3.500A) Proline residue: S2 415 - end of helix Processing helix chain 'S2' and resid 422 through 434 removed outlier: 4.926A pdb=" N ASPS2 434 " --> pdb=" O VALS2 430 " (cutoff:3.500A) Processing helix chain 'S2' and resid 436 through 442 Processing helix chain 'S3' and resid 8 through 16 removed outlier: 4.680A pdb=" N PHES3 12 " --> pdb=" O PROS3 8 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLUS3 16 " --> pdb=" O PHES3 12 " (cutoff:3.500A) Processing helix chain 'S3' and resid 38 through 52 removed outlier: 3.783A pdb=" N PHES3 42 " --> pdb=" O PROS3 38 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYRS3 43 " --> pdb=" O SERS3 39 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SERS3 44 " --> pdb=" O ASNS3 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARGS3 51 " --> pdb=" O LEUS3 47 " (cutoff:3.500A) Processing helix chain 'S3' and resid 84 through 90 removed outlier: 4.183A pdb=" N TYRS3 88 " --> pdb=" O ASNS3 84 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHES3 89 " --> pdb=" O ILES3 85 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHES3 90 " --> pdb=" O GLUS3 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'S3' and resid 84 through 90' Processing helix chain 'S3' and resid 125 through 130 removed outlier: 4.353A pdb=" N ALAS3 130 " --> pdb=" O ASPS3 126 " (cutoff:3.500A) Processing helix chain 'S3' and resid 131 through 144 removed outlier: 3.697A pdb=" N LEUS3 135 " --> pdb=" O ASNS3 131 " (cutoff:3.500A) Processing helix chain 'S4' and resid 13 through 19 removed outlier: 3.607A pdb=" N GLNS4 17 " --> pdb=" O TYRS4 13 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILES4 19 " --> pdb=" O GLUS4 15 " (cutoff:3.500A) Processing helix chain 'S4' and resid 26 through 33 Processing helix chain 'S4' and resid 34 through 43 Processing helix chain 'S4' and resid 138 through 150 Processing helix chain 'S4' and resid 167 through 173 removed outlier: 4.700A pdb=" N ASNS4 171 " --> pdb=" O SERS4 167 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N METS4 172 " --> pdb=" O TYRS4 168 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEUS4 173 " --> pdb=" O ALAS4 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'S4' and resid 167 through 173' Processing helix chain 'S6' and resid 41 through 49 removed outlier: 3.650A pdb=" N HISS6 49 " --> pdb=" O LEUS6 45 " (cutoff:3.500A) Processing helix chain 'S6' and resid 58 through 64 removed outlier: 5.061A pdb=" N TRPS6 62 " --> pdb=" O LYSS6 58 " (cutoff:3.500A) Processing helix chain 'S6' and resid 67 through 76 removed outlier: 3.824A pdb=" N VALS6 75 " --> pdb=" O LEUS6 71 " (cutoff:3.500A) Proline residue: S6 76 - end of helix Processing helix chain 'S7' and resid 2 through 22 removed outlier: 4.197A pdb=" N ILES7 6 " --> pdb=" O ARGS7 2 " (cutoff:3.500A) Proline residue: S7 9 - end of helix removed outlier: 3.913A pdb=" N ALAS7 12 " --> pdb=" O THRS7 8 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALS7 13 " --> pdb=" O PROS7 9 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHES7 22 " --> pdb=" O ARGS7 18 " (cutoff:3.500A) Processing helix chain 'S7' and resid 30 through 42 removed outlier: 4.102A pdb=" N VALS7 34 " --> pdb=" O ALAS7 30 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SERS7 42 " --> pdb=" O HISS7 38 " (cutoff:3.500A) Processing helix chain 'S7' and resid 45 through 50 removed outlier: 4.252A pdb=" N PHES7 49 " --> pdb=" O ASPS7 45 " (cutoff:3.500A) Processing helix chain 'S7' and resid 56 through 61 removed outlier: 3.514A pdb=" N ALAS7 60 " --> pdb=" O THRS7 56 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASPS7 61 " --> pdb=" O PROS7 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'S7' and resid 56 through 61' Processing helix chain 'S7' and resid 70 through 84 Proline residue: S7 75 - end of helix removed outlier: 3.508A pdb=" N THRS7 84 " --> pdb=" O LEUS7 80 " (cutoff:3.500A) Processing helix chain 'S7' and resid 94 through 99 Processing helix chain 'S7' and resid 112 through 117 removed outlier: 4.734A pdb=" N ILES7 116 " --> pdb=" O GLYS7 112 " (cutoff:3.500A) Processing helix chain 'S7' and resid 129 through 148 removed outlier: 4.301A pdb=" N ILES7 148 " --> pdb=" O LEUS7 144 " (cutoff:3.500A) Processing helix chain 'S8' and resid 51 through 57 removed outlier: 3.842A pdb=" N LEUS8 55 " --> pdb=" O ILES8 51 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASPS8 57 " --> pdb=" O GLUS8 53 " (cutoff:3.500A) Processing helix chain 'S8' and resid 58 through 63 removed outlier: 4.578A pdb=" N TYRS8 62 " --> pdb=" O ASPS8 58 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLYS8 63 " --> pdb=" O ILES8 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'S8' and resid 58 through 63' Processing helix chain 'S8' and resid 71 through 83 Processing helix chain 'S8' and resid 85 through 102 removed outlier: 4.734A pdb=" N PHES8 89 " --> pdb=" O CYSS8 85 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HISS8 91 " --> pdb=" O GLUS8 87 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHES8 92 " --> pdb=" O TYRS8 88 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VALS8 98 " --> pdb=" O PHES8 94 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLUS8 102 " --> pdb=" O VALS8 98 " (cutoff:3.500A) Processing helix chain 'S8' and resid 140 through 146 Processing helix chain 'S8' and resid 171 through 176 removed outlier: 5.988A pdb=" N ILES8 176 " --> pdb=" O METS8 172 " (cutoff:3.500A) Processing helix chain 'S8' and resid 179 through 186 Proline residue: S8 186 - end of helix Processing helix chain 'S8' and resid 202 through 208 removed outlier: 4.078A pdb=" N LEUS8 206 " --> pdb=" O LEUS8 202 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHES8 207 " --> pdb=" O HISS8 203 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYRS8 208 " --> pdb=" O GLUS8 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'S8' and resid 202 through 208' Processing helix chain 'S8' and resid 209 through 221 Processing helix chain 'S8' and resid 222 through 236 Proline residue: S8 235 - end of helix Processing helix chain 'B9' and resid 12 through 22 Processing helix chain 'B9' and resid 26 through 31 removed outlier: 4.761A pdb=" N LEUB9 30 " --> pdb=" O TYRB9 26 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASNB9 31 " --> pdb=" O PROB9 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B9' and resid 26 through 31' Processing helix chain 'B9' and resid 32 through 51 Processing helix chain 'B9' and resid 58 through 80 removed outlier: 3.701A pdb=" N ALAB9 78 " --> pdb=" O ASNB9 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEUB9 79 " --> pdb=" O LYSB9 75 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYSB9 80 " --> pdb=" O METB9 76 " (cutoff:3.500A) Processing helix chain 'B9' and resid 83 through 101 Processing helix chain 'B9' and resid 124 through 130 removed outlier: 3.613A pdb=" N PHEB9 130 " --> pdb=" O TYRB9 126 " (cutoff:3.500A) Processing helix chain 'B9' and resid 177 through 187 Processing helix chain 'TX' and resid 30 through 42 Processing helix chain 'TX' and resid 57 through 73 removed outlier: 3.529A pdb=" N ALATX 61 " --> pdb=" O LEUTX 57 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYSTX 63 " --> pdb=" O GLUTX 59 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEUTX 73 " --> pdb=" O SERTX 69 " (cutoff:3.500A) Processing helix chain 'TX' and resid 81 through 86 Proline residue: TX 86 - end of helix Processing helix chain 'TX' and resid 87 through 93 Processing helix chain 'TX' and resid 116 through 135 removed outlier: 5.482A pdb=" N ASNTX 135 " --> pdb=" O VALTX 131 " (cutoff:3.500A) Processing helix chain 'TX' and resid 145 through 166 removed outlier: 4.166A pdb=" N GLNTX 149 " --> pdb=" O GLUTX 145 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYRTX 150 " --> pdb=" O PHETX 146 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLNTX 156 " --> pdb=" O ALATX 152 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYSTX 159 " --> pdb=" O THRTX 155 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLUTX 160 " --> pdb=" O GLNTX 156 " (cutoff:3.500A) Processing helix chain 'A8' and resid 111 through 122 removed outlier: 4.192A pdb=" N TYRA8 120 " --> pdb=" O ILEA8 116 " (cutoff:3.500A) Processing helix chain 'A8' and resid 125 through 137 Processing helix chain 'A8' and resid 145 through 165 removed outlier: 4.137A pdb=" N CYSA8 149 " --> pdb=" O ASPA8 145 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ALAA8 151 " --> pdb=" O ILEA8 147 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLNA8 152 " --> pdb=" O HISA8 148 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLUA8 162 " --> pdb=" O SERA8 158 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYSA8 165 " --> pdb=" O LYSA8 161 " (cutoff:3.500A) Processing helix chain 'A8' and resid 167 through 185 removed outlier: 4.095A pdb=" N LEUA8 171 " --> pdb=" O ASPA8 167 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SERA8 172 " --> pdb=" O PROA8 168 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SERA8 173 " --> pdb=" O ILEA8 169 " (cutoff:3.500A) Processing helix chain 'A8' and resid 187 through 192 Processing helix chain 'A8' and resid 193 through 205 removed outlier: 3.536A pdb=" N CYSA8 201 " --> pdb=" O GLNA8 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASNA8 204 " --> pdb=" O THRA8 200 " (cutoff:3.500A) Proline residue: A8 205 - end of helix Processing helix chain 'A8' and resid 206 through 215 removed outlier: 4.889A pdb=" N GLUA8 210 " --> pdb=" O ALAA8 206 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHEA8 211 " --> pdb=" O ALAA8 207 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SERA8 215 " --> pdb=" O PHEA8 211 " (cutoff:3.500A) Processing helix chain 'A8' and resid 216 through 221 removed outlier: 4.177A pdb=" N LYSA8 221 " --> pdb=" O ALAA8 217 " (cutoff:3.500A) Processing helix chain 'A8' and resid 226 through 231 removed outlier: 4.362A pdb=" N ARGA8 231 " --> pdb=" O PHEA8 227 " (cutoff:3.500A) Processing helix chain 'TB' and resid 74 through 100 removed outlier: 3.540A pdb=" N GLYTB 100 " --> pdb=" O ALATB 96 " (cutoff:3.500A) Processing helix chain 'V1' and resid 52 through 60 Processing helix chain 'V1' and resid 64 through 72 removed outlier: 3.604A pdb=" N ASNV1 71 " --> pdb=" O GLUV1 67 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLYV1 72 " --> pdb=" O ILEV1 68 " (cutoff:3.500A) Processing helix chain 'V1' and resid 73 through 84 removed outlier: 3.620A pdb=" N GLYV1 84 " --> pdb=" O ILEV1 80 " (cutoff:3.500A) Processing helix chain 'V1' and resid 94 through 102 removed outlier: 4.067A pdb=" N METV1 102 " --> pdb=" O LYSV1 98 " (cutoff:3.500A) Processing helix chain 'V1' and resid 126 through 135 removed outlier: 3.932A pdb=" N GLUV1 130 " --> pdb=" O CYSV1 126 " (cutoff:3.500A) Processing helix chain 'V1' and resid 136 through 151 Processing helix chain 'V1' and resid 163 through 181 Processing helix chain 'V1' and resid 204 through 209 removed outlier: 4.399A pdb=" N GLYV1 208 " --> pdb=" O ALAV1 204 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLUV1 209 " --> pdb=" O TYRV1 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'V1' and resid 204 through 209' Processing helix chain 'V1' and resid 210 through 219 removed outlier: 3.884A pdb=" N GLYV1 219 " --> pdb=" O GLUV1 215 " (cutoff:3.500A) Processing helix chain 'V1' and resid 245 through 259 removed outlier: 3.613A pdb=" N VALV1 249 " --> pdb=" O ASNV1 245 " (cutoff:3.500A) Proline residue: V1 253 - end of helix Processing helix chain 'V1' and resid 260 through 266 removed outlier: 4.107A pdb=" N PHEV1 266 " --> pdb=" O TRPV1 262 " (cutoff:3.500A) Processing helix chain 'V1' and resid 296 through 304 Processing helix chain 'V1' and resid 329 through 336 removed outlier: 4.732A pdb=" N ASPV1 335 " --> pdb=" O ASNV1 331 " (cutoff:3.500A) Processing helix chain 'V1' and resid 339 through 347 removed outlier: 3.738A pdb=" N VALV1 346 " --> pdb=" O ALAV1 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLYV1 347 " --> pdb=" O LEUV1 343 " (cutoff:3.500A) Processing helix chain 'V1' and resid 363 through 379 Processing helix chain 'V1' and resid 383 through 403 removed outlier: 4.585A pdb=" N GLYV1 391 " --> pdb=" O ARGV1 387 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGV1 399 " --> pdb=" O ASPV1 395 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALV1 402 " --> pdb=" O GLUV1 398 " (cutoff:3.500A) Processing helix chain 'V1' and resid 406 through 424 removed outlier: 4.040A pdb=" N ILEV1 410 " --> pdb=" O ASPV1 406 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASPV1 411 " --> pdb=" O TYRV1 407 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N METV1 422 " --> pdb=" O GLNV1 418 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HISV1 423 " --> pdb=" O GLNV1 419 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THRV1 424 " --> pdb=" O ILEV1 420 " (cutoff:3.500A) Processing helix chain 'V1' and resid 427 through 443 Proline residue: V1 435 - end of helix Processing helix chain 'V1' and resid 444 through 459 Proline residue: V1 459 - end of helix Processing helix chain 'V2' and resid 45 through 60 removed outlier: 3.707A pdb=" N TYRV2 59 " --> pdb=" O ILEV2 55 " (cutoff:3.500A) Proline residue: V2 60 - end of helix Processing helix chain 'V2' and resid 63 through 80 removed outlier: 4.480A pdb=" N ALAV2 67 " --> pdb=" O GLNV2 63 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VALV2 68 " --> pdb=" O LYSV2 64 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N METV2 69 " --> pdb=" O ARGV2 65 " (cutoff:3.500A) Proline residue: V2 70 - end of helix removed outlier: 4.470A pdb=" N ASNV2 80 " --> pdb=" O GLNV2 76 " (cutoff:3.500A) Processing helix chain 'V2' and resid 84 through 96 Processing helix chain 'V2' and resid 98 through 110 removed outlier: 3.617A pdb=" N VALV2 102 " --> pdb=" O PROV2 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYRV2 109 " --> pdb=" O VALV2 105 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THRV2 110 " --> pdb=" O ALAV2 106 " (cutoff:3.500A) Processing helix chain 'V2' and resid 127 through 134 removed outlier: 3.868A pdb=" N CYSV2 133 " --> pdb=" O PROV2 129 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLYV2 134 " --> pdb=" O CYSV2 130 " (cutoff:3.500A) Processing helix chain 'V2' and resid 135 through 147 Processing helix chain 'V2' and resid 188 through 202 removed outlier: 3.840A pdb=" N VALV2 193 " --> pdb=" O THRV2 189 " (cutoff:3.500A) Processing helix chain 'V2' and resid 226 through 232 removed outlier: 4.344A pdb=" N LEUV2 230 " --> pdb=" O GLUV2 226 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLYV2 232 " --> pdb=" O ASPV2 228 " (cutoff:3.500A) Processing helix chain 'V2' and resid 239 through 256 Processing helix chain 'B6' and resid 79 through 104 Proline residue: B6 90 - end of helix removed outlier: 4.191A pdb=" N ILEB6 104 " --> pdb=" O ARGB6 100 " (cutoff:3.500A) Processing helix chain 'BM' and resid 64 through 69 Processing helix chain 'BM' and resid 100 through 105 Processing helix chain 'BM' and resid 113 through 118 removed outlier: 5.061A pdb=" N GLYBM 118 " --> pdb=" O ASPBM 114 " (cutoff:3.500A) Processing helix chain 'BM' and resid 139 through 158 Processing helix chain 'BM' and resid 160 through 166 Processing helix chain 'BM' and resid 169 through 206 Processing helix chain 'C4' and resid 3 through 24 Processing helix chain 'C4' and resid 34 through 67 removed outlier: 3.532A pdb=" N GLNC4 58 " --> pdb=" O METC4 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUC4 64 " --> pdb=" O CYSC4 60 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYSC4 65 " --> pdb=" O TYRC4 61 " (cutoff:3.500A) Processing helix chain 'C4' and resid 81 through 86 removed outlier: 3.907A pdb=" N SERC4 85 " --> pdb=" O GLYC4 81 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASPC4 86 " --> pdb=" O GLUC4 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C4' and resid 81 through 86' Processing helix chain 'C4' and resid 88 through 97 Processing helix chain 'AN' and resid 4 through 9 removed outlier: 3.580A pdb=" N LYSAN 8 " --> pdb=" O ASNAN 4 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLUAN 9 " --> pdb=" O SERAN 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 4 through 9' Processing helix chain 'AN' and resid 10 through 18 Processing helix chain 'AN' and resid 35 through 50 removed outlier: 3.605A pdb=" N LYSAN 39 " --> pdb=" O SERAN 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VALAN 40 " --> pdb=" O THRAN 36 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYSAN 43 " --> pdb=" O LYSAN 39 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARGAN 44 " --> pdb=" O VALAN 40 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASPAN 45 " --> pdb=" O TYRAN 41 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N METAN 46 " --> pdb=" O ALAAN 42 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEUAN 47 " --> pdb=" O CYSAN 43 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRPAN 48 " --> pdb=" O ARGAN 44 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HISAN 50 " --> pdb=" O METAN 46 " (cutoff:3.500A) Processing helix chain 'AN' and resid 52 through 81 removed outlier: 3.509A pdb=" N GLYAN 76 " --> pdb=" O ALAAN 72 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEUAN 77 " --> pdb=" O SERAN 73 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILEAN 78 " --> pdb=" O GLYAN 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SERAN 79 " --> pdb=" O PHEAN 75 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THRAN 81 " --> pdb=" O LEUAN 77 " (cutoff:3.500A) Processing helix chain 'AN' and resid 83 through 98 removed outlier: 5.169A pdb=" N ASNAN 98 " --> pdb=" O VALAN 94 " (cutoff:3.500A) Processing helix chain 'AN' and resid 99 through 130 removed outlier: 3.836A pdb=" N ARGAN 103 " --> pdb=" O PHEAN 99 " (cutoff:3.500A) Proline residue: AN 111 - end of helix Processing helix chain 'AN' and resid 136 through 156 Processing helix chain 'AN' and resid 161 through 180 Processing helix chain 'AN' and resid 201 through 220 removed outlier: 3.968A pdb=" N GLYAN 218 " --> pdb=" O ILEAN 214 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASNAN 219 " --> pdb=" O GLNAN 215 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYRAN 220 " --> pdb=" O PHEAN 216 " (cutoff:3.500A) Processing helix chain 'AN' and resid 221 through 226 Processing helix chain 'B4' and resid 63 through 76 removed outlier: 4.416A pdb=" N TYRB4 73 " --> pdb=" O PHEB4 69 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASPB4 74 " --> pdb=" O VALB4 70 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASNB4 75 " --> pdb=" O PHEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 82 through 87 removed outlier: 4.468A pdb=" N SERB4 86 " --> pdb=" O GLYB4 82 " (cutoff:3.500A) Processing helix chain 'B4' and resid 89 through 118 Proline residue: B4 100 - end of helix removed outlier: 3.506A pdb=" N ASNB4 116 " --> pdb=" O ASPB4 112 " (cutoff:3.500A) Processing helix chain 'T4' and resid 17 through 29 removed outlier: 3.629A pdb=" N GLUT4 28 " --> pdb=" O GLUT4 24 " (cutoff:3.500A) Processing helix chain 'T4' and resid 39 through 50 Processing helix chain 'T4' and resid 78 through 93 removed outlier: 4.559A pdb=" N THRT4 82 " --> pdb=" O GLNT4 78 " (cutoff:3.500A) Processing helix chain 'T4' and resid 98 through 107 Proline residue: T4 107 - end of helix Processing helix chain 'T4' and resid 111 through 136 Processing helix chain 'T4' and resid 139 through 184 Proline residue: T4 160 - end of helix removed outlier: 3.694A pdb=" N GLNT4 169 " --> pdb=" O GLUT4 165 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THRT4 170 " --> pdb=" O VALT4 166 " (cutoff:3.500A) Proline residue: T4 171 - end of helix Processing helix chain 'T4' and resid 185 through 195 removed outlier: 3.734A pdb=" N PHET4 189 " --> pdb=" O GLYT4 185 " (cutoff:3.500A) Proline residue: T4 195 - end of helix Processing helix chain 'T4' and resid 198 through 205 Processing helix chain 'T4' and resid 30 through 35 removed outlier: 3.938A pdb=" N HIST4 35 " --> pdb=" O SERT4 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'T4' and resid 30 through 35' Processing helix chain 'T8' and resid 7 through 12 removed outlier: 5.195A pdb=" N ASNT8 12 " --> pdb=" O VALT8 8 " (cutoff:3.500A) Processing helix chain 'T8' and resid 17 through 68 Proline residue: T8 51 - end of helix removed outlier: 5.221A pdb=" N TYRT8 57 " --> pdb=" O LEUT8 53 " (cutoff:3.500A) Proline residue: T8 58 - end of helix Processing helix chain 'T8' and resid 78 through 85 Processing helix chain 'T8' and resid 90 through 96 Processing helix chain 'T8' and resid 97 through 106 Processing helix chain 'T8' and resid 107 through 122 removed outlier: 3.772A pdb=" N LEUT8 111 " --> pdb=" O LYST8 107 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYST8 121 " --> pdb=" O GLUT8 117 " (cutoff:3.500A) Processing helix chain 'T8' and resid 125 through 130 removed outlier: 4.112A pdb=" N SERT8 129 " --> pdb=" O VALT8 125 " (cutoff:3.500A) Proline residue: T8 130 - end of helix No H-bonds generated for 'chain 'T8' and resid 125 through 130' Processing helix chain 'T8' and resid 70 through 75 removed outlier: 3.688A pdb=" N ASNT8 73 " --> pdb=" O VALT8 70 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILET8 74 " --> pdb=" O TRPT8 71 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIST8 75 " --> pdb=" O SERT8 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'T8' and resid 70 through 75' Processing helix chain 'B2' and resid 11 through 24 removed outlier: 5.454A pdb=" N TYRB2 23 " --> pdb=" O ASNB2 19 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLNB2 24 " --> pdb=" O ASPB2 20 " (cutoff:3.500A) Processing helix chain 'B2' and resid 41 through 65 Processing helix chain 'B2' and resid 67 through 74 Processing helix chain 'B2' and resid 92 through 120 Processing helix chain 'B2' and resid 85 through 90 removed outlier: 3.958A pdb=" N SERB2 88 " --> pdb=" O LEUB2 85 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASNB2 89 " --> pdb=" O ILEB2 86 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILEB2 90 " --> pdb=" O ASPB2 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 85 through 90' Processing helix chain 'T3' and resid 13 through 19 removed outlier: 3.673A pdb=" N LEUT3 17 " --> pdb=" O CYST3 13 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYST3 19 " --> pdb=" O SERT3 15 " (cutoff:3.500A) Processing helix chain 'T3' and resid 47 through 52 removed outlier: 3.822A pdb=" N GLUT3 51 " --> pdb=" O ARGT3 47 " (cutoff:3.500A) Processing helix chain 'T3' and resid 53 through 78 removed outlier: 4.187A pdb=" N GLNT3 77 " --> pdb=" O GLNT3 73 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VALT3 78 " --> pdb=" O LEUT3 74 " (cutoff:3.500A) Processing helix chain 'T3' and resid 80 through 112 Processing helix chain 'T3' and resid 117 through 130 removed outlier: 3.524A pdb=" N VALT3 121 " --> pdb=" O PROT3 117 " (cutoff:3.500A) Processing helix chain 'T3' and resid 137 through 145 Processing helix chain 'T3' and resid 146 through 154 removed outlier: 3.649A pdb=" N GLUT3 152 " --> pdb=" O PROT3 148 " (cutoff:3.500A) Processing helix chain 'T3' and resid 158 through 173 Processing helix chain 'T3' and resid 177 through 198 removed outlier: 4.327A pdb=" N LEUT3 181 " --> pdb=" O ASPT3 177 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASPT3 192 " --> pdb=" O LEUT3 188 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHET3 193 " --> pdb=" O SERT3 189 " (cutoff:3.500A) Proline residue: T3 194 - end of helix removed outlier: 3.692A pdb=" N LEUT3 197 " --> pdb=" O PHET3 193 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLNT3 198 " --> pdb=" O PROT3 194 " (cutoff:3.500A) Processing helix chain 'T3' and resid 226 through 235 Processing helix chain 'T3' and resid 243 through 263 removed outlier: 3.810A pdb=" N ALAT3 247 " --> pdb=" O LYST3 243 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VALT3 260 " --> pdb=" O SERT3 256 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASNT3 261 " --> pdb=" O PHET3 257 " (cutoff:3.500A) Proline residue: T3 262 - end of helix Processing helix chain 'T3' and resid 278 through 297 removed outlier: 3.861A pdb=" N GLUT3 295 " --> pdb=" O SERT3 291 " (cutoff:3.500A) Processing helix chain 'T3' and resid 300 through 311 Processing helix chain 'P1' and resid 33 through 42 removed outlier: 4.881A pdb=" N TYRP1 39 " --> pdb=" O ASPP1 35 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLNP1 40 " --> pdb=" O ASPP1 36 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARGP1 41 " --> pdb=" O TYRP1 37 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALAP1 42 " --> pdb=" O ASPP1 38 " (cutoff:3.500A) Processing helix chain 'P1' and resid 55 through 63 Processing helix chain 'P1' and resid 64 through 69 removed outlier: 6.058A pdb=" N ARGP1 69 " --> pdb=" O VALP1 65 " (cutoff:3.500A) Processing helix chain 'P1' and resid 70 through 78 removed outlier: 3.599A pdb=" N ASNP1 78 " --> pdb=" O PHEP1 74 " (cutoff:3.500A) Processing helix chain 'P1' and resid 81 through 86 removed outlier: 4.222A pdb=" N VALP1 85 " --> pdb=" O THRP1 81 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SERP1 86 " --> pdb=" O ASNP1 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'P1' and resid 81 through 86' Processing helix chain 'P1' and resid 107 through 130 removed outlier: 4.429A pdb=" N ASNP1 111 " --> pdb=" O ARGP1 107 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLUP1 120 " --> pdb=" O TYRP1 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SERP1 121 " --> pdb=" O ARGP1 117 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILEP1 122 " --> pdb=" O SERP1 118 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEUP1 124 " --> pdb=" O GLUP1 120 " (cutoff:3.500A) Proline residue: P1 125 - end of helix Processing helix chain 'P1' and resid 133 through 148 removed outlier: 3.626A pdb=" N ALAP1 137 " --> pdb=" O TYRP1 133 " (cutoff:3.500A) Proline residue: P1 143 - end of helix Processing helix chain 'P1' and resid 153 through 160 Processing helix chain 'P1' and resid 198 through 207 removed outlier: 4.031A pdb=" N VALP1 202 " --> pdb=" O PROP1 198 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLUP1 204 " --> pdb=" O ASPP1 200 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLNP1 205 " --> pdb=" O GLNP1 201 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASNP1 207 " --> pdb=" O LYSP1 203 " (cutoff:3.500A) Processing helix chain 'P1' and resid 208 through 213 Processing helix chain 'P1' and resid 241 through 247 Processing helix chain 'B3' and resid 15 through 30 removed outlier: 6.203A pdb=" N TYRB3 19 " --> pdb=" O LEUB3 15 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILEB3 20 " --> pdb=" O PHEB3 16 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLNB3 30 " --> pdb=" O SERB3 26 " (cutoff:3.500A) Processing helix chain 'B3' and resid 31 through 43 removed outlier: 4.444A pdb=" N TYRB3 35 " --> pdb=" O LYSB3 31 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TRPB3 40 " --> pdb=" O ARGB3 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARGB3 41 " --> pdb=" O VALB3 37 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRPB3 42 " --> pdb=" O ASNB3 38 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASNB3 43 " --> pdb=" O ARGB3 39 " (cutoff:3.500A) Processing helix chain 'B3' and resid 49 through 74 removed outlier: 4.349A pdb=" N ARGB3 55 " --> pdb=" O PROB3 51 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEUB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N LYSB3 57 " --> pdb=" O PHEB3 53 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N TYRB3 58 " --> pdb=" O LEUB3 54 " (cutoff:3.500A) Proline residue: B3 59 - end of helix Processing helix chain 'TA' and resid 42 through 51 removed outlier: 3.601A pdb=" N TYRTA 51 " --> pdb=" O ASPTA 47 " (cutoff:3.500A) Processing helix chain 'TA' and resid 54 through 59 Processing helix chain 'TA' and resid 68 through 113 removed outlier: 4.705A pdb=" N GLYTA 88 " --> pdb=" O LEUTA 84 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLYTA 89 " --> pdb=" O PHETA 85 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHETA 90 " --> pdb=" O ILETA 86 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THRTA 91 " --> pdb=" O ILETA 87 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THRTA 113 " --> pdb=" O GLUTA 109 " (cutoff:3.500A) Processing helix chain 'S5' and resid 15 through 29 Processing helix chain 'S5' and resid 31 through 36 Processing helix chain 'S5' and resid 37 through 49 removed outlier: 3.816A pdb=" N ARGS5 49 " --> pdb=" O GLUS5 45 " (cutoff:3.500A) Processing helix chain 'S5' and resid 50 through 66 removed outlier: 4.226A pdb=" N ASNS5 65 " --> pdb=" O LYSS5 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILES5 66 " --> pdb=" O GLUS5 62 " (cutoff:3.500A) Processing helix chain 'TC' and resid 4 through 10 Processing helix chain 'TC' and resid 17 through 45 removed outlier: 3.715A pdb=" N TYRTC 39 " --> pdb=" O VALTC 35 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYSTC 40 " --> pdb=" O ASNTC 36 " (cutoff:3.500A) Proline residue: TC 41 - end of helix Processing helix chain 'TC' and resid 56 through 92 Processing helix chain 'P2' and resid 49 through 57 removed outlier: 5.078A pdb=" N ALAP2 57 " --> pdb=" O PHEP2 53 " (cutoff:3.500A) Processing helix chain 'P2' and resid 58 through 75 Proline residue: P2 68 - end of helix Processing helix chain 'P2' and resid 119 through 127 removed outlier: 3.503A pdb=" N TYRP2 123 " --> pdb=" O PROP2 119 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYSP2 127 " --> pdb=" O TYRP2 123 " (cutoff:3.500A) Processing helix chain 'P2' and resid 162 through 168 removed outlier: 3.860A pdb=" N HISP2 168 " --> pdb=" O GLUP2 164 " (cutoff:3.500A) Processing helix chain 'P2' and resid 172 through 177 Processing helix chain 'P2' and resid 178 through 183 Processing helix chain 'A3' and resid 39 through 58 Processing helix chain 'A3' and resid 59 through 82 removed outlier: 4.064A pdb=" N GLUA3 82 " --> pdb=" O ALAA3 78 " (cutoff:3.500A) Processing helix chain 'A3' and resid 90 through 95 removed outlier: 4.751A pdb=" N GLYA3 95 " --> pdb=" O GLNA3 91 " (cutoff:3.500A) Processing helix chain 'A3' and resid 98 through 107 Processing helix chain 'T9' and resid 21 through 36 Processing helix chain 'T9' and resid 37 through 54 removed outlier: 3.520A pdb=" N GLUT9 43 " --> pdb=" O LEUT9 39 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALT9 50 " --> pdb=" O ARGT9 46 " (cutoff:3.500A) Processing helix chain 'T9' and resid 66 through 81 removed outlier: 4.052A pdb=" N ARGT9 70 " --> pdb=" O LEUT9 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEUT9 71 " --> pdb=" O PROT9 67 " (cutoff:3.500A) Processing helix chain 'T9' and resid 92 through 107 removed outlier: 4.052A pdb=" N LEUT9 96 " --> pdb=" O PROT9 92 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASPT9 97 " --> pdb=" O GLUT9 93 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N SERT9 98 " --> pdb=" O ILET9 94 " (cutoff:3.500A) Processing helix chain 'T9' and resid 112 through 131 removed outlier: 4.192A pdb=" N CYST9 116 " --> pdb=" O PROT9 112 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARGT9 117 " --> pdb=" O METT9 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGT9 118 " --> pdb=" O GLNT9 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHET9 119 " --> pdb=" O SERT9 115 " (cutoff:3.500A) Processing helix chain 'TE' and resid 23 through 46 Processing helix chain 'T7' and resid 19 through 38 Processing helix chain 'T7' and resid 40 through 47 Processing helix chain 'T7' and resid 52 through 78 Proline residue: T7 64 - end of helix Processing helix chain 'T7' and resid 83 through 122 removed outlier: 5.755A pdb=" N ARGT7 87 " --> pdb=" O TYRT7 83 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASNT7 117 " --> pdb=" O LEUT7 113 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYRT7 118 " --> pdb=" O TYRT7 114 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIST7 119 " --> pdb=" O THRT7 115 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEUT7 120 " --> pdb=" O ARGT7 116 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHET7 121 " --> pdb=" O ASNT7 117 " (cutoff:3.500A) Proline residue: T7 122 - end of helix Processing helix chain 'T7' and resid 123 through 132 Processing helix chain 'T7' and resid 137 through 142 removed outlier: 3.941A pdb=" N TRPT7 141 " --> pdb=" O CYST7 137 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '3A' and resid 66 through 69 removed outlier: 4.909A pdb=" N LYS3A 66 " --> pdb=" O SER3A 82 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP3A 90 " --> pdb=" O ALA3A 254 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3A' and resid 291 through 297 removed outlier: 3.580A pdb=" N GLY3A 359 " --> pdb=" O SER3A 311 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3B' and resid 64 through 68 removed outlier: 3.701A pdb=" N GLY3B 252 " --> pdb=" O GLU3B 78 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN3B 245 " --> pdb=" O ARG3B 93 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASN3B 136 " --> pdb=" O SER3B 151 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3B' and resid 289 through 295 removed outlier: 3.539A pdb=" N PHE3B 377 " --> pdb=" O PHE3B 308 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR3B 374 " --> pdb=" O TYR3B 371 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR3B 362 " --> pdb=" O ALA3B 333 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '3E' and resid 129 through 134 removed outlier: 5.788A pdb=" N THR3E 250 " --> pdb=" O ILE3E 134 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '3E' and resid 141 through 146 removed outlier: 3.614A pdb=" N GLU3E 141 " --> pdb=" O ARG3E 156 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '3a' and resid 66 through 69 removed outlier: 4.508A pdb=" N LYS3a 66 " --> pdb=" O SER3a 82 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP3a 90 " --> pdb=" O ALA3a 254 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '3a' and resid 346 through 355 removed outlier: 3.826A pdb=" N SER3a 358 " --> pdb=" O PHE3a 355 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY3a 359 " --> pdb=" O SER3a 311 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '3b' and resid 64 through 68 removed outlier: 4.939A pdb=" N ASN3b 136 " --> pdb=" O SER3b 151 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '3b' and resid 289 through 295 removed outlier: 3.600A pdb=" N SER3b 290 " --> pdb=" O LEU3b 476 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE3b 377 " --> pdb=" O PHE3b 308 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR3b 374 " --> pdb=" O TYR3b 371 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N THR3b 362 " --> pdb=" O ALA3b 333 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '3d' and resid 196 through 199 removed outlier: 4.296A pdb=" N MET3d 205 " --> pdb=" O ASN3d 199 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '5' and resid 227 through 232 removed outlier: 6.502A pdb=" N PHE 5 246 " --> pdb=" O LEU 5 232 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE 5 242 " --> pdb=" O TYR 5 237 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR 5 237 " --> pdb=" O PHE 5 242 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL 5 244 " --> pdb=" O TRP 5 235 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY 5 233 " --> pdb=" O PHE 5 246 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A2' and resid 48 through 54 removed outlier: 3.742A pdb=" N LEUA2 15 " --> pdb=" O PROA2 48 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A7' and resid 214 through 218 Processing sheet with id= 15, first strand: chain 'A9' and resid 94 through 99 removed outlier: 5.871A pdb=" N GLNA9 94 " --> pdb=" O SERA9 67 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLNA9 257 " --> pdb=" O ALAA9 193 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A9' and resid 222 through 226 Processing sheet with id= 17, first strand: chain 'AL' and resid 60 through 66 removed outlier: 7.829A pdb=" N GLYAL 60 " --> pdb=" O SERAL 81 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SERAL 81 " --> pdb=" O GLYAL 60 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARGAL 75 " --> pdb=" O ASPAL 66 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'BL' and resid 13 through 16 Processing sheet with id= 19, first strand: chain 'C1' and resid 71 through 76 removed outlier: 4.032A pdb=" N VALC1 93 " --> pdb=" O GLUC1 71 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLUC1 97 " --> pdb=" O TRPC1 75 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C1' and resid 77 through 81 removed outlier: 4.319A pdb=" N VALC1 99 " --> pdb=" O ASNC1 77 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SERC1 127 " --> pdb=" O ASNC1 98 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYSC1 144 " --> pdb=" O LYSC1 126 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SERC1 162 " --> pdb=" O GLYC1 143 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEUC1 147 " --> pdb=" O VALC1 164 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C1' and resid 137 through 141 removed outlier: 3.917A pdb=" N ALAC1 156 " --> pdb=" O GLUC1 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THRC1 174 " --> pdb=" O GLYC1 155 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLYC1 178 " --> pdb=" O ALAC1 159 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEUC1 175 " --> pdb=" O VALC1 184 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C1' and resid 149 through 154 removed outlier: 4.129A pdb=" N ARGC1 168 " --> pdb=" O GLYC1 149 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALAC1 172 " --> pdb=" O GLUC1 153 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C2' and resid 56 through 59 removed outlier: 4.639A pdb=" N VALC2 75 " --> pdb=" O VALC2 56 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C2' and resid 86 through 90 removed outlier: 5.570A pdb=" N VALC2 108 " --> pdb=" O GLYC2 86 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N CYSC2 136 " --> pdb=" O LYSC2 107 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THRC2 153 " --> pdb=" O GLYC2 135 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SERC2 171 " --> pdb=" O ASNC2 152 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUC2 156 " --> pdb=" O VALC2 173 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C2' and resid 141 through 145 removed outlier: 5.818A pdb=" N ARGC2 163 " --> pdb=" O ASPC2 144 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARGC2 177 " --> pdb=" O GLYC2 158 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SERC2 181 " --> pdb=" O GLUC2 162 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C2' and resid 184 through 187 removed outlier: 3.986A pdb=" N LEUC2 184 " --> pdb=" O VALC2 193 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C3' and resid 51 through 54 removed outlier: 4.000A pdb=" N ARGC3 51 " --> pdb=" O SERC3 72 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VALC3 74 " --> pdb=" O ARGC3 51 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C3' and resid 77 through 82 removed outlier: 5.859A pdb=" N ASPC3 77 " --> pdb=" O GLYC3 97 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYSC3 103 " --> pdb=" O LYSC3 81 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C3' and resid 83 through 88 removed outlier: 4.206A pdb=" N THRC3 105 " --> pdb=" O GLYC3 83 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASPC3 109 " --> pdb=" O TRPC3 87 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VALC3 128 " --> pdb=" O GLNC3 104 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C3' and resid 133 through 137 removed outlier: 3.972A pdb=" N SERC3 151 " --> pdb=" O ASNC3 133 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SERC3 169 " --> pdb=" O GLYC3 150 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SERC3 154 " --> pdb=" O VALC3 171 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C3' and resid 156 through 160 Processing sheet with id= 32, first strand: chain 'C3' and resid 162 through 166 removed outlier: 4.426A pdb=" N GLNC3 181 " --> pdb=" O ASNC3 162 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASNC3 180 " --> pdb=" O ILEC3 194 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'J1' and resid 294 through 298 Processing sheet with id= 34, first strand: chain 'FX' and resid 53 through 59 removed outlier: 4.771A pdb=" N GLNFX 53 " --> pdb=" O ASNFX 49 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T2' and resid 41 through 44 removed outlier: 3.594A pdb=" N VALT2 35 " --> pdb=" O TRPT2 44 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T2' and resid 161 through 166 removed outlier: 5.485A pdb=" N VALT2 75 " --> pdb=" O ILET2 100 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEUT2 202 " --> pdb=" O VALT2 95 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T1' and resid 46 through 52 removed outlier: 4.513A pdb=" N ALAT1 126 " --> pdb=" O THRT1 17 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T1' and resid 229 through 233 Processing sheet with id= 39, first strand: chain 'T1' and resid 336 through 340 removed outlier: 4.171A pdb=" N LEUT1 358 " --> pdb=" O ALAT1 270 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILET1 376 " --> pdb=" O PROT1 357 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIST1 407 " --> pdb=" O SERT1 373 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S1' and resid 197 through 202 removed outlier: 3.588A pdb=" N GLYS1 197 " --> pdb=" O GLYS1 208 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARGS1 201 " --> pdb=" O ALAS1 204 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S1' and resid 246 through 251 removed outlier: 6.260A pdb=" N ALAS1 261 " --> pdb=" O ARGS1 277 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'S1' and resid 314 through 318 removed outlier: 4.412A pdb=" N ASNS1 314 " --> pdb=" O SERS1 310 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SERS1 305 " --> pdb=" O PROS1 579 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S1' and resid 441 through 444 Processing sheet with id= 44, first strand: chain 'S1' and resid 501 through 504 removed outlier: 7.605A pdb=" N VALS1 501 " --> pdb=" O GLYS1 510 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S1' and resid 588 through 592 removed outlier: 4.185A pdb=" N ARGS1 596 " --> pdb=" O ASNS1 592 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S2' and resid 26 through 29 removed outlier: 3.747A pdb=" N ARGS2 54 " --> pdb=" O GLNS2 46 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S2' and resid 373 through 381 Processing sheet with id= 48, first strand: chain 'S3' and resid 57 through 61 removed outlier: 8.249A pdb=" N ASNS3 57 " --> pdb=" O TYRS3 103 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASNS3 99 " --> pdb=" O ILES3 61 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S3' and resid 120 through 123 Processing sheet with id= 50, first strand: chain 'S3' and resid 177 through 183 Processing sheet with id= 51, first strand: chain 'S3' and resid 93 through 103 Processing sheet with id= 52, first strand: chain 'S4' and resid 113 through 118 removed outlier: 5.797A pdb=" N ALAS4 113 " --> pdb=" O GLYS4 126 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'S4' and resid 133 through 137 removed outlier: 4.804A pdb=" N ILES4 87 " --> pdb=" O SERS4 156 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S6' and resid 77 through 80 removed outlier: 5.013A pdb=" N LEUS6 120 " --> pdb=" O CYSS6 115 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S6' and resid 84 through 88 Processing sheet with id= 56, first strand: chain 'S7' and resid 52 through 55 removed outlier: 4.163A pdb=" N GLYS7 67 " --> pdb=" O METS7 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILES7 121 " --> pdb=" O VALS7 90 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S8' and resid 123 through 127 removed outlier: 3.668A pdb=" N GLUS8 123 " --> pdb=" O GLYS8 193 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALAS8 189 " --> pdb=" O ARGS8 127 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S8' and resid 151 through 155 Processing sheet with id= 59, first strand: chain 'TX' and resid 25 through 28 Processing sheet with id= 60, first strand: chain 'TB' and resid 31 through 34 Processing sheet with id= 61, first strand: chain 'V1' and resid 194 through 201 removed outlier: 4.014A pdb=" N ALAV1 154 " --> pdb=" O SERV1 112 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARGV1 160 " --> pdb=" O SERV1 118 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'V1' and resid 286 through 289 removed outlier: 3.524A pdb=" N VALV1 357 " --> pdb=" O SERV1 280 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALAV1 317 " --> pdb=" O METV1 358 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'V2' and resid 119 through 126 Processing sheet with id= 64, first strand: chain 'V2' and resid 175 through 178 Processing sheet with id= 65, first strand: chain 'T3' and resid 200 through 203 removed outlier: 5.558A pdb=" N GLNT3 209 " --> pdb=" O HIST3 203 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'P1' and resid 100 through 103 removed outlier: 6.763A pdb=" N METP1 164 " --> pdb=" O VALP1 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILEP1 183 " --> pdb=" O GLYP1 179 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'P1' and resid 194 through 197 removed outlier: 4.475A pdb=" N ILEP1 222 " --> pdb=" O VALP1 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLUP1 230 " --> pdb=" O ASPP1 225 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P2' and resid 36 through 39 removed outlier: 6.721A pdb=" N METP2 86 " --> pdb=" O LEUP2 39 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYSP2 85 " --> pdb=" O ASPP2 98 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P2' and resid 79 through 83 removed outlier: 3.685A pdb=" N PHEP2 152 " --> pdb=" O PROP2 79 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILEP2 143 " --> pdb=" O VALP2 118 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'T9' and resid 2 through 6 No H-bonds generated for sheet with id= 70 7157 hydrogen bonds defined for protein. 21312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 66.88 Time building geometry restraints manager: 50.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 66922 1.41 - 1.65: 89276 1.65 - 1.89: 939 1.89 - 2.13: 24 2.13 - 2.37: 88 Bond restraints: 157249 Sorted by residual: bond pdb=" C2D HEC3D 401 " pdb=" C3D HEC3D 401 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C2D HEC3d 401 " pdb=" C3D HEC3d 401 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" CAC HEC3d 401 " pdb=" CBC HEC3d 401 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" CAC HEC3D 401 " pdb=" CBC HEC3D 401 " ideal model delta sigma weight residual 1.544 1.364 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C2 U103C 605 " pdb=" C3 U103C 605 " ideal model delta sigma weight residual 1.390 1.563 -0.173 2.00e-02 2.50e+03 7.51e+01 ... (remaining 157244 not shown) Histogram of bond angle deviations from ideal: 63.44 - 86.48: 80 86.48 - 109.51: 13457 109.51 - 132.55: 198692 132.55 - 155.58: 290 155.58 - 178.62: 12 Bond angle restraints: 212531 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 134.34 -26.60 1.95e+00 2.62e-01 1.85e+02 angle pdb=" C5B NDPA9 401 " pdb=" O5B NDPA9 401 " pdb=" PA NDPA9 401 " ideal model delta sigma weight residual 103.84 120.30 -16.46 1.91e+00 2.73e-01 7.39e+01 angle pdb=" S2 SF4S7 201 " pdb="FE1 SF4S7 201 " pdb=" S3 SF4S7 201 " ideal model delta sigma weight residual 104.10 115.67 -11.57 1.50e+00 4.44e-01 5.95e+01 angle pdb=" S2 SF4S1 801 " pdb="FE3 SF4S1 801 " pdb=" S4 SF4S1 801 " ideal model delta sigma weight residual 104.10 115.53 -11.43 1.50e+00 4.44e-01 5.81e+01 angle pdb=" C5D NDPA9 401 " pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 104.93 124.98 -20.05 2.66e+00 1.41e-01 5.69e+01 ... (remaining 212526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 90959 35.74 - 71.48: 2488 71.48 - 107.21: 203 107.21 - 142.95: 12 142.95 - 178.69: 8 Dihedral angle restraints: 93670 sinusoidal: 39791 harmonic: 53879 Sorted by residual: dihedral pdb=" CB CYSC2 31 " pdb=" SG CYSC2 31 " pdb=" SG CYSC2 39 " pdb=" CB CYSC2 39 " ideal model delta sinusoidal sigma weight residual 93.00 -178.68 -88.32 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" C12 U105B 202 " pdb=" C13 U105B 202 " pdb=" C14 U105B 202 " pdb=" C16 U105B 202 " ideal model delta sinusoidal sigma weight residual 178.80 0.11 178.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C22 U103C 605 " pdb=" C23 U103C 605 " pdb=" C24 U103C 605 " pdb=" C26 U103C 605 " ideal model delta sinusoidal sigma weight residual -178.11 0.21 -178.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 93667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 22344 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.960: 0 16.960 - 21.200: 24 Chirality restraints: 22368 Sorted by residual: chirality pdb="FE1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " pdb=" S4 SF4S1 802 " both_signs ideal model delta sigma weight residual False -10.55 10.65 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S3 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4S8 302 " pdb=" S2 SF4S8 302 " pdb=" S3 SF4S8 302 " pdb=" S4 SF4S8 302 " both_signs ideal model delta sigma weight residual False -10.55 10.62 -21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 22365 not shown) Planarity restraints: 26786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.016 2.00e-02 2.50e+03 2.27e-02 2.45e+01 pdb=" C10 FMNV1 501 " 0.015 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.023 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.004 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.020 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " 0.024 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.007 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.053 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.005 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.016 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " 0.014 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.024 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.005 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.020 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.018 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " 0.026 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.047 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERC2 188 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PROC2 189 " -0.185 5.00e-02 4.00e+02 pdb=" CA PROC2 189 " 0.056 5.00e-02 4.00e+02 pdb=" CD PROC2 189 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILES1 282 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C ILES1 282 " 0.050 2.00e-02 2.50e+03 pdb=" O ILES1 282 " -0.019 2.00e-02 2.50e+03 pdb=" N ASNS1 283 " -0.017 2.00e-02 2.50e+03 ... (remaining 26783 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 2023 2.67 - 3.23: 144039 3.23 - 3.79: 244690 3.79 - 4.34: 351385 4.34 - 4.90: 567252 Nonbonded interactions: 1309389 Sorted by model distance: nonbonded pdb=" OG1 THR3E 198 " pdb=" O LEU3E 235 " model vdw 2.115 2.440 nonbonded pdb=" NE2 HIS3C 199 " pdb="FE HEM3C 601 " model vdw 2.124 3.080 nonbonded pdb=" OH TYRC1 220 " pdb=" OD2 ASPC2 27 " model vdw 2.129 2.440 nonbonded pdb=" NE2 HIS3c 185 " pdb="FE HEM3c 502 " model vdw 2.143 3.080 nonbonded pdb=" OH TYR 2 108 " pdb=" OD1 ASN2B 147 " model vdw 2.143 2.440 ... (remaining 1309384 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 '3A' and resid 24 through 481) selection = chain '3a' } ncs_group { reference = (chain '3B' and resid 36 through 513) selection = (chain '3b' and resid 36 through 513) } ncs_group { reference = (chain '3C' and (resid 1 through 425 or (resid 426 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 602 or (resid 606 and (name N or name C1 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ ame C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain '3c' and (resid 1 through 426 or resid 502 or (resid 506 and (name N or n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name O11 or \ name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) } ncs_group { reference = (chain '3D' and (resid 35 through 319 or resid 401)) selection = (chain '3d' and (resid 35 through 318 or (resid 319 and (name N or name CA or na \ me C or name O or name CB )) or resid 401)) } ncs_group { reference = (chain '3G' and (resid 22 through 273 or resid 280 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain '3g' and resid 22 through 328) } ncs_group { reference = (chain '3H' and resid 1 through 124) selection = chain '3h' } ncs_group { reference = (chain '3I' and (resid 2 through 112 or resid 604)) selection = (chain '3i' and (resid 2 through 112 or (resid 201 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C51 \ or name C71 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name \ CA7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or na \ me OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 o \ r name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name P \ A1 or name PB2)))) } ncs_group { reference = (chain '3J' and (resid 1 through 51 or (resid 101 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C3A or name O11 or name O12 or na \ me O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P ))) \ ) selection = chain '3j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 47.240 Check model and map are aligned: 1.660 Set scattering table: 1.080 Process input model: 413.960 Find NCS groups from input model: 7.310 Set up NCS constraints: 0.760 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: 0.020 Load rotamer database and sin/cos tables:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 496.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.005 0.219 157249 Z= 0.309 Angle : 0.592 26.597 212531 Z= 0.305 Chirality : 0.686 21.200 22368 Planarity : 0.004 0.107 26786 Dihedral : 16.315 178.691 58966 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 0.01 % Allowed : 0.24 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % 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: 0.89 (0.06), residues: 17880 helix: 1.48 (0.06), residues: 8981 sheet: 0.61 (0.16), residues: 1082 loop : -0.41 (0.07), residues: 7817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRPS1 286 HIS 0.008 0.001 HISP2 78 PHE 0.041 0.001 PHES7 46 TYR 0.048 0.001 TYR 1 245 ARG 0.011 0.000 ARGT7 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1328 time to evaluate : 13.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 118 ASP cc_start: 0.7861 (p0) cc_final: 0.7602 (p0) REVERT: 2 21 PHE cc_start: 0.8078 (m-80) cc_final: 0.7875 (t80) REVERT: 3F 56 MET cc_start: 0.6762 (mtm) cc_final: 0.6421 (mtp) REVERT: 3G 286 GLU cc_start: 0.6896 (tp30) cc_final: 0.6385 (tp30) REVERT: 3G 290 ASN cc_start: 0.7960 (m-40) cc_final: 0.6409 (m-40) REVERT: 3d 242 MET cc_start: 0.8689 (mmm) cc_final: 0.8370 (mmm) REVERT: BL 10 ASP cc_start: 0.7852 (p0) cc_final: 0.7417 (p0) REVERT: X1 60 PHE cc_start: 0.7677 (t80) cc_final: 0.7056 (t80) REVERT: S8 74 ASP cc_start: 0.7087 (t70) cc_final: 0.6821 (t0) REVERT: V2 242 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7399 (ttmt) REVERT: T4 194 ASN cc_start: 0.7735 (t0) cc_final: 0.7491 (t0) REVERT: B3 25 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7973 (mtmt) REVERT: P2 48 ASN cc_start: 0.7774 (p0) cc_final: 0.7564 (p0) REVERT: T7 75 ILE cc_start: 0.6995 (pt) cc_final: 0.6778 (pp) outliers start: 2 outliers final: 0 residues processed: 1330 average time/residue: 2.3193 time to fit residues: 4446.4141 Evaluate side-chains 993 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 993 time to evaluate : 13.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1508 optimal weight: 10.0000 chunk 1353 optimal weight: 6.9990 chunk 751 optimal weight: 0.0020 chunk 462 optimal weight: 9.9990 chunk 913 optimal weight: 8.9990 chunk 723 optimal weight: 5.9990 chunk 1399 optimal weight: 0.5980 chunk 541 optimal weight: 6.9990 chunk 851 optimal weight: 20.0000 chunk 1041 optimal weight: 5.9990 chunk 1621 optimal weight: 10.0000 overall best weight: 3.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 2 106 ASN ** 2 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 141 ASN 3 12 ASN 3A 302 ASN ** 3A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 176 GLN 3B 194 ASN 3B 507 ASN 3C 316 HIS ** 3E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3F 27 HIS ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 112 GLN 3c 321 GLN 3f 16 GLN 3g 11 GLN ** 3g 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 90 ASN 4 93 ASN ** 4 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 17 ASN A5 163 GLN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 359 ASN AB 81 ASN AC 133 ASN AL 9 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 35 GLN C2 61 HIS ** C3 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 133 ASN TD 61 GLN TD 64 GLN FX 29 HIS FX 163 ASN T2 130 ASN T2 208 GLN T1 250 GLN T1 388 GLN A1 81 ASN T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S1 599 GLN S3 57 ASN ** S6 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 99 GLN B9 187 ASN A8 187 ASN AN 127 GLN B2 25 ASN T3 43 ASN T3 73 GLN P1 237 GLN P1 251 ASN TA 102 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 97 GLN TE 26 ASN T7 107 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.267 157249 Z= 0.448 Angle : 1.131 50.859 212531 Z= 0.713 Chirality : 0.215 6.557 22368 Planarity : 0.004 0.077 26786 Dihedral : 13.129 176.618 23676 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.67 % Rotamer: Outliers : 1.28 % Allowed : 6.62 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 0.89 (0.06), residues: 17880 helix: 1.54 (0.05), residues: 9074 sheet: 0.62 (0.16), residues: 1073 loop : -0.54 (0.07), residues: 7733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPS2 149 HIS 0.009 0.001 HISS2 58 PHE 0.036 0.002 PHES7 46 TYR 0.035 0.002 TYRA5 138 ARG 0.007 0.000 ARG3b 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1044 time to evaluate : 13.296 Fit side-chains revert: symmetry clash REVERT: 1 29 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7648 (mtt) REVERT: 1 118 ASP cc_start: 0.7921 (p0) cc_final: 0.7690 (p0) REVERT: 2 21 PHE cc_start: 0.8110 (m-80) cc_final: 0.7907 (t80) REVERT: 3A 56 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6925 (tpp80) REVERT: 3A 286 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8051 (ttpp) REVERT: 3C 213 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7965 (ttt) REVERT: 3C 286 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6433 (tpp) REVERT: 3E 32 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7537 (mp-120) REVERT: 3G 189 TYR cc_start: 0.2732 (OUTLIER) cc_final: 0.1669 (p90) REVERT: 3G 286 GLU cc_start: 0.7046 (tp30) cc_final: 0.6506 (tp30) REVERT: 3G 290 ASN cc_start: 0.7726 (m-40) cc_final: 0.6432 (m-40) REVERT: 3H 31 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: 3H 55 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: 3I 35 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: 3c 213 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7873 (ttt) REVERT: 3c 236 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5831 (mm-30) REVERT: 3c 286 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.5105 (tpp) REVERT: 3d 242 MET cc_start: 0.8796 (mmm) cc_final: 0.8511 (mmm) REVERT: 3f 15 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: 3f 23 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7630 (tp) REVERT: 3h 1 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6673 (mtp) REVERT: 5 191 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (tt) REVERT: 5 283 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6605 (mt-10) REVERT: 5 693 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6988 (p0) REVERT: 6 79 GLU cc_start: 0.7747 (mp0) cc_final: 0.7467 (mp0) REVERT: A5 73 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: AB 69 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8179 (ttmt) REVERT: AB 86 GLN cc_start: 0.8641 (tp40) cc_final: 0.8400 (tp-100) REVERT: AM 70 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6953 (mm-30) REVERT: B8 56 MET cc_start: 0.8750 (mmt) cc_final: 0.8466 (tpt) REVERT: BL 10 ASP cc_start: 0.7887 (p0) cc_final: 0.7440 (p0) REVERT: BL 94 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7840 (mtp) REVERT: FX 41 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8483 (mmpt) REVERT: T1 216 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7911 (mptt) REVERT: A1 63 ASP cc_start: 0.7990 (m-30) cc_final: 0.7735 (m-30) REVERT: T6 99 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7870 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8628 (mttp) REVERT: S1 481 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: S2 194 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: S2 318 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6383 (m-40) REVERT: S4 1 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6310 (ppp) REVERT: S4 15 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: S4 25 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7279 (ptpt) REVERT: S4 93 MET cc_start: 0.8468 (mmm) cc_final: 0.8241 (mmm) REVERT: S4 183 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: S8 29 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: V1 122 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: V2 242 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7500 (ttmt) REVERT: T4 194 ASN cc_start: 0.7694 (t0) cc_final: 0.7463 (t0) REVERT: P1 77 ARG cc_start: 0.6783 (mtm-85) cc_final: 0.6561 (ptp-110) REVERT: P2 48 ASN cc_start: 0.7766 (p0) cc_final: 0.7456 (p0) REVERT: P2 87 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: A3 56 ASN cc_start: 0.8368 (m-40) cc_final: 0.8163 (m-40) REVERT: T9 43 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: T7 31 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: T7 75 ILE cc_start: 0.7190 (pt) cc_final: 0.6971 (pp) REVERT: T7 124 ASP cc_start: 0.8680 (p0) cc_final: 0.8474 (p0) outliers start: 205 outliers final: 69 residues processed: 1145 average time/residue: 2.2229 time to fit residues: 3677.5169 Evaluate side-chains 1091 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 983 time to evaluate : 11.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2B residue 66 LEU Chi-restraints excluded: chain 3A residue 56 ARG Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 482 LYS Chi-restraints excluded: chain 3C residue 213 MET Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3E residue 32 GLN Chi-restraints excluded: chain 3E residue 150 THR Chi-restraints excluded: chain 3E residue 160 ASN Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3b residue 230 ASP Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 236 GLU Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3g residue 231 THR Chi-restraints excluded: chain 3h residue 1 MET Chi-restraints excluded: chain 3h residue 81 THR Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 283 GLU Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 6 residue 20 ILE Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 73 MET Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain BL residue 94 MET Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T1 residue 216 LYS Chi-restraints excluded: chain T1 residue 278 ILE Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain S1 residue 256 ASP Chi-restraints excluded: chain S1 residue 372 HIS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S2 residue 194 GLU Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S3 residue 22 MET Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 1 MET Chi-restraints excluded: chain S4 residue 15 GLU Chi-restraints excluded: chain S4 residue 25 LYS Chi-restraints excluded: chain S4 residue 183 GLU Chi-restraints excluded: chain S8 residue 26 ILE Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TX residue 155 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 122 GLU Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V2 residue 189 THR Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain B2 residue 110 LYS Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain A3 residue 83 LYS Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 31 GLN Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 901 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 1349 optimal weight: 6.9990 chunk 1104 optimal weight: 9.9990 chunk 447 optimal weight: 5.9990 chunk 1624 optimal weight: 6.9990 chunk 1755 optimal weight: 0.0000 chunk 1447 optimal weight: 5.9990 chunk 1611 optimal weight: 6.9990 chunk 553 optimal weight: 6.9990 chunk 1303 optimal weight: 1.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 ASN 2 237 ASN ** 2B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3A 302 ASN ** 3A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 176 GLN 3B 194 ASN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3E 119 ASN 3G 76 HIS 3I 43 ASN ** 3a 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 90 ASN ** 4 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 163 GLN ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 102 HIS C2 131 ASN C3 31 GLN ** C3 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN TD 66 GLN T2 130 ASN T2 208 GLN T1 214 ASN T1 250 GLN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN ** S6 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 22 GLN S8 108 ASN A8 187 ASN TB 103 GLN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 191 ASN T8 104 GLN B2 25 ASN P1 237 GLN ** P1 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 102 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 157249 Z= 0.459 Angle : 1.131 50.588 212531 Z= 0.713 Chirality : 0.214 6.528 22368 Planarity : 0.004 0.056 26786 Dihedral : 12.779 179.193 23676 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.62 % Rotamer: Outliers : 1.70 % Allowed : 9.17 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 0.79 (0.06), residues: 17880 helix: 1.51 (0.05), residues: 9071 sheet: 0.51 (0.16), residues: 1068 loop : -0.64 (0.07), residues: 7741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPS2 149 HIS 0.011 0.001 HISS2 130 PHE 0.032 0.002 PHES7 46 TYR 0.041 0.002 TYRB9 5 ARG 0.006 0.000 ARGC3 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1017 time to evaluate : 13.413 Fit side-chains REVERT: 1 29 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7675 (mtt) REVERT: 1 109 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8412 (tpp) REVERT: 3A 286 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8077 (ttpp) REVERT: 3B 257 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (tp40) REVERT: 3C 286 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6436 (tpp) REVERT: 3E 144 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: 3G 189 TYR cc_start: 0.2726 (OUTLIER) cc_final: 0.1868 (p90) REVERT: 3G 286 GLU cc_start: 0.7044 (tp30) cc_final: 0.6505 (tp30) REVERT: 3G 290 ASN cc_start: 0.7819 (m-40) cc_final: 0.6453 (m-40) REVERT: 3H 31 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: 3H 55 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: 3I 35 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: 3I 114 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: 3a 349 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: 3b 230 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7019 (p0) REVERT: 3c 213 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7876 (ttt) REVERT: 3c 286 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5055 (tpp) REVERT: 3d 242 MET cc_start: 0.8778 (mmm) cc_final: 0.8467 (mmm) REVERT: 3f 15 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: 3f 23 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7603 (tp) REVERT: 3f 26 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: 3h 1 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6892 (mtp) REVERT: 3l 22 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5503 (tm-30) REVERT: 5 191 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8737 (tt) REVERT: 5 693 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7066 (p0) REVERT: AB 69 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8155 (ttmt) REVERT: AB 83 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7084 (mtm-85) REVERT: AM 34 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7363 (mmmm) REVERT: AM 41 ASP cc_start: 0.7161 (p0) cc_final: 0.6859 (p0) REVERT: AM 70 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: B8 56 MET cc_start: 0.8752 (mmt) cc_final: 0.8514 (tpt) REVERT: J1 21 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: T1 216 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7919 (mptt) REVERT: A1 63 ASP cc_start: 0.7990 (m-30) cc_final: 0.7684 (m-30) REVERT: T6 99 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7833 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8594 (mttp) REVERT: S1 481 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: S2 318 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6419 (m-40) REVERT: S2 434 ASP cc_start: 0.5911 (p0) cc_final: 0.5701 (p0) REVERT: S4 15 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: S4 25 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7334 (ptpt) REVERT: S4 183 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: S7 1 MET cc_start: 0.4975 (mmp) cc_final: 0.4611 (mmm) REVERT: S8 29 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: V1 457 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7857 (mmtt) REVERT: V2 242 LYS cc_start: 0.7829 (ttpp) cc_final: 0.7567 (ttmt) REVERT: BM 196 ASP cc_start: 0.7985 (t70) cc_final: 0.7439 (t70) REVERT: T4 194 ASN cc_start: 0.7646 (t0) cc_final: 0.7411 (t0) REVERT: B2 98 ASN cc_start: 0.7846 (m110) cc_final: 0.7305 (m-40) REVERT: T3 231 TYR cc_start: 0.8058 (t80) cc_final: 0.7653 (t80) REVERT: P1 50 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6707 (pp20) REVERT: P1 77 ARG cc_start: 0.6866 (mtm-85) cc_final: 0.6607 (ptp-110) REVERT: S5 86 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: P2 37 ILE cc_start: 0.8149 (mt) cc_final: 0.7825 (mp) REVERT: P2 48 ASN cc_start: 0.7736 (p0) cc_final: 0.7383 (p0) REVERT: P2 84 ILE cc_start: 0.8468 (mt) cc_final: 0.8168 (mm) REVERT: P2 87 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: P2 163 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: T9 43 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: T7 27 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7942 (mtpt) REVERT: T7 75 ILE cc_start: 0.7333 (pt) cc_final: 0.7076 (pp) REVERT: T7 124 ASP cc_start: 0.8696 (p0) cc_final: 0.8431 (p0) outliers start: 272 outliers final: 102 residues processed: 1182 average time/residue: 2.2523 time to fit residues: 3873.4625 Evaluate side-chains 1107 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 963 time to evaluate : 13.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 109 MET Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 482 LYS Chi-restraints excluded: chain 3B residue 257 GLN Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 40 LEU Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 144 GLN Chi-restraints excluded: chain 3E residue 150 THR Chi-restraints excluded: chain 3E residue 160 ASN Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3G residue 62 LEU Chi-restraints excluded: chain 3G residue 95 ARG Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 349 GLU Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3b residue 230 ASP Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 325 THR Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3h residue 1 MET Chi-restraints excluded: chain 3h residue 18 GLU Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 1 MET Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 319 ASP Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 5B residue 29 SER Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 94 VAL Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 34 LYS Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 79 ASP Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B7 residue 48 GLU Chi-restraints excluded: chain B8 residue 105 THR Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 41 MET Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 116 ASP Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T2 residue 242 SER Chi-restraints excluded: chain T1 residue 216 LYS Chi-restraints excluded: chain T1 residue 333 THR Chi-restraints excluded: chain T1 residue 374 VAL Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S4 residue 15 GLU Chi-restraints excluded: chain S4 residue 25 LYS Chi-restraints excluded: chain S4 residue 183 GLU Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 26 ILE Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain S8 residue 142 CYS Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TX residue 155 THR Chi-restraints excluded: chain A8 residue 109 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 457 LYS Chi-restraints excluded: chain V2 residue 189 THR Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain P1 residue 27 LYS Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain P2 residue 163 GLU Chi-restraints excluded: chain A3 residue 83 LYS Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 27 LYS Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1605 optimal weight: 30.0000 chunk 1221 optimal weight: 9.9990 chunk 843 optimal weight: 0.0270 chunk 179 optimal weight: 1.9990 chunk 775 optimal weight: 8.9990 chunk 1091 optimal weight: 10.0000 chunk 1630 optimal weight: 6.9990 chunk 1726 optimal weight: 5.9990 chunk 851 optimal weight: 10.0000 chunk 1545 optimal weight: 9.9990 chunk 465 optimal weight: 10.0000 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN ** 2 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 ASN ** 3A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 98 GLN 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN 3d 183 HIS ** 4 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 163 GLN ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 28 GLN AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3 242 HIS TD 61 GLN TD 64 GLN T2 130 ASN T1 102 ASN T1 132 ASN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 59 GLN T5 69 HIS T5 181 GLN S1 134 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN ** S6 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 22 GLN TX 128 GLN A8 187 ASN V1 223 GLN V1 233 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 25 ASN T3 233 HIS P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.247 157249 Z= 0.488 Angle : 1.145 50.666 212531 Z= 0.720 Chirality : 0.213 6.507 22368 Planarity : 0.005 0.059 26786 Dihedral : 12.686 179.403 23676 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.51 % Favored : 96.48 % Rotamer: Outliers : 2.10 % Allowed : 10.83 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.68 (0.06), residues: 17880 helix: 1.44 (0.05), residues: 9074 sheet: 0.47 (0.16), residues: 1044 loop : -0.72 (0.07), residues: 7762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP4L 8 HIS 0.011 0.001 HISS2 130 PHE 0.028 0.002 PHEA6 22 TYR 0.042 0.002 TYRB9 5 ARG 0.006 0.000 ARGA3 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 988 time to evaluate : 13.160 Fit side-chains revert: symmetry clash REVERT: 1 29 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7642 (mtt) REVERT: 1 109 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8505 (tpp) REVERT: 3A 286 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8096 (ttpp) REVERT: 3C 213 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8032 (ttt) REVERT: 3C 286 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6479 (tpp) REVERT: 3E 32 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7565 (mp-120) REVERT: 3G 189 TYR cc_start: 0.2732 (OUTLIER) cc_final: 0.1916 (p90) REVERT: 3G 286 GLU cc_start: 0.7064 (tp30) cc_final: 0.6641 (tp30) REVERT: 3G 290 ASN cc_start: 0.7846 (m-40) cc_final: 0.6719 (m-40) REVERT: 3H 31 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: 3H 55 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: 3I 35 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: 3I 114 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: 3a 349 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6972 (tp30) REVERT: 3c 213 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7870 (ttt) REVERT: 3c 286 MET cc_start: 0.5490 (OUTLIER) cc_final: 0.5090 (tpp) REVERT: 3c 415 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7099 (t80) REVERT: 3f 15 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: 3f 23 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7696 (tp) REVERT: 3f 26 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: 3g 16 LYS cc_start: 0.6516 (mttp) cc_final: 0.6060 (ttpp) REVERT: 3h 75 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6556 (mmt) REVERT: 3j 44 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7794 (mp) REVERT: 4L 32 MET cc_start: 0.9132 (mmm) cc_final: 0.8853 (mmm) REVERT: 5 191 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8773 (tt) REVERT: 5 693 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7074 (p0) REVERT: 5 720 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7376 (ptt90) REVERT: 6 160 GLU cc_start: 0.7471 (pm20) cc_final: 0.7263 (pm20) REVERT: A5 73 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: A5 128 GLN cc_start: 0.8089 (mt0) cc_final: 0.7702 (mt0) REVERT: AB 69 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8153 (ttmt) REVERT: AC 70 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (mtpt) REVERT: AM 34 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7400 (mmmm) REVERT: AM 70 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: B8 56 MET cc_start: 0.8738 (mmt) cc_final: 0.8524 (tpt) REVERT: B8 190 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (mppt) REVERT: C1 44 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.6826 (p90) REVERT: J1 21 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: FX 41 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8566 (mmpt) REVERT: T1 216 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7982 (mptt) REVERT: T1 447 MET cc_start: 0.8441 (tpt) cc_final: 0.8207 (mmt) REVERT: A1 63 ASP cc_start: 0.8037 (m-30) cc_final: 0.7690 (m-30) REVERT: T6 99 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7854 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: S1 311 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7546 (tptt) REVERT: S1 481 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: S2 318 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.6430 (m-40) REVERT: S2 434 ASP cc_start: 0.5888 (p0) cc_final: 0.5676 (p0) REVERT: S2 442 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7164 (ptt90) REVERT: S4 15 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6663 (pp20) REVERT: S4 25 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7361 (ptpt) REVERT: S4 183 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: S8 29 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: TX 128 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8404 (tp40) REVERT: V1 457 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7886 (mmtt) REVERT: V2 242 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7564 (ttmt) REVERT: C4 13 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8476 (tp) REVERT: T4 25 MET cc_start: 0.8388 (mtt) cc_final: 0.8012 (mtt) REVERT: T4 194 ASN cc_start: 0.7687 (t0) cc_final: 0.7467 (t0) REVERT: B2 98 ASN cc_start: 0.7889 (m110) cc_final: 0.7367 (m-40) REVERT: T3 231 TYR cc_start: 0.8021 (t80) cc_final: 0.7800 (t80) REVERT: P1 50 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6617 (pp20) REVERT: P1 77 ARG cc_start: 0.6874 (mtm-85) cc_final: 0.6560 (ptp-110) REVERT: TA 48 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8590 (tp40) REVERT: S5 86 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: P2 37 ILE cc_start: 0.8209 (mt) cc_final: 0.7848 (mp) REVERT: P2 48 ASN cc_start: 0.7743 (p0) cc_final: 0.7379 (p0) REVERT: P2 84 ILE cc_start: 0.8454 (mt) cc_final: 0.8158 (mm) REVERT: P2 87 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: P2 163 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: T9 43 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: T7 27 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7906 (mtpt) REVERT: T7 124 ASP cc_start: 0.8703 (p0) cc_final: 0.8442 (p0) outliers start: 335 outliers final: 155 residues processed: 1216 average time/residue: 2.1928 time to fit residues: 3882.7307 Evaluate side-chains 1164 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 957 time to evaluate : 13.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 MET Chi-restraints excluded: chain 1 residue 109 MET Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 344 THR Chi-restraints excluded: chain 3A residue 70 THR Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3A residue 482 LYS Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 40 LEU Chi-restraints excluded: chain 3C residue 213 MET Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 340 ASP Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 30 ASP Chi-restraints excluded: chain 3D residue 191 ASP Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3D residue 214 VAL Chi-restraints excluded: chain 3E residue 32 GLN Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 150 THR Chi-restraints excluded: chain 3E residue 160 ASN Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3G residue 62 LEU Chi-restraints excluded: chain 3G residue 95 ARG Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 241 LEU Chi-restraints excluded: chain 3a residue 349 GLU Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 172 GLU Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 325 THR Chi-restraints excluded: chain 3c residue 351 ASP Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3g residue 170 THR Chi-restraints excluded: chain 3g residue 231 THR Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 18 GLU Chi-restraints excluded: chain 3h residue 75 MET Chi-restraints excluded: chain 3h residue 81 THR Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 4 residue 58 PHE Chi-restraints excluded: chain 4 residue 319 ASP Chi-restraints excluded: chain 4 residue 467 MET Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 720 ARG Chi-restraints excluded: chain 5B residue 29 SER Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 188 ILE Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 73 MET Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 70 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 94 VAL Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AL residue 115 ASN Chi-restraints excluded: chain AM residue 34 LYS Chi-restraints excluded: chain AM residue 59 LEU Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 79 ASP Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 105 THR Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 41 MET Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain C3 residue 327 THR Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 57 ILE Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 208 GLN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T2 residue 242 SER Chi-restraints excluded: chain T1 residue 87 VAL Chi-restraints excluded: chain T1 residue 216 LYS Chi-restraints excluded: chain T1 residue 333 THR Chi-restraints excluded: chain T1 residue 374 VAL Chi-restraints excluded: chain T1 residue 391 ASN Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 65 ILE Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 311 LYS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 442 ARG Chi-restraints excluded: chain S3 residue 22 MET Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S3 residue 95 LEU Chi-restraints excluded: chain S4 residue 15 GLU Chi-restraints excluded: chain S4 residue 25 LYS Chi-restraints excluded: chain S4 residue 183 GLU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S8 residue 26 ILE Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain S8 residue 142 CYS Chi-restraints excluded: chain B9 residue 5 TYR Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TX residue 155 THR Chi-restraints excluded: chain A8 residue 109 THR Chi-restraints excluded: chain A8 residue 138 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 122 GLU Chi-restraints excluded: chain V1 residue 132 LEU Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V1 residue 457 LYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 189 THR Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain C4 residue 13 LEU Chi-restraints excluded: chain C4 residue 29 THR Chi-restraints excluded: chain C4 residue 90 GLU Chi-restraints excluded: chain AN residue 81 THR Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T4 residue 117 LEU Chi-restraints excluded: chain B2 residue 110 LYS Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain TA residue 48 GLN Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain P2 residue 163 GLU Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 27 LYS Chi-restraints excluded: chain T7 residue 115 THR Chi-restraints excluded: chain T7 residue 123 LYS Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1437 optimal weight: 0.9980 chunk 979 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 1285 optimal weight: 2.9990 chunk 712 optimal weight: 4.9990 chunk 1473 optimal weight: 8.9990 chunk 1193 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 881 optimal weight: 0.9990 chunk 1549 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 3 12 ASN 3A 302 ASN 3B 176 GLN 3B 227 ASN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 316 HIS ** 3a 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN ** 3g 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 163 GLN A7 41 ASN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 112 ASN TD 61 GLN TD 64 GLN T2 130 ASN T2 208 GLN T1 102 ASN T1 132 ASN T1 146 GLN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN ** S6 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 22 GLN A8 187 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T8 105 GLN T8 135 ASN B2 25 ASN T3 56 GLN T3 233 HIS P1 55 GLN P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T9 51 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.249 157249 Z= 0.384 Angle : 1.095 50.629 212531 Z= 0.699 Chirality : 0.211 6.414 22368 Planarity : 0.004 0.055 26786 Dihedral : 12.198 178.733 23676 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.18 % Favored : 96.81 % Rotamer: Outliers : 1.82 % Allowed : 12.15 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 0.96 (0.06), residues: 17880 helix: 1.71 (0.05), residues: 9067 sheet: 0.48 (0.16), residues: 1070 loop : -0.63 (0.07), residues: 7743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP4L 8 HIS 0.006 0.001 HISAN 12 PHE 0.024 0.001 PHEA6 22 TYR 0.032 0.001 TYR3C 304 ARG 0.006 0.000 ARGA3 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1031 time to evaluate : 18.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: 2 184 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8788 (mp) REVERT: 3A 286 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8117 (ttpp) REVERT: 3A 382 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: 3C 65 MET cc_start: 0.8401 (mtp) cc_final: 0.8152 (mtt) REVERT: 3E 144 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: 3F 36 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: 3G 189 TYR cc_start: 0.2762 (OUTLIER) cc_final: 0.1944 (p90) REVERT: 3G 286 GLU cc_start: 0.7012 (tp30) cc_final: 0.6564 (tp30) REVERT: 3G 290 ASN cc_start: 0.7824 (m-40) cc_final: 0.6654 (m-40) REVERT: 3H 55 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: 3I 114 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: 3a 349 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: 3c 213 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7761 (ttt) REVERT: 3c 286 MET cc_start: 0.5424 (OUTLIER) cc_final: 0.5052 (tpp) REVERT: 3c 415 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7063 (t80) REVERT: 3d 242 MET cc_start: 0.8788 (mmm) cc_final: 0.8485 (mmm) REVERT: 3f 15 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: 3f 22 GLU cc_start: 0.6615 (pm20) cc_final: 0.6387 (pm20) REVERT: 3f 23 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.6779 (tp) REVERT: 3f 26 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: 3f 27 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6490 (m90) REVERT: 3f 56 MET cc_start: 0.3403 (tpt) cc_final: 0.2975 (tpt) REVERT: 3g 16 LYS cc_start: 0.6374 (mttp) cc_final: 0.5933 (ttpp) REVERT: 3h 1 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6833 (mtp) REVERT: 3j 44 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7771 (mp) REVERT: 3l 22 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5390 (tm-30) REVERT: 5 191 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8640 (tt) REVERT: 5 693 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6863 (p0) REVERT: AB 69 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8125 (ttmt) REVERT: AM 70 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6916 (mm-30) REVERT: B8 56 MET cc_start: 0.8698 (mmt) cc_final: 0.8470 (tpt) REVERT: B8 190 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7887 (mppt) REVERT: C1 44 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6810 (p90) REVERT: FX 41 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8591 (mmpt) REVERT: T1 111 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7011 (mppt) REVERT: T1 216 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: T1 447 MET cc_start: 0.8422 (tpt) cc_final: 0.8133 (mmt) REVERT: A1 22 VAL cc_start: 0.8495 (m) cc_final: 0.8268 (t) REVERT: A1 63 ASP cc_start: 0.8057 (m-30) cc_final: 0.7714 (m-30) REVERT: T6 99 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7780 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8603 (mttp) REVERT: S1 311 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7503 (tptt) REVERT: S1 481 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: S2 318 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6404 (m-40) REVERT: S2 442 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7099 (ptt90) REVERT: S7 1 MET cc_start: 0.5068 (mmp) cc_final: 0.4708 (mmm) REVERT: S8 29 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: S8 94 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6903 (t80) REVERT: V2 242 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7448 (ttmt) REVERT: C4 67 GLU cc_start: 0.7605 (tp30) cc_final: 0.7356 (tm-30) REVERT: T4 25 MET cc_start: 0.8358 (mtt) cc_final: 0.8034 (mtt) REVERT: T3 137 ASN cc_start: 0.7458 (p0) cc_final: 0.6635 (p0) REVERT: T3 231 TYR cc_start: 0.8005 (t80) cc_final: 0.7794 (t80) REVERT: P1 50 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6469 (pp20) REVERT: P1 77 ARG cc_start: 0.6788 (mtm-85) cc_final: 0.6484 (ptp-110) REVERT: P2 48 ASN cc_start: 0.7679 (p0) cc_final: 0.7285 (p0) REVERT: P2 84 ILE cc_start: 0.8406 (mt) cc_final: 0.8126 (mm) REVERT: P2 87 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: T9 43 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: T7 75 ILE cc_start: 0.7361 (pt) cc_final: 0.7059 (pp) REVERT: T7 106 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6995 (ttm170) REVERT: T7 124 ASP cc_start: 0.8703 (p0) cc_final: 0.8424 (p0) outliers start: 291 outliers final: 128 residues processed: 1230 average time/residue: 2.1593 time to fit residues: 3900.7069 Evaluate side-chains 1130 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 962 time to evaluate : 13.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3A residue 122 LEU Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 382 GLU Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 178 ILE Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 30 ASP Chi-restraints excluded: chain 3E residue 144 GLN Chi-restraints excluded: chain 3E residue 160 ASN Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3F residue 78 ILE Chi-restraints excluded: chain 3G residue 62 LEU Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 263 THR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 349 GLU Chi-restraints excluded: chain 3a residue 454 VAL Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 27 HIS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3h residue 1 MET Chi-restraints excluded: chain 3h residue 18 GLU Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 1 MET Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 58 PHE Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 425 SER Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 5B residue 41 SER Chi-restraints excluded: chain 6 residue 226 ASP Chi-restraints excluded: chain A2 residue 46 ASN Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 108 ASN Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 105 THR Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 41 MET Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C1 residue 103 THR Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C3 residue 195 THR Chi-restraints excluded: chain TD residue 72 LYS Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 216 LYS Chi-restraints excluded: chain T1 residue 313 ASP Chi-restraints excluded: chain T1 residue 333 THR Chi-restraints excluded: chain T1 residue 391 ASN Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 17 LYS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 296 ASP Chi-restraints excluded: chain S1 residue 311 LYS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S1 residue 669 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 442 ARG Chi-restraints excluded: chain S3 residue 22 MET Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S6 residue 63 THR Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain S8 residue 94 PHE Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TB residue 26 THR Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain B4 residue 42 LEU Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T4 residue 117 LEU Chi-restraints excluded: chain B2 residue 110 LYS Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 135 VAL Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 84 PHE Chi-restraints excluded: chain T7 residue 115 THR Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 580 optimal weight: 0.9990 chunk 1554 optimal weight: 8.9990 chunk 341 optimal weight: 0.8980 chunk 1013 optimal weight: 9.9990 chunk 426 optimal weight: 3.9990 chunk 1728 optimal weight: 0.3980 chunk 1434 optimal weight: 20.0000 chunk 800 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 571 optimal weight: 10.0000 chunk 907 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 3 12 ASN ** 3A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3D 120 HIS 3a 302 ASN ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN ** 3g 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 241 GLN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3 114 GLN C3 305 GLN TD 61 GLN TD 64 GLN J1 39 GLN T2 130 ASN T1 63 GLN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN ** S6 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 22 GLN TX 128 GLN A8 187 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 25 ASN T3 56 GLN T3 233 HIS P1 55 GLN P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 157249 Z= 0.382 Angle : 1.093 50.607 212531 Z= 0.697 Chirality : 0.211 6.403 22368 Planarity : 0.004 0.055 26786 Dihedral : 11.964 177.889 23676 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Rotamer: Outliers : 1.99 % Allowed : 12.66 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.06), residues: 17880 helix: 1.80 (0.05), residues: 9073 sheet: 0.47 (0.16), residues: 1075 loop : -0.59 (0.07), residues: 7732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP4L 8 HIS 0.005 0.001 HIS3I 79 PHE 0.024 0.001 PHEV2 229 TYR 0.027 0.001 TYR 5 605 ARG 0.006 0.000 ARGA3 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 1004 time to evaluate : 12.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: 1 109 MET cc_start: 0.8555 (tpp) cc_final: 0.8096 (mmm) REVERT: 2 184 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8750 (mp) REVERT: 3A 286 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8116 (ttpp) REVERT: 3A 382 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: 3E 144 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: 3F 36 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: 3G 189 TYR cc_start: 0.2814 (OUTLIER) cc_final: 0.2022 (p90) REVERT: 3G 286 GLU cc_start: 0.7033 (tp30) cc_final: 0.6500 (tp30) REVERT: 3G 290 ASN cc_start: 0.7836 (m-40) cc_final: 0.6580 (m-40) REVERT: 3H 31 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: 3H 55 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: 3I 35 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: 3a 349 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: 3c 213 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7735 (ttt) REVERT: 3c 286 MET cc_start: 0.5416 (OUTLIER) cc_final: 0.5051 (tpp) REVERT: 3c 415 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7033 (t80) REVERT: 3d 242 MET cc_start: 0.8779 (mmm) cc_final: 0.8385 (mmm) REVERT: 3f 15 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: 3f 22 GLU cc_start: 0.6582 (pm20) cc_final: 0.6343 (pm20) REVERT: 3f 23 LEU cc_start: 0.7929 (tm) cc_final: 0.7473 (tp) REVERT: 3f 26 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6684 (mp10) REVERT: 3g 16 LYS cc_start: 0.6398 (mttp) cc_final: 0.5964 (ttpp) REVERT: 3g 89 MET cc_start: 0.7494 (mtt) cc_final: 0.7261 (mtp) REVERT: 3j 44 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7769 (mp) REVERT: 3l 22 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5385 (tm-30) REVERT: 4L 32 MET cc_start: 0.9025 (mmm) cc_final: 0.8763 (mmm) REVERT: 5 191 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (tt) REVERT: 5 283 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: 5 693 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6724 (p0) REVERT: A5 73 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: AB 69 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8111 (ttmt) REVERT: AB 83 ARG cc_start: 0.7450 (mtm110) cc_final: 0.7171 (mtm-85) REVERT: AM 70 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: B8 56 MET cc_start: 0.8692 (mmt) cc_final: 0.8466 (tpt) REVERT: B8 112 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B8 190 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7592 (mppt) REVERT: C1 44 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.6769 (p90) REVERT: C2 82 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8564 (m) REVERT: C2 172 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9007 (tp) REVERT: J1 21 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: FX 41 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8606 (mmpt) REVERT: FX 153 MET cc_start: 0.9146 (mtt) cc_final: 0.8918 (mtt) REVERT: T1 111 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.6984 (mppt) REVERT: T1 447 MET cc_start: 0.8431 (tpt) cc_final: 0.8116 (mmt) REVERT: A1 13 ILE cc_start: 0.8453 (pt) cc_final: 0.8246 (pp) REVERT: A1 63 ASP cc_start: 0.8042 (m-30) cc_final: 0.7689 (m-30) REVERT: T6 99 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7753 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: S1 311 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7527 (tptt) REVERT: S1 481 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: S2 194 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: S2 318 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6356 (m-40) REVERT: S2 442 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7071 (ptt90) REVERT: S8 29 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: S8 94 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6901 (t80) REVERT: V2 242 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7509 (ttmt) REVERT: BM 159 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7939 (mtt) REVERT: C4 67 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: B2 110 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8166 (mttt) REVERT: T3 137 ASN cc_start: 0.7483 (p0) cc_final: 0.6691 (p0) REVERT: T3 200 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7774 (m) REVERT: T3 231 TYR cc_start: 0.8013 (t80) cc_final: 0.7796 (t80) REVERT: T3 234 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: P1 50 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6468 (pp20) REVERT: P1 77 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6498 (ptp-110) REVERT: TA 48 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8565 (tp40) REVERT: S5 86 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.7043 (pt0) REVERT: P2 48 ASN cc_start: 0.7688 (p0) cc_final: 0.7265 (p0) REVERT: P2 84 ILE cc_start: 0.8414 (mt) cc_final: 0.8126 (mm) REVERT: P2 87 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: T9 43 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: T7 19 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6507 (t0) REVERT: T7 75 ILE cc_start: 0.7354 (pt) cc_final: 0.7064 (pp) REVERT: T7 124 ASP cc_start: 0.8718 (p0) cc_final: 0.8431 (p0) outliers start: 318 outliers final: 155 residues processed: 1234 average time/residue: 2.1424 time to fit residues: 3863.7403 Evaluate side-chains 1179 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 972 time to evaluate : 12.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 3A residue 122 LEU Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 382 GLU Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 40 LEU Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 30 ASP Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 144 GLN Chi-restraints excluded: chain 3E residue 150 THR Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 263 THR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3J residue 43 MET Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 241 LEU Chi-restraints excluded: chain 3a residue 349 GLU Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 58 CYS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 18 GLU Chi-restraints excluded: chain 3h residue 41 VAL Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 319 ASP Chi-restraints excluded: chain 4 residue 425 SER Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 283 GLU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 5B residue 29 SER Chi-restraints excluded: chain 5B residue 41 SER Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 188 ILE Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 73 MET Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain A9 residue 200 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 79 ASP Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 105 THR Chi-restraints excluded: chain B8 residue 112 ILE Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 41 MET Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C2 residue 32 LYS Chi-restraints excluded: chain C2 residue 82 VAL Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C2 residue 172 LEU Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain TD residue 72 LYS Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 258 LEU Chi-restraints excluded: chain T1 residue 278 ILE Chi-restraints excluded: chain T1 residue 333 THR Chi-restraints excluded: chain T1 residue 391 ASN Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain X1 residue 59 LEU Chi-restraints excluded: chain T6 residue 68 CYS Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 296 ASP Chi-restraints excluded: chain S1 residue 311 LYS Chi-restraints excluded: chain S1 residue 372 HIS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S1 residue 669 VAL Chi-restraints excluded: chain S2 residue 194 GLU Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 442 ARG Chi-restraints excluded: chain S3 residue 22 MET Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 99 ILE Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S7 residue 29 LEU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 46 PHE Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 26 ILE Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain S8 residue 94 PHE Chi-restraints excluded: chain B9 residue 5 TYR Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 293 MET Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 189 THR Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain BM residue 159 MET Chi-restraints excluded: chain BM residue 205 LEU Chi-restraints excluded: chain C4 residue 67 GLU Chi-restraints excluded: chain AN residue 81 THR Chi-restraints excluded: chain B4 residue 42 LEU Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T4 residue 117 LEU Chi-restraints excluded: chain B2 residue 110 LYS Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 200 VAL Chi-restraints excluded: chain T3 residue 234 GLU Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain TA residue 48 GLN Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain TC residue 92 LYS Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain A3 residue 12 ASP Chi-restraints excluded: chain A3 residue 70 CYS Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 19 ASP Chi-restraints excluded: chain T7 residue 84 PHE Chi-restraints excluded: chain T7 residue 115 THR Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1666 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 984 optimal weight: 20.0000 chunk 1261 optimal weight: 0.9980 chunk 977 optimal weight: 10.0000 chunk 1454 optimal weight: 7.9990 chunk 964 optimal weight: 30.0000 chunk 1721 optimal weight: 5.9990 chunk 1077 optimal weight: 7.9990 chunk 1049 optimal weight: 8.9990 chunk 794 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 2 237 ASN 2 308 ASN 3 12 ASN ** 3A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 302 ASN ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN A5 163 GLN A7 41 ASN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN J1 39 GLN T2 130 ASN T1 63 GLN T1 250 GLN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN X1 140 ASN T5 69 HIS T5 181 GLN ** T5 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN S8 22 GLN A8 187 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 25 ASN T3 233 HIS P1 55 GLN P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 157249 Z= 0.458 Angle : 1.131 50.595 212531 Z= 0.713 Chirality : 0.213 6.484 22368 Planarity : 0.004 0.071 26786 Dihedral : 12.184 179.431 23676 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 2.14 % Allowed : 13.13 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % 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: 0.84 (0.06), residues: 17880 helix: 1.61 (0.05), residues: 9075 sheet: 0.44 (0.16), residues: 1065 loop : -0.68 (0.07), residues: 7740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP4L 8 HIS 0.008 0.001 HISS2 130 PHE 0.027 0.002 PHEV2 229 TYR 0.035 0.002 TYRB9 5 ARG 0.014 0.000 ARGT7 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 981 time to evaluate : 12.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6317 (mt-10) REVERT: 2 184 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8801 (mp) REVERT: 3A 286 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8156 (ttpp) REVERT: 3A 382 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: 3E 32 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: 3E 144 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: 3F 36 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7057 (tp30) REVERT: 3G 95 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7606 (mmp-170) REVERT: 3G 189 TYR cc_start: 0.2952 (OUTLIER) cc_final: 0.2248 (p90) REVERT: 3G 286 GLU cc_start: 0.7052 (tp30) cc_final: 0.6500 (tp30) REVERT: 3G 290 ASN cc_start: 0.7844 (m-40) cc_final: 0.6626 (m-40) REVERT: 3H 31 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: 3H 55 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: 3I 35 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: 3I 114 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6044 (mp0) REVERT: 3a 349 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: 3c 213 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7653 (tmt) REVERT: 3c 286 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.5093 (tpp) REVERT: 3c 415 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.6954 (t80) REVERT: 3d 113 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8159 (m) REVERT: 3d 242 MET cc_start: 0.8779 (mmm) cc_final: 0.8432 (mmm) REVERT: 3f 15 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: 3f 23 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7727 (tp) REVERT: 3f 26 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: 3g 16 LYS cc_start: 0.6554 (mttp) cc_final: 0.6108 (ttpp) REVERT: 3g 292 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6254 (mp) REVERT: 3j 44 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7747 (mp) REVERT: 3l 22 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5418 (tm-30) REVERT: 5 191 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8719 (tt) REVERT: 5 693 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6948 (p0) REVERT: A5 73 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7656 (mtp) REVERT: AB 69 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8142 (ttmt) REVERT: AM 34 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (mmmm) REVERT: AM 70 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: B8 56 MET cc_start: 0.8707 (mmt) cc_final: 0.8500 (tpt) REVERT: B8 112 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7986 (pp) REVERT: C1 44 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6879 (p90) REVERT: C1 191 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: C2 82 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8588 (m) REVERT: J1 21 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: FX 41 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8601 (mmpt) REVERT: T1 111 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6995 (mppt) REVERT: T1 216 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7890 (mttt) REVERT: T1 447 MET cc_start: 0.8455 (tpt) cc_final: 0.8133 (mmt) REVERT: A1 63 ASP cc_start: 0.8029 (m-30) cc_final: 0.7654 (m-30) REVERT: T6 99 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7815 (ttm-80) REVERT: T5 79 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: S1 311 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7493 (tptt) REVERT: S1 481 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: S2 318 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6396 (m-40) REVERT: S2 442 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7198 (ptt90) REVERT: S4 93 MET cc_start: 0.8491 (mmm) cc_final: 0.8192 (mmm) REVERT: S8 29 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: S8 94 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6961 (t80) REVERT: V1 122 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: V2 242 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7533 (ttmt) REVERT: C4 67 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: T3 137 ASN cc_start: 0.7505 (p0) cc_final: 0.6705 (p0) REVERT: T3 200 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7831 (m) REVERT: T3 231 TYR cc_start: 0.8027 (t80) cc_final: 0.7797 (t80) REVERT: P1 50 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: P1 77 ARG cc_start: 0.6868 (mtm-85) cc_final: 0.6518 (ptp-110) REVERT: TA 48 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8572 (tp40) REVERT: TA 92 TYR cc_start: 0.7825 (t80) cc_final: 0.7554 (t80) REVERT: S5 86 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.7051 (pt0) REVERT: TC 79 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7963 (mptp) REVERT: P2 37 ILE cc_start: 0.8199 (mt) cc_final: 0.7840 (mp) REVERT: P2 48 ASN cc_start: 0.7710 (p0) cc_final: 0.7318 (p0) REVERT: P2 84 ILE cc_start: 0.8449 (mt) cc_final: 0.8157 (mm) REVERT: P2 87 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: T9 43 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: T7 19 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6742 (t0) REVERT: T7 124 ASP cc_start: 0.8719 (p0) cc_final: 0.8445 (p0) outliers start: 342 outliers final: 185 residues processed: 1238 average time/residue: 2.1539 time to fit residues: 3919.0507 Evaluate side-chains 1202 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 961 time to evaluate : 13.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 131 ILE Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 237 ASN Chi-restraints excluded: chain 2 residue 344 THR Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3A residue 70 THR Chi-restraints excluded: chain 3A residue 122 LEU Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 272 GLN Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 382 GLU Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 40 LEU Chi-restraints excluded: chain 3C residue 178 ILE Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 30 ASP Chi-restraints excluded: chain 3D residue 191 ASP Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3E residue 32 GLN Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 144 GLN Chi-restraints excluded: chain 3E residue 150 THR Chi-restraints excluded: chain 3E residue 160 ASN Chi-restraints excluded: chain 3E residue 226 PHE Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3G residue 62 LEU Chi-restraints excluded: chain 3G residue 95 ARG Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 263 THR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3I residue 80 VAL Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 241 LEU Chi-restraints excluded: chain 3a residue 272 GLN Chi-restraints excluded: chain 3a residue 349 GLU Chi-restraints excluded: chain 3a residue 454 VAL Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 172 VAL Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 213 MET Chi-restraints excluded: chain 3c residue 236 GLU Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 325 THR Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 113 THR Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 55 GLU Chi-restraints excluded: chain 3f residue 58 CYS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3g residue 244 THR Chi-restraints excluded: chain 3g residue 292 LEU Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 18 GLU Chi-restraints excluded: chain 3h residue 41 VAL Chi-restraints excluded: chain 3h residue 81 THR Chi-restraints excluded: chain 3h residue 114 THR Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 58 PHE Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 425 SER Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 384 PHE Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 5B residue 29 SER Chi-restraints excluded: chain 5B residue 41 SER Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 188 ILE Chi-restraints excluded: chain 6 residue 226 ASP Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 73 MET Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A7 residue 26 THR Chi-restraints excluded: chain A7 residue 30 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain A9 residue 200 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 34 LYS Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 79 ASP Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 105 THR Chi-restraints excluded: chain B8 residue 112 ILE Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 41 MET Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C1 residue 103 THR Chi-restraints excluded: chain C1 residue 191 GLU Chi-restraints excluded: chain C2 residue 32 LYS Chi-restraints excluded: chain C2 residue 82 VAL Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 57 ILE Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 216 LYS Chi-restraints excluded: chain T1 residue 258 LEU Chi-restraints excluded: chain T1 residue 278 ILE Chi-restraints excluded: chain T1 residue 313 ASP Chi-restraints excluded: chain T1 residue 333 THR Chi-restraints excluded: chain T1 residue 391 ASN Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain X1 residue 59 LEU Chi-restraints excluded: chain T6 residue 68 CYS Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T5 residue 79 LYS Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 17 LYS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 296 ASP Chi-restraints excluded: chain S1 residue 311 LYS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S1 residue 669 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 356 GLU Chi-restraints excluded: chain S2 residue 442 ARG Chi-restraints excluded: chain S3 residue 22 MET Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S3 residue 95 LEU Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 99 ILE Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S7 residue 29 LEU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 46 PHE Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain S8 residue 48 ILE Chi-restraints excluded: chain S8 residue 94 PHE Chi-restraints excluded: chain B9 residue 5 TYR Chi-restraints excluded: chain B9 residue 26 TYR Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain A8 residue 109 THR Chi-restraints excluded: chain TB residue 45 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 122 GLU Chi-restraints excluded: chain V1 residue 132 LEU Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 189 THR Chi-restraints excluded: chain V2 residue 215 VAL Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain BM residue 205 LEU Chi-restraints excluded: chain C4 residue 67 GLU Chi-restraints excluded: chain AN residue 81 THR Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T4 residue 117 LEU Chi-restraints excluded: chain B2 residue 110 LYS Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 200 VAL Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain TA residue 48 GLN Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain TC residue 79 LYS Chi-restraints excluded: chain TC residue 92 LYS Chi-restraints excluded: chain P2 residue 44 THR Chi-restraints excluded: chain P2 residue 61 THR Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain A3 residue 70 CYS Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 19 ASP Chi-restraints excluded: chain T7 residue 115 THR Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1064 optimal weight: 10.0000 chunk 687 optimal weight: 0.9990 chunk 1028 optimal weight: 5.9990 chunk 518 optimal weight: 0.9980 chunk 338 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 1094 optimal weight: 6.9990 chunk 1172 optimal weight: 5.9990 chunk 851 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 1353 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 2 106 ASN 3 12 ASN 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3C 316 HIS ** 3H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3a 302 ASN ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN 3g 188 GLN A5 163 GLN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN J1 39 GLN T2 130 ASN T1 63 GLN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 57 ASN S8 22 GLN A8 187 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 25 ASN T3 233 HIS P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 157249 Z= 0.370 Angle : 1.088 50.807 212531 Z= 0.695 Chirality : 0.211 6.424 22368 Planarity : 0.004 0.064 26786 Dihedral : 11.783 177.142 23676 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 1.70 % Allowed : 13.73 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.06), residues: 17880 helix: 1.83 (0.05), residues: 9077 sheet: 0.48 (0.16), residues: 1062 loop : -0.58 (0.07), residues: 7741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP4L 8 HIS 0.005 0.001 HIS 4 367 PHE 0.028 0.001 PHEV2 229 TYR 0.027 0.001 TYR 5 605 ARG 0.007 0.000 ARGA3 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1017 time to evaluate : 13.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6315 (mt-10) REVERT: 1 109 MET cc_start: 0.8558 (tpp) cc_final: 0.7993 (mmm) REVERT: 2 184 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8739 (mp) REVERT: 2 290 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8759 (mt) REVERT: 2B 33 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7746 (tmt) REVERT: 3A 286 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: 3A 382 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: 3B 257 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: 3C 65 MET cc_start: 0.8359 (mtp) cc_final: 0.8115 (mtt) REVERT: 3C 286 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6327 (tpp) REVERT: 3F 36 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: 3G 189 TYR cc_start: 0.2868 (OUTLIER) cc_final: 0.2156 (p90) REVERT: 3G 286 GLU cc_start: 0.7038 (tp30) cc_final: 0.6504 (tp30) REVERT: 3G 290 ASN cc_start: 0.7838 (m-40) cc_final: 0.6687 (m-40) REVERT: 3H 31 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: 3H 55 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7143 (pt0) REVERT: 3I 35 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: 3I 114 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: 3c 286 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5221 (tpp) REVERT: 3c 415 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6981 (t80) REVERT: 3d 242 MET cc_start: 0.8795 (mmm) cc_final: 0.8405 (mmm) REVERT: 3f 15 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: 3f 22 GLU cc_start: 0.6696 (pm20) cc_final: 0.6382 (pm20) REVERT: 3f 23 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7584 (tp) REVERT: 3f 26 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: 3g 16 LYS cc_start: 0.6359 (mttp) cc_final: 0.5935 (ttpp) REVERT: 3g 292 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6231 (mp) REVERT: 3h 75 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6627 (mmt) REVERT: 3j 44 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7765 (mp) REVERT: 3l 22 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5411 (tm-30) REVERT: 5 191 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8602 (tt) REVERT: 5 693 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6703 (p0) REVERT: A5 73 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7622 (mtp) REVERT: AB 69 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8095 (ttmt) REVERT: AM 70 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: B8 56 MET cc_start: 0.8689 (mmt) cc_final: 0.8468 (tpt) REVERT: B8 112 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7969 (pp) REVERT: B8 190 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7784 (mppt) REVERT: C1 44 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6736 (p90) REVERT: C1 191 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: C2 172 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8988 (tp) REVERT: C3 250 MET cc_start: 0.8332 (mtp) cc_final: 0.8128 (mtp) REVERT: FX 41 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8611 (mmpt) REVERT: FX 153 MET cc_start: 0.9132 (mtt) cc_final: 0.8912 (mtt) REVERT: T1 111 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6906 (mppt) REVERT: T1 447 MET cc_start: 0.8432 (tpt) cc_final: 0.8113 (mmt) REVERT: A1 13 ILE cc_start: 0.8442 (pt) cc_final: 0.8239 (pp) REVERT: A1 22 VAL cc_start: 0.8488 (m) cc_final: 0.8269 (t) REVERT: A1 44 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8634 (pmt170) REVERT: A1 63 ASP cc_start: 0.8053 (m-30) cc_final: 0.7682 (m-30) REVERT: X1 150 ASP cc_start: 0.6559 (m-30) cc_final: 0.6323 (m-30) REVERT: T6 99 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7735 (ttm-80) REVERT: T5 178 GLN cc_start: 0.8595 (tp40) cc_final: 0.8328 (mm-40) REVERT: S1 481 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: S1 698 MET cc_start: 0.8931 (mmp) cc_final: 0.8233 (mmp) REVERT: S2 194 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: S2 318 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6384 (m-40) REVERT: S2 442 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7093 (ptt90) REVERT: S4 1 MET cc_start: 0.7206 (ppp) cc_final: 0.5986 (pmt) REVERT: S4 93 MET cc_start: 0.8489 (mmm) cc_final: 0.8237 (mmm) REVERT: S7 1 MET cc_start: 0.4470 (mmp) cc_final: 0.3874 (mmm) REVERT: S8 29 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: B9 76 MET cc_start: 0.8596 (mtm) cc_final: 0.8369 (mtp) REVERT: V1 122 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: V2 242 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7496 (ttmt) REVERT: B6 73 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: C4 67 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: T3 137 ASN cc_start: 0.7464 (p0) cc_final: 0.6704 (p0) REVERT: T3 200 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7754 (m) REVERT: T3 231 TYR cc_start: 0.7998 (t80) cc_final: 0.7741 (t80) REVERT: P1 50 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6446 (pp20) REVERT: P1 77 ARG cc_start: 0.6828 (mtm-85) cc_final: 0.6510 (ptp-110) REVERT: S5 86 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: TC 79 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7882 (mptp) REVERT: P2 48 ASN cc_start: 0.7686 (p0) cc_final: 0.7266 (p0) REVERT: P2 84 ILE cc_start: 0.8401 (mt) cc_final: 0.8127 (mm) REVERT: P2 87 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7181 (mm-30) REVERT: T9 43 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: T7 124 ASP cc_start: 0.8709 (p0) cc_final: 0.8437 (p0) outliers start: 272 outliers final: 142 residues processed: 1224 average time/residue: 2.1233 time to fit residues: 3812.1947 Evaluate side-chains 1168 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 975 time to evaluate : 12.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 184 ILE Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2B residue 33 MET Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3A residue 122 LEU Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 382 GLU Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 82 VAL Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 257 GLN Chi-restraints excluded: chain 3C residue 138 CYS Chi-restraints excluded: chain 3C residue 167 ILE Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 30 ASP Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3D residue 214 VAL Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 226 PHE Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 35 GLN Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 197 LEU Chi-restraints excluded: chain 3a residue 272 GLN Chi-restraints excluded: chain 3a residue 454 VAL Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 172 VAL Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3e residue 112 MET Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 58 CYS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3g residue 231 THR Chi-restraints excluded: chain 3g residue 244 THR Chi-restraints excluded: chain 3g residue 292 LEU Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 41 VAL Chi-restraints excluded: chain 3h residue 75 MET Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 1 MET Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 58 PHE Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 603 VAL Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 6 residue 188 ILE Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 73 MET Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A5 residue 175 VAL Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A6 residue 138 THR Chi-restraints excluded: chain A7 residue 30 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain A9 residue 200 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 70 GLU Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 65 VAL Chi-restraints excluded: chain B8 residue 112 ILE Chi-restraints excluded: chain B8 residue 189 GLU Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C1 residue 191 GLU Chi-restraints excluded: chain C2 residue 32 LYS Chi-restraints excluded: chain C2 residue 172 LEU Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain TD residue 72 LYS Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain FX residue 166 SER Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T2 residue 214 ASP Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 278 ILE Chi-restraints excluded: chain T1 residue 313 ASP Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain A1 residue 44 ARG Chi-restraints excluded: chain T6 residue 68 CYS Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain R residue 6 TRP Chi-restraints excluded: chain R residue 17 LYS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 100 MET Chi-restraints excluded: chain S1 residue 372 HIS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S2 residue 194 GLU Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 356 GLU Chi-restraints excluded: chain S2 residue 442 ARG Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S7 residue 29 LEU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 29 GLU Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TB residue 26 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 122 GLU Chi-restraints excluded: chain V1 residue 293 MET Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 215 VAL Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain B6 residue 73 GLN Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain BM residue 205 LEU Chi-restraints excluded: chain C4 residue 67 GLU Chi-restraints excluded: chain AN residue 81 THR Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T4 residue 117 LEU Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 200 VAL Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain B3 residue 46 ASP Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain TC residue 79 LYS Chi-restraints excluded: chain TC residue 92 LYS Chi-restraints excluded: chain P2 residue 87 GLU Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain T9 residue 43 GLU Chi-restraints excluded: chain T7 residue 84 PHE Chi-restraints excluded: chain T7 residue 115 THR Chi-restraints excluded: chain T7 residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1565 optimal weight: 6.9990 chunk 1649 optimal weight: 20.0000 chunk 1504 optimal weight: 2.9990 chunk 1604 optimal weight: 1.9990 chunk 1648 optimal weight: 5.9990 chunk 965 optimal weight: 9.9990 chunk 698 optimal weight: 7.9990 chunk 1259 optimal weight: 0.0050 chunk 492 optimal weight: 0.0670 chunk 1449 optimal weight: 0.6980 chunk 1517 optimal weight: 4.9990 overall best weight: 1.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 3 12 ASN 3A 104 ASN 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN 3g 188 GLN A5 163 GLN A7 98 GLN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN TD 70 HIS J1 39 GLN T2 130 ASN T1 250 GLN T1 359 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 425 ASN S3 57 ASN S6 99 GLN S8 22 GLN V1 468 ASN ** V2 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 191 ASN B2 25 ASN T3 233 HIS P1 55 GLN P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 157249 Z= 0.362 Angle : 1.079 50.750 212531 Z= 0.691 Chirality : 0.211 6.460 22368 Planarity : 0.004 0.058 26786 Dihedral : 11.377 175.210 23676 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 1.46 % Allowed : 14.15 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.06), residues: 17880 helix: 1.96 (0.06), residues: 9087 sheet: 0.54 (0.16), residues: 1062 loop : -0.52 (0.07), residues: 7731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPS4 119 HIS 0.005 0.001 HIS 4 367 PHE 0.028 0.001 PHEV2 229 TYR 0.035 0.001 TYR3C 304 ARG 0.008 0.000 ARGA3 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1021 time to evaluate : 13.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6347 (mt-10) REVERT: 1 109 MET cc_start: 0.8538 (tpp) cc_final: 0.8042 (mtp) REVERT: 2 290 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (mt) REVERT: 2B 33 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7725 (tmt) REVERT: 3A 142 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8100 (ttt) REVERT: 3A 286 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8136 (ttpp) REVERT: 3C 286 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.6312 (tpp) REVERT: 3F 36 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7041 (tp30) REVERT: 3G 189 TYR cc_start: 0.2879 (OUTLIER) cc_final: 0.2074 (p90) REVERT: 3G 286 GLU cc_start: 0.7034 (tp30) cc_final: 0.6368 (tp30) REVERT: 3G 290 ASN cc_start: 0.7907 (m-40) cc_final: 0.6689 (m-40) REVERT: 3H 31 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: 3H 55 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: 3I 114 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: 3c 286 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5260 (tpp) REVERT: 3c 415 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7001 (t80) REVERT: 3d 113 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7713 (t) REVERT: 3d 242 MET cc_start: 0.8786 (mmm) cc_final: 0.8519 (mmm) REVERT: 3f 15 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.6892 (mp-120) REVERT: 3f 22 GLU cc_start: 0.6689 (pm20) cc_final: 0.6376 (pm20) REVERT: 3f 23 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7535 (tp) REVERT: 3f 26 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: 3g 16 LYS cc_start: 0.6382 (mttp) cc_final: 0.5939 (ttpp) REVERT: 3h 75 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6581 (mmt) REVERT: 3h 117 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6164 (mpp) REVERT: 3j 44 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7745 (mp) REVERT: 3l 22 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5329 (tm-30) REVERT: 4L 32 MET cc_start: 0.8946 (mmm) cc_final: 0.8674 (mmm) REVERT: 5 191 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8523 (tt) REVERT: 5 693 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6408 (p0) REVERT: 6 79 GLU cc_start: 0.7536 (mp0) cc_final: 0.7285 (mp0) REVERT: A2 46 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7074 (t0) REVERT: A2 80 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7166 (mp0) REVERT: AB 69 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8097 (ttmt) REVERT: B8 56 MET cc_start: 0.8706 (mmt) cc_final: 0.8470 (tpt) REVERT: B8 112 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7989 (pp) REVERT: B8 190 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7881 (mppt) REVERT: C1 44 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6851 (p90) REVERT: C1 191 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: TD 72 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5618 (tmmt) REVERT: J1 21 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: FX 41 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8613 (mmpt) REVERT: T1 111 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6851 (mppt) REVERT: T1 447 MET cc_start: 0.8398 (tpt) cc_final: 0.8085 (mmt) REVERT: X1 150 ASP cc_start: 0.6433 (m-30) cc_final: 0.6218 (m-30) REVERT: T6 99 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7737 (ttm-80) REVERT: T5 178 GLN cc_start: 0.8593 (tp40) cc_final: 0.8298 (mm-40) REVERT: S1 481 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: S2 206 MET cc_start: 0.7804 (mtm) cc_final: 0.7553 (mtm) REVERT: S2 318 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.6278 (m-40) REVERT: S4 93 MET cc_start: 0.8486 (mmm) cc_final: 0.8221 (mmm) REVERT: S7 1 MET cc_start: 0.4508 (mmp) cc_final: 0.3930 (mmm) REVERT: B9 76 MET cc_start: 0.8578 (mtm) cc_final: 0.8345 (mtp) REVERT: V2 242 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7447 (ttmt) REVERT: B6 73 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: C4 67 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: AN 103 ARG cc_start: 0.7154 (mpt180) cc_final: 0.6901 (mpt180) REVERT: AN 105 MET cc_start: 0.7921 (mmm) cc_final: 0.7601 (mmm) REVERT: T3 137 ASN cc_start: 0.7521 (p0) cc_final: 0.6717 (p0) REVERT: T3 200 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7753 (m) REVERT: T3 231 TYR cc_start: 0.7902 (t80) cc_final: 0.7663 (t80) REVERT: P1 50 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6470 (pp20) REVERT: P1 77 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6499 (ptp-110) REVERT: TC 79 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7874 (mptp) REVERT: P2 48 ASN cc_start: 0.7722 (p0) cc_final: 0.7279 (p0) REVERT: P2 84 ILE cc_start: 0.8391 (mt) cc_final: 0.8102 (mm) REVERT: T7 75 ILE cc_start: 0.7203 (pt) cc_final: 0.6928 (pp) REVERT: T7 124 ASP cc_start: 0.8725 (p0) cc_final: 0.8449 (p0) outliers start: 233 outliers final: 132 residues processed: 1197 average time/residue: 2.1290 time to fit residues: 3736.6092 Evaluate side-chains 1155 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 982 time to evaluate : 12.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 2 residue 290 LEU Chi-restraints excluded: chain 2B residue 33 MET Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 82 VAL Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 269 THR Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 138 CYS Chi-restraints excluded: chain 3C residue 167 ILE Chi-restraints excluded: chain 3C residue 269 ASN Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3D residue 214 VAL Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 226 PHE Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 263 THR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 80 VAL Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 56 ARG Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 272 GLN Chi-restraints excluded: chain 3a residue 454 VAL Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 172 VAL Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 351 ASP Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 113 THR Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 58 CYS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3g residue 231 THR Chi-restraints excluded: chain 3g residue 244 THR Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 41 VAL Chi-restraints excluded: chain 3h residue 75 MET Chi-restraints excluded: chain 3h residue 117 MET Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 440 ILE Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain A2 residue 46 ASN Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A7 residue 30 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain A9 residue 200 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 112 ILE Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C1 residue 191 GLU Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain TD residue 72 LYS Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 258 LEU Chi-restraints excluded: chain T1 residue 313 ASP Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain A1 residue 88 THR Chi-restraints excluded: chain T6 residue 68 CYS Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T6 residue 130 GLU Chi-restraints excluded: chain R residue 17 LYS Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 372 HIS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 356 GLU Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S7 residue 29 LEU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain B9 residue 5 TYR Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TB residue 26 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 215 VAL Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain B6 residue 73 GLN Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain BM residue 205 LEU Chi-restraints excluded: chain C4 residue 66 LEU Chi-restraints excluded: chain C4 residue 67 GLU Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 200 VAL Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain TC residue 79 LYS Chi-restraints excluded: chain TC residue 92 LYS Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain T7 residue 84 PHE Chi-restraints excluded: chain T7 residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 1598 optimal weight: 0.8980 chunk 1053 optimal weight: 1.9990 chunk 1696 optimal weight: 3.9990 chunk 1035 optimal weight: 8.9990 chunk 804 optimal weight: 5.9990 chunk 1179 optimal weight: 6.9990 chunk 1779 optimal weight: 6.9990 chunk 1637 optimal weight: 2.9990 chunk 1416 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 1094 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 3 12 ASN 3 36 GLN 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 273 ASN ** 3H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN 3g 188 GLN A5 163 GLN ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 98 GLN ** A9 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 359 ASN AC 133 ASN AL 183 ASN B7 11 GLN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN J1 39 GLN T2 130 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 181 GLN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 57 ASN S6 99 GLN S8 22 GLN TX 128 GLN V2 123 GLN V2 191 ASN B2 25 ASN B2 91 ASN T3 56 GLN T3 233 HIS P1 55 GLN P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 157249 Z= 0.369 Angle : 1.084 50.603 212531 Z= 0.693 Chirality : 0.211 6.452 22368 Planarity : 0.004 0.054 26786 Dihedral : 11.252 174.892 23676 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.88 % Rotamer: Outliers : 1.41 % Allowed : 14.43 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.06), residues: 17880 helix: 1.97 (0.05), residues: 9082 sheet: 0.59 (0.16), residues: 1060 loop : -0.51 (0.07), residues: 7738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP4L 8 HIS 0.005 0.001 HIS 4 367 PHE 0.025 0.001 PHEA6 22 TYR 0.027 0.001 TYR 5 605 ARG 0.007 0.000 ARGA3 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35760 Ramachandran restraints generated. 17880 Oldfield, 0 Emsley, 17880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1003 time to evaluate : 13.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 83 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: 1 109 MET cc_start: 0.8559 (tpp) cc_final: 0.8075 (mmm) REVERT: 3A 286 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8132 (ttpp) REVERT: 3C 286 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6320 (tpp) REVERT: 3F 36 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: 3G 189 TYR cc_start: 0.2900 (OUTLIER) cc_final: 0.2172 (p90) REVERT: 3G 286 GLU cc_start: 0.7039 (tp30) cc_final: 0.6374 (tp30) REVERT: 3G 290 ASN cc_start: 0.7930 (m-40) cc_final: 0.6632 (m-40) REVERT: 3H 31 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: 3H 55 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7038 (pt0) REVERT: 3I 114 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: 3a 146 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: 3c 286 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5265 (tpp) REVERT: 3c 415 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.6979 (t80) REVERT: 3d 113 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7728 (t) REVERT: 3d 242 MET cc_start: 0.8790 (mmm) cc_final: 0.8508 (mmm) REVERT: 3f 15 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7012 (mp-120) REVERT: 3f 22 GLU cc_start: 0.6673 (pm20) cc_final: 0.6363 (pm20) REVERT: 3f 23 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7541 (tp) REVERT: 3f 26 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6610 (mp10) REVERT: 3g 16 LYS cc_start: 0.6422 (mttp) cc_final: 0.5973 (ttpp) REVERT: 3h 1 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6521 (mtp) REVERT: 3h 75 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6646 (mmt) REVERT: 3h 117 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6023 (mpp) REVERT: 3j 44 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7741 (mp) REVERT: 3l 22 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5287 (tm-30) REVERT: 4L 32 MET cc_start: 0.8984 (mmm) cc_final: 0.8698 (mmm) REVERT: 5 191 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8557 (tt) REVERT: 5 693 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6379 (p0) REVERT: 6 79 GLU cc_start: 0.7555 (mp0) cc_final: 0.7307 (mp0) REVERT: A2 46 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7103 (t0) REVERT: A2 80 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7242 (mp0) REVERT: AB 69 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8096 (ttmt) REVERT: B8 56 MET cc_start: 0.8694 (mmt) cc_final: 0.8456 (tpt) REVERT: B8 112 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7992 (pp) REVERT: B8 190 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7862 (mppt) REVERT: C1 44 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6829 (p90) REVERT: C1 191 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: TD 72 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.5609 (tmmt) REVERT: J1 21 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: FX 41 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8609 (mmpt) REVERT: FX 153 MET cc_start: 0.9104 (mtt) cc_final: 0.8881 (mtt) REVERT: T1 111 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6857 (mppt) REVERT: T1 447 MET cc_start: 0.8378 (tpt) cc_final: 0.8055 (mmt) REVERT: X1 150 ASP cc_start: 0.6410 (m-30) cc_final: 0.6196 (m-30) REVERT: T6 99 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7733 (ttm-80) REVERT: T5 178 GLN cc_start: 0.8617 (tp40) cc_final: 0.8324 (mm-40) REVERT: S1 311 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7502 (tptt) REVERT: S1 481 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: S2 318 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6286 (m-40) REVERT: S4 93 MET cc_start: 0.8497 (mmm) cc_final: 0.8229 (mmm) REVERT: S7 1 MET cc_start: 0.4714 (mmp) cc_final: 0.4030 (mmm) REVERT: S8 56 LYS cc_start: 0.8642 (ptmm) cc_final: 0.8061 (ptpp) REVERT: B9 76 MET cc_start: 0.8566 (mtm) cc_final: 0.8329 (mtp) REVERT: A8 213 GLU cc_start: 0.7604 (pp20) cc_final: 0.7384 (pp20) REVERT: V2 242 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7495 (ttmt) REVERT: B6 73 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: C4 67 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: AN 103 ARG cc_start: 0.7170 (mpt180) cc_final: 0.6922 (mpt180) REVERT: T3 137 ASN cc_start: 0.7514 (p0) cc_final: 0.6715 (p0) REVERT: T3 200 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7771 (m) REVERT: T3 231 TYR cc_start: 0.7889 (t80) cc_final: 0.7660 (t80) REVERT: P1 50 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6475 (pp20) REVERT: P1 77 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6475 (ptp-110) REVERT: S5 86 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6974 (pt0) REVERT: TC 79 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7846 (mptp) REVERT: P2 48 ASN cc_start: 0.7727 (p0) cc_final: 0.7301 (p0) REVERT: P2 84 ILE cc_start: 0.8394 (mt) cc_final: 0.8103 (mm) REVERT: T7 75 ILE cc_start: 0.7206 (pt) cc_final: 0.6926 (pp) REVERT: T7 124 ASP cc_start: 0.8723 (p0) cc_final: 0.8469 (p0) outliers start: 225 outliers final: 141 residues processed: 1177 average time/residue: 2.1062 time to fit residues: 3632.7437 Evaluate side-chains 1168 residues out of total 15990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 985 time to evaluate : 13.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 83 GLU Chi-restraints excluded: chain 1 residue 175 ILE Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 283 ILE Chi-restraints excluded: chain 2 residue 54 GLN Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3A residue 142 MET Chi-restraints excluded: chain 3A residue 286 LYS Chi-restraints excluded: chain 3A residue 454 VAL Chi-restraints excluded: chain 3B residue 82 VAL Chi-restraints excluded: chain 3B residue 207 THR Chi-restraints excluded: chain 3B residue 269 THR Chi-restraints excluded: chain 3B residue 374 THR Chi-restraints excluded: chain 3C residue 138 CYS Chi-restraints excluded: chain 3C residue 269 ASN Chi-restraints excluded: chain 3C residue 286 MET Chi-restraints excluded: chain 3C residue 314 VAL Chi-restraints excluded: chain 3C residue 369 VAL Chi-restraints excluded: chain 3D residue 194 LYS Chi-restraints excluded: chain 3D residue 214 VAL Chi-restraints excluded: chain 3E residue 68 VAL Chi-restraints excluded: chain 3E residue 226 PHE Chi-restraints excluded: chain 3E residue 254 MET Chi-restraints excluded: chain 3F residue 36 GLU Chi-restraints excluded: chain 3G residue 62 LEU Chi-restraints excluded: chain 3G residue 110 TYR Chi-restraints excluded: chain 3G residue 189 TYR Chi-restraints excluded: chain 3G residue 263 THR Chi-restraints excluded: chain 3G residue 270 ASP Chi-restraints excluded: chain 3H residue 31 ASP Chi-restraints excluded: chain 3H residue 41 VAL Chi-restraints excluded: chain 3H residue 55 GLU Chi-restraints excluded: chain 3I residue 80 VAL Chi-restraints excluded: chain 3I residue 114 GLU Chi-restraints excluded: chain 3J residue 55 VAL Chi-restraints excluded: chain 3M residue 8 PHE Chi-restraints excluded: chain 3a residue 52 VAL Chi-restraints excluded: chain 3a residue 91 MET Chi-restraints excluded: chain 3a residue 146 GLN Chi-restraints excluded: chain 3a residue 272 GLN Chi-restraints excluded: chain 3a residue 454 VAL Chi-restraints excluded: chain 3b residue 122 ASN Chi-restraints excluded: chain 3b residue 172 VAL Chi-restraints excluded: chain 3b residue 228 ILE Chi-restraints excluded: chain 3b residue 369 LEU Chi-restraints excluded: chain 3c residue 22 VAL Chi-restraints excluded: chain 3c residue 112 GLN Chi-restraints excluded: chain 3c residue 175 THR Chi-restraints excluded: chain 3c residue 286 MET Chi-restraints excluded: chain 3c residue 308 ILE Chi-restraints excluded: chain 3c residue 351 ASP Chi-restraints excluded: chain 3c residue 415 PHE Chi-restraints excluded: chain 3d residue 46 GLU Chi-restraints excluded: chain 3d residue 47 VAL Chi-restraints excluded: chain 3d residue 113 THR Chi-restraints excluded: chain 3d residue 157 VAL Chi-restraints excluded: chain 3d residue 218 VAL Chi-restraints excluded: chain 3d residue 246 VAL Chi-restraints excluded: chain 3f residue 15 GLN Chi-restraints excluded: chain 3f residue 23 LEU Chi-restraints excluded: chain 3f residue 26 GLN Chi-restraints excluded: chain 3f residue 58 CYS Chi-restraints excluded: chain 3g residue 80 LEU Chi-restraints excluded: chain 3g residue 134 VAL Chi-restraints excluded: chain 3g residue 244 THR Chi-restraints excluded: chain 3h residue 1 MET Chi-restraints excluded: chain 3h residue 4 THR Chi-restraints excluded: chain 3h residue 41 VAL Chi-restraints excluded: chain 3h residue 75 MET Chi-restraints excluded: chain 3h residue 117 MET Chi-restraints excluded: chain 3i residue 33 ARG Chi-restraints excluded: chain 3j residue 29 LEU Chi-restraints excluded: chain 3j residue 32 SER Chi-restraints excluded: chain 3j residue 44 ILE Chi-restraints excluded: chain 3l residue 22 GLU Chi-restraints excluded: chain 4 residue 224 THR Chi-restraints excluded: chain 4 residue 282 SER Chi-restraints excluded: chain 4 residue 440 ILE Chi-restraints excluded: chain 4L residue 91 ASP Chi-restraints excluded: chain 5 residue 191 LEU Chi-restraints excluded: chain 5 residue 423 VAL Chi-restraints excluded: chain 5 residue 472 LEU Chi-restraints excluded: chain 5 residue 501 THR Chi-restraints excluded: chain 5 residue 693 ASP Chi-restraints excluded: chain 5 residue 750 LEU Chi-restraints excluded: chain 6 residue 188 ILE Chi-restraints excluded: chain A2 residue 46 ASN Chi-restraints excluded: chain A5 residue 40 VAL Chi-restraints excluded: chain A5 residue 57 THR Chi-restraints excluded: chain A5 residue 95 THR Chi-restraints excluded: chain A5 residue 138 TYR Chi-restraints excluded: chain A5 residue 171 SER Chi-restraints excluded: chain A6 residue 67 ILE Chi-restraints excluded: chain A7 residue 30 THR Chi-restraints excluded: chain A9 residue 69 VAL Chi-restraints excluded: chain A9 residue 200 THR Chi-restraints excluded: chain AB residue 69 LYS Chi-restraints excluded: chain AC residue 75 SER Chi-restraints excluded: chain AC residue 120 GLU Chi-restraints excluded: chain AL residue 3 LEU Chi-restraints excluded: chain AM residue 31 LEU Chi-restraints excluded: chain AM residue 135 ASP Chi-restraints excluded: chain B8 residue 65 VAL Chi-restraints excluded: chain B8 residue 112 ILE Chi-restraints excluded: chain B8 residue 190 LYS Chi-restraints excluded: chain BL residue 107 SER Chi-restraints excluded: chain C1 residue 44 TYR Chi-restraints excluded: chain C1 residue 72 THR Chi-restraints excluded: chain C1 residue 93 VAL Chi-restraints excluded: chain C1 residue 191 GLU Chi-restraints excluded: chain C2 residue 122 VAL Chi-restraints excluded: chain C2 residue 190 VAL Chi-restraints excluded: chain TD residue 72 LYS Chi-restraints excluded: chain J1 residue 21 GLN Chi-restraints excluded: chain J1 residue 81 SER Chi-restraints excluded: chain FX residue 41 LYS Chi-restraints excluded: chain T2 residue 187 ASN Chi-restraints excluded: chain T1 residue 111 LYS Chi-restraints excluded: chain T1 residue 258 LEU Chi-restraints excluded: chain T1 residue 313 ASP Chi-restraints excluded: chain A1 residue 31 SER Chi-restraints excluded: chain A1 residue 88 THR Chi-restraints excluded: chain T6 residue 68 CYS Chi-restraints excluded: chain T6 residue 99 ARG Chi-restraints excluded: chain T6 residue 130 GLU Chi-restraints excluded: chain T5 residue 117 LYS Chi-restraints excluded: chain T5 residue 184 ILE Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S1 residue 223 VAL Chi-restraints excluded: chain S1 residue 311 LYS Chi-restraints excluded: chain S1 residue 372 HIS Chi-restraints excluded: chain S1 residue 481 GLU Chi-restraints excluded: chain S1 residue 613 ASP Chi-restraints excluded: chain S1 residue 626 VAL Chi-restraints excluded: chain S2 residue 318 ASN Chi-restraints excluded: chain S2 residue 356 GLU Chi-restraints excluded: chain S3 residue 55 PHE Chi-restraints excluded: chain S3 residue 81 ASP Chi-restraints excluded: chain S4 residue 47 VAL Chi-restraints excluded: chain S4 residue 128 THR Chi-restraints excluded: chain S7 residue 29 LEU Chi-restraints excluded: chain S7 residue 31 CYS Chi-restraints excluded: chain S7 residue 153 LYS Chi-restraints excluded: chain S8 residue 38 LYS Chi-restraints excluded: chain B9 residue 5 TYR Chi-restraints excluded: chain B9 residue 26 TYR Chi-restraints excluded: chain B9 residue 31 ASN Chi-restraints excluded: chain TX residue 24 ARG Chi-restraints excluded: chain TB residue 26 THR Chi-restraints excluded: chain TB residue 47 THR Chi-restraints excluded: chain V1 residue 331 ASN Chi-restraints excluded: chain V1 residue 332 VAL Chi-restraints excluded: chain V1 residue 383 CYS Chi-restraints excluded: chain V2 residue 150 LEU Chi-restraints excluded: chain V2 residue 215 VAL Chi-restraints excluded: chain V2 residue 227 LYS Chi-restraints excluded: chain B6 residue 73 GLN Chi-restraints excluded: chain BM residue 99 LEU Chi-restraints excluded: chain BM residue 205 LEU Chi-restraints excluded: chain C4 residue 29 THR Chi-restraints excluded: chain C4 residue 67 GLU Chi-restraints excluded: chain AN residue 81 THR Chi-restraints excluded: chain B4 residue 99 VAL Chi-restraints excluded: chain B4 residue 120 ASN Chi-restraints excluded: chain T8 residue 16 LEU Chi-restraints excluded: chain B2 residue 111 LEU Chi-restraints excluded: chain T3 residue 200 VAL Chi-restraints excluded: chain T3 residue 251 LEU Chi-restraints excluded: chain T3 residue 291 SER Chi-restraints excluded: chain P1 residue 50 GLU Chi-restraints excluded: chain P1 residue 65 VAL Chi-restraints excluded: chain TA residue 31 THR Chi-restraints excluded: chain TA residue 35 VAL Chi-restraints excluded: chain S5 residue 78 ASN Chi-restraints excluded: chain S5 residue 86 GLN Chi-restraints excluded: chain TC residue 77 LEU Chi-restraints excluded: chain TC residue 79 LYS Chi-restraints excluded: chain TC residue 92 LYS Chi-restraints excluded: chain P2 residue 103 GLN Chi-restraints excluded: chain P2 residue 140 THR Chi-restraints excluded: chain A3 residue 70 CYS Chi-restraints excluded: chain T7 residue 84 PHE Chi-restraints excluded: chain T7 residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1786 random chunks: chunk 868 optimal weight: 8.9990 chunk 1125 optimal weight: 0.8980 chunk 1509 optimal weight: 0.8980 chunk 434 optimal weight: 0.9990 chunk 1306 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 393 optimal weight: 7.9990 chunk 1419 optimal weight: 4.9990 chunk 593 optimal weight: 4.9990 chunk 1457 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 2 31 ASN 3 12 ASN 3 36 GLN 3B 176 GLN ** 3B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3G 273 ASN ** 3a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3b 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3c 321 GLN 3g 188 GLN ** 3g 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 100 ASN A5 163 GLN ** A7 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 98 GLN A9 102 ASN A9 359 ASN AB 87 ASN AC 133 ASN AL 183 ASN B7 11 GLN B8 147 ASN ** BL 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** TD 61 GLN TD 64 GLN J1 39 GLN T2 130 ASN ** T1 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 81 ASN T5 181 GLN T5 182 ASN ** S1 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 57 ASN S6 99 GLN S8 22 GLN V2 191 ASN BM 204 GLN B2 25 ASN T3 56 GLN T3 233 HIS P1 237 GLN ** P2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.097851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082211 restraints weight = 287546.554| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.43 r_work: 0.3289 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 157249 Z= 0.357 Angle : 1.073 50.581 212531 Z= 0.689 Chirality : 0.210 6.406 22368 Planarity : 0.003 0.064 26786 Dihedral : 10.901 173.153 23676 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.99 % Favored : 97.00 % Rotamer: Outliers : 1.20 % Allowed : 14.69 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.06), residues: 17880 helix: 2.06 (0.06), residues: 9103 sheet: 0.61 (0.16), residues: 1072 loop : -0.46 (0.07), residues: 7705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPS4 119 HIS 0.006 0.001 HIS 4 367 PHE 0.034 0.001 PHEV2 229 TYR 0.038 0.001 TYR3C 304 ARG 0.008 0.000 ARGA3 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 56724.96 seconds wall clock time: 983 minutes 32.96 seconds (59012.96 seconds total)