Starting phenix.real_space_refine on Wed Mar 13 06:21:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yam_10761/03_2024/6yam_10761_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.006 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 8 7.16 5 P 1865 5.49 5 Mg 1 5.21 5 S 426 5.16 5 C 67568 2.51 5 N 21382 2.21 5 O 27286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l ARG 9": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "S PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 80": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ARG 14": "NH1" <-> "NH2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j GLU 48": "OE1" <-> "OE2" Residue "j ASP 83": "OD1" <-> "OD2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k GLU 40": "OE1" <-> "OE2" Residue "k ARG 96": "NH1" <-> "NH2" Residue "k ARG 101": "NH1" <-> "NH2" Residue "k GLU 151": "OE1" <-> "OE2" Residue "k TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 190": "NH1" <-> "NH2" Residue "k GLU 193": "OE1" <-> "OE2" Residue "k ARG 267": "NH1" <-> "NH2" Residue "k TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 306": "NH1" <-> "NH2" Residue "k GLU 320": "OE1" <-> "OE2" Residue "k ARG 325": "NH1" <-> "NH2" Residue "k GLU 335": "OE1" <-> "OE2" Residue "k GLU 340": "OE1" <-> "OE2" Residue "k GLU 341": "OE1" <-> "OE2" Residue "k GLU 359": "OE1" <-> "OE2" Residue "k ARG 390": "NH1" <-> "NH2" Residue "k ARG 395": "NH1" <-> "NH2" Residue "k ARG 502": "NH1" <-> "NH2" Residue "k ARG 531": "NH1" <-> "NH2" Residue "k PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 563": "OE1" <-> "OE2" Residue "k ARG 567": "NH1" <-> "NH2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "m ARG 183": "NH1" <-> "NH2" Residue "m ARG 212": "NH1" <-> "NH2" Residue "m ARG 218": "NH1" <-> "NH2" Residue "m ARG 271": "NH1" <-> "NH2" Residue "m ARG 329": "NH1" <-> "NH2" Residue "m ARG 362": "NH1" <-> "NH2" Residue "m ARG 402": "NH1" <-> "NH2" Residue "m ARG 434": "NH1" <-> "NH2" Residue "m ARG 462": "NH1" <-> "NH2" Residue "m GLU 475": "OE1" <-> "OE2" Residue "y ARG 7": "NH1" <-> "NH2" Residue "y ARG 158": "NH1" <-> "NH2" Residue "y ASP 176": "OD1" <-> "OD2" Residue "y GLU 248": "OE1" <-> "OE2" Residue "y ARG 321": "NH1" <-> "NH2" Residue "y ASP 345": "OD1" <-> "OD2" Residue "y ARG 353": "NH1" <-> "NH2" Residue "y ARG 354": "NH1" <-> "NH2" Residue "y PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 323": "OE1" <-> "OE2" Residue "v ARG 340": "NH1" <-> "NH2" Residue "v TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 396": "OE1" <-> "OE2" Residue "v PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 429": "OE1" <-> "OE2" Residue "v GLU 449": "OE1" <-> "OE2" Residue "v ARG 450": "NH1" <-> "NH2" Residue "v ASP 452": "OD1" <-> "OD2" Residue "v TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 484": "OE1" <-> "OE2" Residue "v GLU 491": "OE1" <-> "OE2" Residue "v TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 115": "NH1" <-> "NH2" Residue "r ARG 280": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 118536 Number of models: 1 Model: "" Number of chains: 51 Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1741 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 208} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1019 Classifications: {'peptide': 126} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "V" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1112 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1107 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "a" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1021 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 789 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 76} Chain: "d" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain: "n" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 37187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1743, 37187 Inner-chain residues flagged as termini: ['pdbres=" G 2 270 "', 'pdbres=" G 21765 "'] Classifications: {'RNA': 1743} Modifications used: {'5*END': 3, 'rna2p_pur': 149, 'rna2p_pyr': 121, 'rna3p': 1, 'rna3p_pur': 764, 'rna3p_pyr': 708} Link IDs: {'rna2p': 270, 'rna3p': 1472} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3214 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PTRANS': 22, 'TRANS': 394} Chain: "j" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 882 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "k" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4693 Classifications: {'peptide': 595} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 561} Chain: "U" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1194 Classifications: {'peptide': 145} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 130} Chain: "3" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 960 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna2p': 11, 'rna3p': 33} Chain: "m" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2955 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 13, 'TRANS': 351} Chain: "y" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4971 Classifications: {'peptide': 603} Link IDs: {'CIS': 2, 'PTRANS': 23, 'TRANS': 577} Chain: "v" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4508 Classifications: {'peptide': 554} Link IDs: {'CIS': 4, 'PTRANS': 18, 'TRANS': 531} Chain: "w" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3465 Classifications: {'peptide': 419} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 403} Chain: "q" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 257} Chain: "r" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2624 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 13, 'TRANS': 307} Chain: "s" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1737 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 208} Chain: "t" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3109 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "u" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2918 Classifications: {'peptide': 365} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 354} Chain: "k" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 81 Unusual residues: {' MG': 1, 'GNP': 2, 'SF4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 82265 SG CYS k 29 115.865 104.735 82.845 1.00 0.82 S ATOM 82465 SG CYS k 55 120.689 105.533 78.494 1.00 0.73 S ATOM 82501 SG CYS k 61 120.065 101.117 82.651 1.00 0.77 S ATOM 82483 SG CYS k 58 121.153 106.325 83.707 1.00 0.73 S ATOM 82235 SG CYS k 25 116.614 96.251 83.059 1.00 0.79 S ATOM 82200 SG CYS k 21 113.388 91.168 84.230 1.00 0.76 S ATOM 82533 SG CYS k 65 118.502 93.421 84.041 1.00 0.68 S ATOM 82160 SG CYS k 16 117.289 91.128 78.145 1.00 0.73 S Residues with excluded nonbonded symmetry interactions: 413 residue: pdb=" N GLN B 52 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN B 52 " occ=0.00 residue: pdb=" N ALA B 53 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 53 " occ=0.00 residue: pdb=" N THR B 54 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 54 " occ=0.00 residue: pdb=" N ILE B 55 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 55 " occ=0.00 residue: pdb=" N ASN B 56 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 56 " occ=0.00 residue: pdb=" N ILE B 57 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 57 " occ=0.00 residue: pdb=" N GLY B 58 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 58 " occ=0.00 residue: pdb=" N THR B 59 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 59 " occ=0.00 residue: pdb=" N ILE B 60 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 60 " occ=0.00 residue: pdb=" N GLY B 61 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 61 " occ=0.00 residue: pdb=" N HIS B 62 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 62 " occ=0.00 residue: pdb=" N VAL B 63 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 63 " occ=0.00 ... (remaining 401 not shown) Time building chain proxies: 44.21, per 1000 atoms: 0.37 Number of scatterers: 118536 At special positions: 0 Unit cell: (233.2, 235.4, 338.8, 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) Fe 8 26.01 S 426 16.00 P 1865 15.00 Mg 1 11.99 O 27286 8.00 N 21382 7.00 C 67568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.42 Conformation dependent library (CDL) restraints added in 10.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 k 701 " pdb="FE3 SF4 k 701 " - pdb=" SG CYS k 61 " pdb="FE2 SF4 k 701 " - pdb=" SG CYS k 55 " pdb="FE4 SF4 k 701 " - pdb=" SG CYS k 58 " pdb="FE1 SF4 k 701 " - pdb=" SG CYS k 29 " pdb=" SF4 k 702 " pdb="FE3 SF4 k 702 " - pdb=" SG CYS k 65 " pdb="FE2 SF4 k 702 " - pdb=" SG CYS k 21 " pdb="FE1 SF4 k 702 " - pdb=" SG CYS k 25 " pdb="FE4 SF4 k 702 " - pdb=" SG CYS k 16 " Number of angles added : 24 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18460 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: 343 helices and 84 sheets defined 48.3% alpha, 13.1% beta 504 base pairs and 888 stacking pairs defined. Time for finding SS restraints: 64.09 Creating SS restraints... Processing helix chain 'l' and resid 1 through 25 removed outlier: 3.573A pdb=" N MET l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.883A pdb=" N VAL C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 39 removed outlier: 3.578A pdb=" N GLU C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 39' Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.775A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 removed outlier: 4.428A pdb=" N ARG C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 132 through 141 removed outlier: 3.670A pdb=" N SER C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 186 removed outlier: 4.424A pdb=" N GLY C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 removed outlier: 3.516A pdb=" N LYS D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 29' Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.539A pdb=" N GLY D 61 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.716A pdb=" N LEU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 4.084A pdb=" N MET D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS D 115 " --> pdb=" O CYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 3.546A pdb=" N VAL D 161 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.577A pdb=" N VAL D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'D' and resid 192 through 203 removed outlier: 3.571A pdb=" N ILE D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER D 203 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.784A pdb=" N GLU D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.522A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 removed outlier: 4.171A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 83 removed outlier: 4.971A pdb=" N ILE E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP E 80 " --> pdb=" O SER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.840A pdb=" N ALA E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 removed outlier: 3.633A pdb=" N LYS E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 235 removed outlier: 3.800A pdb=" N PHE E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.997A pdb=" N TRP E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS E 242 " --> pdb=" O PRO E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 237 through 242' Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.909A pdb=" N THR E 255 " --> pdb=" O TYR E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.792A pdb=" N VAL E 259 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS E 260 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR E 261 " --> pdb=" O LEU E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'F' and resid 6 through 29 removed outlier: 3.764A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 60 removed outlier: 3.921A pdb=" N VAL F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 removed outlier: 3.556A pdb=" N PHE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.950A pdb=" N CYS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA F 98 " --> pdb=" O ARG F 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 98' Processing helix chain 'F' and resid 99 through 112 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.697A pdb=" N ALA F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.221A pdb=" N TYR F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 50 removed outlier: 3.676A pdb=" N PHE G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 3.721A pdb=" N VAL G 61 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 120 removed outlier: 4.160A pdb=" N LYS G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 259 removed outlier: 3.529A pdb=" N ARG G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 removed outlier: 4.341A pdb=" N GLN H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 37' Processing helix chain 'H' and resid 59 through 66 removed outlier: 4.068A pdb=" N LYS H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA H 64 " --> pdb=" O ARG H 60 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 66' Processing helix chain 'H' and resid 67 through 77 removed outlier: 3.974A pdb=" N MET H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 104 removed outlier: 3.822A pdb=" N ILE H 92 " --> pdb=" O MET H 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.940A pdb=" N VAL H 111 " --> pdb=" O ASN H 107 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY H 120 " --> pdb=" O ILE H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 165 removed outlier: 3.586A pdb=" N LEU H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS H 155 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.984A pdb=" N GLY H 183 " --> pdb=" O ASN H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 204 removed outlier: 3.848A pdb=" N LYS H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 28 removed outlier: 3.620A pdb=" N LEU I 24 " --> pdb=" O ASP I 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE I 27 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 43 removed outlier: 4.355A pdb=" N GLY I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU I 43 " --> pdb=" O ASP I 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 38 through 43' Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.753A pdb=" N ILE I 141 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 237 removed outlier: 3.744A pdb=" N LEU I 185 " --> pdb=" O THR I 181 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET I 217 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU I 237 " --> pdb=" O ARG I 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 34 removed outlier: 4.153A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 5.386A pdb=" N LEU J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 41' Processing helix chain 'J' and resid 65 through 76 removed outlier: 6.535A pdb=" N LEU J 69 " --> pdb=" O PRO J 65 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 72 " --> pdb=" O GLN J 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J 74 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE J 75 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 88 removed outlier: 3.664A pdb=" N SER J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 122 removed outlier: 6.596A pdb=" N LEU J 122 " --> pdb=" O ARG J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 135 removed outlier: 3.866A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL J 134 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 168 removed outlier: 4.162A pdb=" N VAL J 166 " --> pdb=" O GLN J 162 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS J 168 " --> pdb=" O ASN J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 removed outlier: 4.336A pdb=" N SER J 174 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY J 175 " --> pdb=" O GLU J 171 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 176 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 removed outlier: 5.670A pdb=" N VAL J 9 " --> pdb=" O ALA J 6 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS J 10 " --> pdb=" O LYS J 7 " (cutoff:3.500A) Proline residue: J 11 - end of helix No H-bonds generated for 'chain 'J' and resid 6 through 11' Processing helix chain 'K' and resid 87 through 94 removed outlier: 4.910A pdb=" N VAL K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG K 92 " --> pdb=" O ASN K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.976A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 132 removed outlier: 4.783A pdb=" N LEU K 129 " --> pdb=" O LYS K 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR K 130 " --> pdb=" O GLY K 126 " (cutoff:3.500A) Proline residue: K 131 - end of helix No H-bonds generated for 'chain 'K' and resid 125 through 132' Processing helix chain 'K' and resid 133 through 138 removed outlier: 4.119A pdb=" N LEU K 137 " --> pdb=" O GLU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 153 removed outlier: 4.654A pdb=" N LYS K 148 " --> pdb=" O LYS K 144 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR K 149 " --> pdb=" O ILE K 145 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 169 removed outlier: 4.265A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE K 166 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 removed outlier: 3.547A pdb=" N GLU K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU K 199 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 36 removed outlier: 3.608A pdb=" N ASP L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 64 removed outlier: 3.951A pdb=" N VAL L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU L 60 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR L 62 " --> pdb=" O ARG L 58 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 85 removed outlier: 3.554A pdb=" N ARG L 79 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 101 removed outlier: 4.286A pdb=" N ILE L 97 " --> pdb=" O LYS L 93 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU L 98 " --> pdb=" O LEU L 94 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS L 101 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 110 removed outlier: 3.908A pdb=" N LEU L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG L 109 " --> pdb=" O PHE L 105 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 117 Processing helix chain 'L' and resid 122 through 133 removed outlier: 3.539A pdb=" N ALA L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG L 133 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 removed outlier: 3.832A pdb=" N GLN L 154 " --> pdb=" O ARG L 150 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 150 through 155' Processing helix chain 'L' and resid 171 through 183 removed outlier: 3.643A pdb=" N LYS L 176 " --> pdb=" O ARG L 172 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.905A pdb=" N ARG M 8 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE M 9 " --> pdb=" O LYS M 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 16 " --> pdb=" O TYR M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 56 removed outlier: 4.176A pdb=" N LYS M 47 " --> pdb=" O LEU M 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 84 Processing helix chain 'N' and resid 47 through 53 removed outlier: 3.924A pdb=" N ILE N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 26 removed outlier: 3.731A pdb=" N LEU O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS O 23 " --> pdb=" O GLN O 19 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 45 removed outlier: 4.415A pdb=" N ARG O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 4.839A pdb=" N VAL O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 90 removed outlier: 4.410A pdb=" N LEU O 85 " --> pdb=" O ASP O 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY O 90 " --> pdb=" O GLY O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 132 removed outlier: 4.792A pdb=" N VAL O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE O 128 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS O 131 " --> pdb=" O TYR O 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 44 removed outlier: 3.580A pdb=" N GLU P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY P 44 " --> pdb=" O LEU P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 57 removed outlier: 4.164A pdb=" N SER P 57 " --> pdb=" O ILE P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 67 removed outlier: 4.197A pdb=" N VAL P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N THR P 67 " --> pdb=" O VAL P 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 62 through 67' Processing helix chain 'P' and resid 70 through 79 removed outlier: 3.545A pdb=" N ILE P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU P 75 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 106 removed outlier: 3.556A pdb=" N VAL P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG P 106 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 133 removed outlier: 3.616A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU P 117 " --> pdb=" O PHE P 113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS P 132 " --> pdb=" O TYR P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 151 removed outlier: 3.654A pdb=" N ALA P 151 " --> pdb=" O SER P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Proline residue: P 23 - end of helix No H-bonds generated for 'chain 'P' and resid 20 through 25' Processing helix chain 'Q' and resid 57 through 62 removed outlier: 3.584A pdb=" N LYS Q 61 " --> pdb=" O THR Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 89 removed outlier: 3.679A pdb=" N ASP Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 123 removed outlier: 4.107A pdb=" N SER Q 114 " --> pdb=" O PRO Q 110 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY Q 123 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 53 removed outlier: 6.820A pdb=" N GLN S 48 " --> pdb=" O PRO S 44 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR S 49 " --> pdb=" O ARG S 45 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU S 51 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU S 52 " --> pdb=" O GLN S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 59 Processing helix chain 'S' and resid 60 through 65 removed outlier: 4.267A pdb=" N ALA S 64 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY S 65 " --> pdb=" O GLU S 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 60 through 65' Processing helix chain 'S' and resid 76 through 99 removed outlier: 3.558A pdb=" N GLN S 80 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR S 82 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 116 removed outlier: 4.118A pdb=" N LYS S 105 " --> pdb=" O ASP S 101 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR S 115 " --> pdb=" O ILE S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 20 removed outlier: 3.531A pdb=" N LYS T 10 " --> pdb=" O THR T 6 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 39 Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.903A pdb=" N ARG T 47 " --> pdb=" O SER T 43 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY T 52 " --> pdb=" O ASN T 48 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG T 63 " --> pdb=" O LYS T 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 84 removed outlier: 3.636A pdb=" N GLU T 75 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR T 84 " --> pdb=" O ARG T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 110 removed outlier: 4.007A pdb=" N LYS T 103 " --> pdb=" O ASP T 99 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU T 104 " --> pdb=" O PRO T 100 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET T 105 " --> pdb=" O ASP T 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 109 " --> pdb=" O MET T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 10 removed outlier: 4.649A pdb=" N VAL V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASN V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 5 through 10' Processing helix chain 'V' and resid 11 through 26 removed outlier: 3.992A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER V 25 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY V 26 " --> pdb=" O LEU V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 67 removed outlier: 3.612A pdb=" N ALA V 58 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU V 64 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 80 removed outlier: 3.625A pdb=" N THR V 76 " --> pdb=" O VAL V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 111 removed outlier: 5.441A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 143 removed outlier: 3.750A pdb=" N GLY V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA V 139 " --> pdb=" O ALA V 135 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS V 143 " --> pdb=" O ALA V 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 47 removed outlier: 3.848A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU W 39 " --> pdb=" O VAL W 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS W 46 " --> pdb=" O GLY W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 105 removed outlier: 3.754A pdb=" N VAL W 98 " --> pdb=" O PRO W 94 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER W 103 " --> pdb=" O LYS W 99 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE W 104 " --> pdb=" O GLN W 100 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER W 105 " --> pdb=" O ILE W 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 63 Processing helix chain 'X' and resid 64 through 77 removed outlier: 3.657A pdb=" N HIS X 76 " --> pdb=" O LEU X 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY X 77 " --> pdb=" O ALA X 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 21 removed outlier: 3.832A pdb=" N ASP Y 9 " --> pdb=" O ASN Y 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS Y 12 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 45 removed outlier: 3.555A pdb=" N VAL Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY Y 45 " --> pdb=" O MET Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 94 removed outlier: 6.332A pdb=" N LEU Y 86 " --> pdb=" O GLN Y 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS Y 88 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 120 removed outlier: 3.521A pdb=" N ALA Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 24 removed outlier: 3.875A pdb=" N HIS Z 16 " --> pdb=" O LYS Z 12 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG Z 18 " --> pdb=" O ARG Z 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP Z 19 " --> pdb=" O SER Z 15 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS Z 23 " --> pdb=" O ASP Z 19 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP Z 24 " --> pdb=" O GLN Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 33 removed outlier: 3.521A pdb=" N LYS Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU Z 32 " --> pdb=" O LYS Z 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 33 " --> pdb=" O LYS Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 39 Processing helix chain 'Z' and resid 89 through 95 removed outlier: 4.208A pdb=" N PHE Z 93 " --> pdb=" O GLY Z 89 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Z 94 " --> pdb=" O CYS Z 90 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU Z 95 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 89 through 95' Processing helix chain 'Z' and resid 129 through 136 Processing helix chain 'a' and resid 36 through 49 removed outlier: 3.760A pdb=" N ILE a 40 " --> pdb=" O PRO a 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 56 removed outlier: 4.366A pdb=" N ILE a 55 " --> pdb=" O THR a 51 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE a 56 " --> pdb=" O PRO a 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 51 through 56' Processing helix chain 'a' and resid 78 through 86 removed outlier: 3.846A pdb=" N ALA a 82 " --> pdb=" O SER a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 95 removed outlier: 3.663A pdb=" N LEU a 91 " --> pdb=" O PRO a 87 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS a 94 " --> pdb=" O ARG a 90 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 118 removed outlier: 3.937A pdb=" N ARG a 110 " --> pdb=" O GLN a 106 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS a 116 " --> pdb=" O ASN a 112 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL a 117 " --> pdb=" O ARG a 113 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG a 118 " --> pdb=" O MET a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 127 Processing helix chain 'b' and resid 46 through 57 removed outlier: 3.896A pdb=" N VAL b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG b 51 " --> pdb=" O ALA b 47 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 82 removed outlier: 3.618A pdb=" N ILE b 79 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER b 81 " --> pdb=" O CYS b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 93 removed outlier: 5.384A pdb=" N LYS b 93 " --> pdb=" O ARG b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 17 removed outlier: 4.900A pdb=" N LYS c 16 " --> pdb=" O PRO c 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 12 through 17' Processing helix chain 'e' and resid 15 through 20 removed outlier: 4.264A pdb=" N ARG e 19 " --> pdb=" O GLY e 15 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER e 20 " --> pdb=" O GLN e 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 15 through 20' Processing helix chain 'e' and resid 40 through 48 removed outlier: 3.954A pdb=" N GLN e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 65 removed outlier: 3.599A pdb=" N CYS n 59 " --> pdb=" O TYR n 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS n 60 " --> pdb=" O ASP n 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL n 62 " --> pdb=" O LEU n 58 " (cutoff:3.500A) Proline residue: n 63 - end of helix Processing helix chain 'n' and resid 69 through 77 removed outlier: 3.842A pdb=" N GLU n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 95 removed outlier: 6.552A pdb=" N ALA n 84 " --> pdb=" O ARG n 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER n 93 " --> pdb=" O GLN n 89 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS n 94 " --> pdb=" O GLU n 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 90 removed outlier: 3.776A pdb=" N THR i 90 " --> pdb=" O VAL i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 116 removed outlier: 4.103A pdb=" N ARG i 108 " --> pdb=" O GLY i 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG i 115 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 5.826A pdb=" N LEU A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 63' Processing helix chain 'A' and resid 91 through 117 removed outlier: 3.703A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 143 removed outlier: 4.571A pdb=" N GLU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.888A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 6.060A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.840A pdb=" N VAL A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.676A pdb=" N LYS A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 removed outlier: 7.104A pdb=" N GLY A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 removed outlier: 4.790A pdb=" N VAL B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 166 removed outlier: 4.231A pdb=" N VAL B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.951A pdb=" N SER B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 removed outlier: 4.269A pdb=" N GLN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.691A pdb=" N GLU B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.407A pdb=" N CYS B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 107 Processing helix chain 'j' and resid 10 through 16 removed outlier: 5.938A pdb=" N ARG j 13 " --> pdb=" O LYS j 10 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG j 14 " --> pdb=" O ASN j 11 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY j 15 " --> pdb=" O ARG j 12 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS j 16 " --> pdb=" O ARG j 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 10 through 16' Processing helix chain 'k' and resid 17 through 22 removed outlier: 3.713A pdb=" N CYS k 21 " --> pdb=" O LYS k 17 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG k 22 " --> pdb=" O PRO k 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 17 through 22' Processing helix chain 'k' and resid 23 through 29 removed outlier: 3.717A pdb=" N CYS k 29 " --> pdb=" O CYS k 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 35 removed outlier: 3.833A pdb=" N GLY k 35 " --> pdb=" O VAL k 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 65 removed outlier: 3.518A pdb=" N LYS k 64 " --> pdb=" O ILE k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 115 through 125 removed outlier: 3.551A pdb=" N GLY k 125 " --> pdb=" O LYS k 121 " (cutoff:3.500A) Processing helix chain 'k' and resid 139 through 148 removed outlier: 6.187A pdb=" N ILE k 143 " --> pdb=" O ASP k 139 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU k 144 " --> pdb=" O TRP k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 151 through 162 removed outlier: 3.703A pdb=" N TYR k 155 " --> pdb=" O GLU k 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP k 162 " --> pdb=" O LYS k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 181 Proline residue: k 177 - end of helix removed outlier: 5.919A pdb=" N ALA k 180 " --> pdb=" O ILE k 176 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LYS k 181 " --> pdb=" O PRO k 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 173 through 181' Processing helix chain 'k' and resid 184 through 192 removed outlier: 6.076A pdb=" N LEU k 188 " --> pdb=" O VAL k 184 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP k 192 " --> pdb=" O LEU k 188 " (cutoff:3.500A) Processing helix chain 'k' and resid 194 through 205 removed outlier: 3.784A pdb=" N ALA k 198 " --> pdb=" O THR k 194 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP k 205 " --> pdb=" O CYS k 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 213 through 218 removed outlier: 4.191A pdb=" N LEU k 217 " --> pdb=" O ASN k 213 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER k 218 " --> pdb=" O VAL k 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 213 through 218' Processing helix chain 'k' and resid 219 through 233 Processing helix chain 'k' and resid 248 through 263 removed outlier: 3.604A pdb=" N LEU k 253 " --> pdb=" O VAL k 249 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU k 262 " --> pdb=" O THR k 258 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE k 263 " --> pdb=" O ILE k 259 " (cutoff:3.500A) Processing helix chain 'k' and resid 278 through 283 Processing helix chain 'k' and resid 304 through 314 removed outlier: 3.901A pdb=" N ASN k 310 " --> pdb=" O ARG k 306 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE k 311 " --> pdb=" O GLU k 307 " (cutoff:3.500A) Processing helix chain 'k' and resid 384 through 394 removed outlier: 4.279A pdb=" N PHE k 388 " --> pdb=" O GLY k 384 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE k 389 " --> pdb=" O LYS k 385 " (cutoff:3.500A) Processing helix chain 'k' and resid 423 through 432 removed outlier: 3.761A pdb=" N LEU k 427 " --> pdb=" O SER k 423 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS k 429 " --> pdb=" O ARG k 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU k 430 " --> pdb=" O GLN k 426 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS k 431 " --> pdb=" O LEU k 427 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE k 432 " --> pdb=" O LEU k 428 " (cutoff:3.500A) Processing helix chain 'k' and resid 439 through 444 removed outlier: 4.277A pdb=" N THR k 443 " --> pdb=" O PRO k 439 " (cutoff:3.500A) Processing helix chain 'k' and resid 450 through 456 removed outlier: 5.043A pdb=" N ILE k 454 " --> pdb=" O GLN k 450 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP k 456 " --> pdb=" O GLU k 452 " (cutoff:3.500A) Processing helix chain 'k' and resid 463 through 478 removed outlier: 4.037A pdb=" N CYS k 475 " --> pdb=" O ALA k 471 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU k 476 " --> pdb=" O LEU k 472 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY k 477 " --> pdb=" O ALA k 473 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS k 478 " --> pdb=" O LEU k 474 " (cutoff:3.500A) Processing helix chain 'k' and resid 494 through 512 removed outlier: 4.103A pdb=" N MET k 499 " --> pdb=" O GLU k 495 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA k 511 " --> pdb=" O PHE k 507 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS k 512 " --> pdb=" O ILE k 508 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 529 removed outlier: 4.565A pdb=" N LEU k 528 " --> pdb=" O MET k 524 " (cutoff:3.500A) Processing helix chain 'k' and resid 551 through 563 removed outlier: 3.634A pdb=" N GLN k 561 " --> pdb=" O LYS k 557 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU k 562 " --> pdb=" O PHE k 558 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU k 563 " --> pdb=" O LEU k 559 " (cutoff:3.500A) Processing helix chain 'k' and resid 582 through 592 removed outlier: 4.544A pdb=" N VAL k 586 " --> pdb=" O SER k 582 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU k 587 " --> pdb=" O ILE k 583 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS k 589 " --> pdb=" O ASP k 585 " (cutoff:3.500A) Processing helix chain 'k' and resid 206 through 211 removed outlier: 5.019A pdb=" N LEU k 209 " --> pdb=" O LEU k 206 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS k 210 " --> pdb=" O THR k 207 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU k 211 " --> pdb=" O HIS k 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 206 through 211' Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.506A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 49 removed outlier: 3.995A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG U 46 " --> pdb=" O HIS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 74 removed outlier: 3.647A pdb=" N ARG U 66 " --> pdb=" O ASP U 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Proline residue: U 74 - end of helix Processing helix chain 'U' and resid 100 through 118 removed outlier: 3.865A pdb=" N ASP U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG U 118 " --> pdb=" O LEU U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 128 removed outlier: 3.769A pdb=" N LEU U 123 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 29 removed outlier: 3.617A pdb=" N LEU R 25 " --> pdb=" O ASP R 21 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 36 removed outlier: 3.808A pdb=" N GLN R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 48 removed outlier: 4.253A pdb=" N ARG R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 67 removed outlier: 5.523A pdb=" N LEU R 56 " --> pdb=" O LYS R 52 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 121 removed outlier: 4.819A pdb=" N PHE R 119 " --> pdb=" O TYR R 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE R 121 " --> pdb=" O GLY R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 115 through 121' Processing helix chain 'm' and resid 175 through 183 removed outlier: 4.276A pdb=" N LYS m 181 " --> pdb=" O PRO m 177 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET m 182 " --> pdb=" O GLN m 178 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG m 183 " --> pdb=" O LEU m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 203 through 209 removed outlier: 4.857A pdb=" N ASP m 207 " --> pdb=" O ASP m 203 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG m 208 " --> pdb=" O LYS m 204 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE m 209 " --> pdb=" O ALA m 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 203 through 209' Processing helix chain 'm' and resid 232 through 242 removed outlier: 3.568A pdb=" N ALA m 239 " --> pdb=" O ILE m 235 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS m 240 " --> pdb=" O ARG m 236 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR m 241 " --> pdb=" O LYS m 237 " (cutoff:3.500A) Processing helix chain 'm' and resid 248 through 258 removed outlier: 3.647A pdb=" N LEU m 255 " --> pdb=" O ILE m 251 " (cutoff:3.500A) Processing helix chain 'm' and resid 308 through 329 removed outlier: 4.271A pdb=" N HIS m 321 " --> pdb=" O THR m 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN m 322 " --> pdb=" O TYR m 318 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER m 324 " --> pdb=" O ASN m 320 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN m 325 " --> pdb=" O HIS m 321 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN m 326 " --> pdb=" O ASN m 322 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU m 328 " --> pdb=" O SER m 324 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG m 329 " --> pdb=" O GLN m 325 " (cutoff:3.500A) Processing helix chain 'm' and resid 400 through 405 removed outlier: 4.725A pdb=" N CYS m 404 " --> pdb=" O ASP m 400 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN m 405 " --> pdb=" O SER m 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 400 through 405' Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 416 through 428 removed outlier: 3.798A pdb=" N ILE m 421 " --> pdb=" O ARG m 417 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU m 424 " --> pdb=" O VAL m 420 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS m 426 " --> pdb=" O ALA m 422 " (cutoff:3.500A) Processing helix chain 'm' and resid 429 through 443 Processing helix chain 'm' and resid 472 through 481 Processing helix chain 'm' and resid 483 through 499 removed outlier: 4.509A pdb=" N ALA m 487 " --> pdb=" O SER m 483 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY m 489 " --> pdb=" O GLU m 485 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE m 490 " --> pdb=" O ASN m 486 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU m 491 " --> pdb=" O ALA m 487 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE m 497 " --> pdb=" O CYS m 493 " (cutoff:3.500A) Processing helix chain 'y' and resid 8 through 22 removed outlier: 4.676A pdb=" N LEU y 12 " --> pdb=" O PRO y 8 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS y 13 " --> pdb=" O GLU y 9 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL y 21 " --> pdb=" O GLU y 17 " (cutoff:3.500A) Processing helix chain 'y' and resid 23 through 37 removed outlier: 3.899A pdb=" N ALA y 27 " --> pdb=" O LYS y 23 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU y 28 " --> pdb=" O LYS y 24 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP y 29 " --> pdb=" O GLN y 25 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL y 34 " --> pdb=" O VAL y 30 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER y 37 " --> pdb=" O ASP y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 46 through 62 Processing helix chain 'y' and resid 63 through 79 removed outlier: 3.623A pdb=" N GLU y 69 " --> pdb=" O HIS y 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN y 76 " --> pdb=" O TYR y 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 82 through 118 removed outlier: 4.832A pdb=" N LEU y 86 " --> pdb=" O ASN y 82 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL y 112 " --> pdb=" O SER y 108 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU y 113 " --> pdb=" O GLN y 109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP y 114 " --> pdb=" O GLN y 110 " (cutoff:3.500A) Processing helix chain 'y' and resid 124 through 132 removed outlier: 5.718A pdb=" N LEU y 128 " --> pdb=" O PRO y 124 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU y 129 " --> pdb=" O GLU y 125 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER y 130 " --> pdb=" O SER y 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA y 131 " --> pdb=" O VAL y 127 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL y 132 " --> pdb=" O LEU y 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 124 through 132' Processing helix chain 'y' and resid 136 through 146 removed outlier: 4.630A pdb=" N LEU y 144 " --> pdb=" O ARG y 140 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU y 145 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 165 removed outlier: 4.218A pdb=" N LEU y 161 " --> pdb=" O TYR y 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP y 162 " --> pdb=" O ARG y 158 " (cutoff:3.500A) Processing helix chain 'y' and resid 172 through 188 removed outlier: 5.429A pdb=" N ASP y 176 " --> pdb=" O ARG y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 210 removed outlier: 4.278A pdb=" N PHE y 194 " --> pdb=" O ARG y 190 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG y 195 " --> pdb=" O LYS y 191 " (cutoff:3.500A) Processing helix chain 'y' and resid 221 through 244 removed outlier: 3.661A pdb=" N SER y 225 " --> pdb=" O ASN y 221 " (cutoff:3.500A) Processing helix chain 'y' and resid 245 through 264 removed outlier: 3.918A pdb=" N ALA y 249 " --> pdb=" O LEU y 245 " (cutoff:3.500A) Processing helix chain 'y' and resid 270 through 284 removed outlier: 6.223A pdb=" N ASN y 274 " --> pdb=" O GLN y 270 " (cutoff:3.500A) Processing helix chain 'y' and resid 288 through 310 Processing helix chain 'y' and resid 314 through 331 removed outlier: 3.713A pdb=" N MET y 318 " --> pdb=" O GLU y 314 " (cutoff:3.500A) Proline residue: y 330 - end of helix Processing helix chain 'y' and resid 337 through 343 Processing helix chain 'y' and resid 346 through 360 removed outlier: 6.113A pdb=" N GLU y 350 " --> pdb=" O GLY y 346 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS y 351 " --> pdb=" O ILE y 347 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN y 352 " --> pdb=" O ILE y 348 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 376 removed outlier: 3.614A pdb=" N ILE y 371 " --> pdb=" O ARG y 367 " (cutoff:3.500A) Processing helix chain 'y' and resid 378 through 383 removed outlier: 3.714A pdb=" N TYR y 382 " --> pdb=" O ASN y 378 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL y 383 " --> pdb=" O VAL y 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 378 through 383' Processing helix chain 'y' and resid 384 through 395 removed outlier: 4.751A pdb=" N ASP y 389 " --> pdb=" O PRO y 385 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU y 390 " --> pdb=" O GLU y 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR y 391 " --> pdb=" O VAL y 387 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN y 392 " --> pdb=" O LYS y 388 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP y 393 " --> pdb=" O ASP y 389 " (cutoff:3.500A) Processing helix chain 'y' and resid 402 through 416 removed outlier: 3.707A pdb=" N THR y 408 " --> pdb=" O CYS y 404 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS y 409 " --> pdb=" O GLU y 405 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL y 410 " --> pdb=" O ARG y 406 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU y 416 " --> pdb=" O ASN y 412 " (cutoff:3.500A) Processing helix chain 'y' and resid 422 through 447 removed outlier: 3.752A pdb=" N GLN y 426 " --> pdb=" O PRO y 422 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR y 427 " --> pdb=" O GLU y 423 " (cutoff:3.500A) Proline residue: y 429 - end of helix removed outlier: 3.515A pdb=" N GLN y 441 " --> pdb=" O LEU y 437 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN y 442 " --> pdb=" O ARG y 438 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL y 443 " --> pdb=" O LEU y 439 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA y 444 " --> pdb=" O LEU y 440 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN y 445 " --> pdb=" O GLN y 441 " (cutoff:3.500A) Processing helix chain 'y' and resid 451 through 460 removed outlier: 3.753A pdb=" N SER y 457 " --> pdb=" O SER y 453 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL y 459 " --> pdb=" O LEU y 455 " (cutoff:3.500A) Proline residue: y 460 - end of helix Processing helix chain 'y' and resid 463 through 478 removed outlier: 3.569A pdb=" N LEU y 467 " --> pdb=" O ASP y 463 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG y 469 " --> pdb=" O PHE y 465 " (cutoff:3.500A) Processing helix chain 'y' and resid 500 through 505 removed outlier: 4.421A pdb=" N ASP y 504 " --> pdb=" O ALA y 500 " (cutoff:3.500A) Processing helix chain 'y' and resid 522 through 539 removed outlier: 4.116A pdb=" N LYS y 532 " --> pdb=" O SER y 528 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA y 533 " --> pdb=" O VAL y 529 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU y 535 " --> pdb=" O ALA y 531 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL y 536 " --> pdb=" O LYS y 532 " (cutoff:3.500A) Proline residue: y 539 - end of helix Processing helix chain 'y' and resid 540 through 569 removed outlier: 5.264A pdb=" N GLN y 544 " --> pdb=" O ALA y 540 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU y 545 " --> pdb=" O HIS y 541 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS y 546 " --> pdb=" O ILE y 542 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS y 563 " --> pdb=" O LYS y 559 " (cutoff:3.500A) Processing helix chain 'y' and resid 570 through 605 removed outlier: 3.690A pdb=" N ARG y 578 " --> pdb=" O THR y 574 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG y 581 " --> pdb=" O GLU y 577 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU y 583 " --> pdb=" O LYS y 579 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER y 584 " --> pdb=" O GLU y 580 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU y 594 " --> pdb=" O GLU y 590 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU y 595 " --> pdb=" O LYS y 591 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU y 600 " --> pdb=" O GLN y 596 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU y 601 " --> pdb=" O ARG y 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS y 603 " --> pdb=" O ALA y 599 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG y 605 " --> pdb=" O LEU y 601 " (cutoff:3.500A) Processing helix chain 'v' and resid 327 through 340 removed outlier: 4.725A pdb=" N ALA v 339 " --> pdb=" O GLU v 335 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ARG v 340 " --> pdb=" O ILE v 336 " (cutoff:3.500A) Processing helix chain 'v' and resid 346 through 361 removed outlier: 5.995A pdb=" N GLN v 350 " --> pdb=" O ASP v 346 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE v 351 " --> pdb=" O ARG v 347 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU v 353 " --> pdb=" O ALA v 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL v 358 " --> pdb=" O LEU v 354 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE v 360 " --> pdb=" O LEU v 356 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA v 361 " --> pdb=" O LEU v 357 " (cutoff:3.500A) Processing helix chain 'v' and resid 365 through 385 removed outlier: 4.651A pdb=" N GLY v 369 " --> pdb=" O ASN v 365 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL v 370 " --> pdb=" O LEU v 366 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE v 371 " --> pdb=" O GLY v 367 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL v 372 " --> pdb=" O GLU v 368 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS v 373 " --> pdb=" O GLY v 369 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE v 374 " --> pdb=" O VAL v 370 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR v 385 " --> pdb=" O SER v 381 " (cutoff:3.500A) Processing helix chain 'v' and resid 394 through 415 removed outlier: 5.932A pdb=" N LEU v 412 " --> pdb=" O LEU v 408 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN v 415 " --> pdb=" O ILE v 411 " (cutoff:3.500A) Processing helix chain 'v' and resid 430 through 435 removed outlier: 5.320A pdb=" N VAL v 434 " --> pdb=" O ASN v 430 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP v 435 " --> pdb=" O LEU v 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 430 through 435' Processing helix chain 'v' and resid 436 through 462 removed outlier: 4.053A pdb=" N VAL v 440 " --> pdb=" O GLN v 436 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE v 444 " --> pdb=" O VAL v 440 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU v 445 " --> pdb=" O ARG v 441 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR v 446 " --> pdb=" O GLY v 442 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU v 447 " --> pdb=" O CYS v 443 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN v 460 " --> pdb=" O THR v 456 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN v 461 " --> pdb=" O LYS v 457 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR v 462 " --> pdb=" O ILE v 458 " (cutoff:3.500A) Processing helix chain 'v' and resid 468 through 490 removed outlier: 4.450A pdb=" N HIS v 472 " --> pdb=" O GLU v 468 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN v 487 " --> pdb=" O ILE v 483 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG v 488 " --> pdb=" O GLU v 484 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR v 489 " --> pdb=" O ARG v 485 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU v 490 " --> pdb=" O VAL v 486 " (cutoff:3.500A) Processing helix chain 'v' and resid 499 through 511 removed outlier: 3.719A pdb=" N TYR v 503 " --> pdb=" O ILE v 499 " (cutoff:3.500A) Processing helix chain 'v' and resid 514 through 523 removed outlier: 5.955A pdb=" N ARG v 521 " --> pdb=" O LYS v 517 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN v 522 " --> pdb=" O ALA v 518 " (cutoff:3.500A) Processing helix chain 'v' and resid 532 through 545 removed outlier: 3.783A pdb=" N GLN v 536 " --> pdb=" O SER v 532 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP v 543 " --> pdb=" O ASN v 539 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA v 545 " --> pdb=" O GLY v 541 " (cutoff:3.500A) Processing helix chain 'v' and resid 546 through 560 removed outlier: 3.983A pdb=" N ARG v 550 " --> pdb=" O VAL v 546 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR v 554 " --> pdb=" O ARG v 550 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE v 555 " --> pdb=" O LEU v 551 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS v 558 " --> pdb=" O TYR v 554 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP v 559 " --> pdb=" O ILE v 555 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG v 560 " --> pdb=" O TYR v 556 " (cutoff:3.500A) Processing helix chain 'v' and resid 561 through 579 removed outlier: 4.139A pdb=" N CYS v 567 " --> pdb=" O ARG v 563 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU v 570 " --> pdb=" O THR v 566 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS v 571 " --> pdb=" O CYS v 567 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR v 574 " --> pdb=" O LEU v 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS v 575 " --> pdb=" O CYS v 571 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS v 576 " --> pdb=" O HIS v 572 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA v 577 " --> pdb=" O ILE v 573 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU v 578 " --> pdb=" O TYR v 574 " (cutoff:3.500A) Processing helix chain 'v' and resid 581 through 593 removed outlier: 3.705A pdb=" N ALA v 585 " --> pdb=" O ARG v 581 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET v 589 " --> pdb=" O ALA v 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU v 590 " --> pdb=" O ARG v 586 " (cutoff:3.500A) Processing helix chain 'v' and resid 594 through 602 removed outlier: 4.502A pdb=" N GLN v 599 " --> pdb=" O GLN v 595 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS v 600 " --> pdb=" O ASP v 596 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP v 602 " --> pdb=" O ILE v 598 " (cutoff:3.500A) Processing helix chain 'v' and resid 603 through 624 removed outlier: 3.996A pdb=" N ILE v 607 " --> pdb=" O PRO v 603 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN v 615 " --> pdb=" O ARG v 611 " (cutoff:3.500A) Processing helix chain 'v' and resid 627 through 638 removed outlier: 4.071A pdb=" N ASP v 635 " --> pdb=" O ASN v 631 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE v 636 " --> pdb=" O ALA v 632 " (cutoff:3.500A) Processing helix chain 'v' and resid 641 through 647 Processing helix chain 'v' and resid 659 through 670 removed outlier: 3.534A pdb=" N LYS v 664 " --> pdb=" O GLN v 660 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL v 665 " --> pdb=" O GLU v 661 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU v 666 " --> pdb=" O GLN v 662 " (cutoff:3.500A) Processing helix chain 'v' and resid 678 through 699 removed outlier: 3.730A pdb=" N LEU v 692 " --> pdb=" O VAL v 688 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU v 693 " --> pdb=" O SER v 689 " (cutoff:3.500A) Proline residue: v 696 - end of helix Processing helix chain 'v' and resid 713 through 723 removed outlier: 4.076A pdb=" N GLY v 721 " --> pdb=" O GLN v 717 " (cutoff:3.500A) Processing helix chain 'v' and resid 732 through 747 Processing helix chain 'v' and resid 748 through 764 removed outlier: 4.184A pdb=" N CYS v 752 " --> pdb=" O ASP v 748 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER v 754 " --> pdb=" O LYS v 750 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE v 755 " --> pdb=" O THR v 751 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS v 760 " --> pdb=" O ILE v 756 " (cutoff:3.500A) Processing helix chain 'v' and resid 771 through 800 removed outlier: 3.843A pdb=" N THR v 777 " --> pdb=" O ASP v 773 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS v 782 " --> pdb=" O MET v 778 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU v 788 " --> pdb=" O GLN v 784 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR v 794 " --> pdb=" O THR v 790 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER v 797 " --> pdb=" O PHE v 793 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL v 798 " --> pdb=" O THR v 794 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP v 800 " --> pdb=" O SER v 796 " (cutoff:3.500A) Processing helix chain 'v' and resid 803 through 812 removed outlier: 3.906A pdb=" N LEU v 807 " --> pdb=" O SER v 803 " (cutoff:3.500A) Processing helix chain 'v' and resid 814 through 828 Processing helix chain 'v' and resid 849 through 876 removed outlier: 4.707A pdb=" N GLN v 853 " --> pdb=" O PRO v 849 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA v 856 " --> pdb=" O GLN v 852 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY v 864 " --> pdb=" O ALA v 860 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER v 865 " --> pdb=" O GLU v 861 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU v 866 " --> pdb=" O LYS v 862 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN v 870 " --> pdb=" O LEU v 866 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 14 removed outlier: 3.765A pdb=" N THR w 8 " --> pdb=" O TYR w 4 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG w 9 " --> pdb=" O ASP w 5 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS w 12 " --> pdb=" O THR w 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE w 13 " --> pdb=" O ARG w 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU w 14 " --> pdb=" O ILE w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 32 through 47 removed outlier: 3.822A pdb=" N GLU w 36 " --> pdb=" O TYR w 32 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU w 38 " --> pdb=" O GLU w 34 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN w 39 " --> pdb=" O LYS w 35 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU w 44 " --> pdb=" O GLY w 40 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP w 47 " --> pdb=" O ASP w 43 " (cutoff:3.500A) Processing helix chain 'w' and resid 49 through 60 removed outlier: 7.178A pdb=" N ALA w 54 " --> pdb=" O MET w 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET w 55 " --> pdb=" O VAL w 51 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP w 56 " --> pdb=" O ASP w 52 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL w 57 " --> pdb=" O PHE w 53 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS w 59 " --> pdb=" O MET w 55 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN w 60 " --> pdb=" O ASP w 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 72 Proline residue: w 67 - end of helix removed outlier: 4.229A pdb=" N ARG w 71 " --> pdb=" O PRO w 67 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU w 72 " --> pdb=" O HIS w 68 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 88 removed outlier: 3.988A pdb=" N GLN w 80 " --> pdb=" O THR w 76 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN w 83 " --> pdb=" O ALA w 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU w 84 " --> pdb=" O GLN w 80 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN w 85 " --> pdb=" O LEU w 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR w 88 " --> pdb=" O LEU w 84 " (cutoff:3.500A) Processing helix chain 'w' and resid 94 through 120 Proline residue: w 98 - end of helix removed outlier: 3.621A pdb=" N ARG w 102 " --> pdb=" O PRO w 98 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN w 105 " --> pdb=" O THR w 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER w 106 " --> pdb=" O ARG w 102 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY w 110 " --> pdb=" O SER w 106 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG w 111 " --> pdb=" O THR w 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU w 113 " --> pdb=" O ASP w 109 " (cutoff:3.500A) Processing helix chain 'w' and resid 124 through 142 removed outlier: 3.602A pdb=" N THR w 130 " --> pdb=" O GLU w 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE w 137 " --> pdb=" O ARG w 133 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU w 140 " --> pdb=" O LYS w 136 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS w 141 " --> pdb=" O PHE w 137 " (cutoff:3.500A) Processing helix chain 'w' and resid 144 through 155 removed outlier: 3.942A pdb=" N ALA w 148 " --> pdb=" O TYR w 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU w 149 " --> pdb=" O SER w 145 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE w 154 " --> pdb=" O TYR w 150 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG w 155 " --> pdb=" O LEU w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 162 through 180 Processing helix chain 'w' and resid 181 through 199 removed outlier: 3.684A pdb=" N THR w 190 " --> pdb=" O MET w 186 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG w 191 " --> pdb=" O GLU w 187 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS w 193 " --> pdb=" O LEU w 189 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU w 194 " --> pdb=" O THR w 190 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN w 199 " --> pdb=" O THR w 195 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 220 removed outlier: 3.992A pdb=" N GLN w 209 " --> pdb=" O LEU w 205 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE w 215 " --> pdb=" O ARG w 211 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP w 217 " --> pdb=" O TRP w 213 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER w 218 " --> pdb=" O LEU w 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU w 219 " --> pdb=" O ILE w 215 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE w 220 " --> pdb=" O HIS w 216 " (cutoff:3.500A) Processing helix chain 'w' and resid 224 through 237 removed outlier: 3.786A pdb=" N GLY w 228 " --> pdb=" O ASN w 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP w 234 " --> pdb=" O ASP w 230 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU w 235 " --> pdb=" O ASN w 231 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE w 236 " --> pdb=" O ILE w 232 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU w 237 " --> pdb=" O ILE w 233 " (cutoff:3.500A) Processing helix chain 'w' and resid 250 through 263 removed outlier: 4.786A pdb=" N LEU w 254 " --> pdb=" O CYS w 250 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG w 255 " --> pdb=" O PRO w 251 " (cutoff:3.500A) Processing helix chain 'w' and resid 266 through 277 removed outlier: 5.095A pdb=" N ARG w 270 " --> pdb=" O ASP w 266 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG w 271 " --> pdb=" O VAL w 267 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN w 272 " --> pdb=" O ARG w 268 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL w 273 " --> pdb=" O LYS w 269 " (cutoff:3.500A) Processing helix chain 'w' and resid 280 through 290 removed outlier: 3.920A pdb=" N SER w 285 " --> pdb=" O ILE w 281 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR w 288 " --> pdb=" O GLU w 284 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS w 289 " --> pdb=" O SER w 285 " (cutoff:3.500A) Processing helix chain 'w' and resid 291 through 303 removed outlier: 3.618A pdb=" N GLU w 297 " --> pdb=" O THR w 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU w 299 " --> pdb=" O PHE w 295 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR w 300 " --> pdb=" O VAL w 296 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 322 removed outlier: 3.685A pdb=" N GLU w 316 " --> pdb=" O LEU w 312 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER w 317 " --> pdb=" O ARG w 313 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL w 318 " --> pdb=" O GLU w 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL w 320 " --> pdb=" O GLU w 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN w 321 " --> pdb=" O SER w 317 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP w 322 " --> pdb=" O VAL w 318 " (cutoff:3.500A) Processing helix chain 'w' and resid 328 through 348 removed outlier: 3.547A pdb=" N PHE w 332 " --> pdb=" O CYS w 328 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE w 333 " --> pdb=" O LEU w 329 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG w 337 " --> pdb=" O ILE w 333 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE w 340 " --> pdb=" O ALA w 336 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR w 343 " --> pdb=" O PHE w 339 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE w 347 " --> pdb=" O THR w 343 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N HIS w 348 " --> pdb=" O PHE w 344 " (cutoff:3.500A) Processing helix chain 'w' and resid 352 through 361 Processing helix chain 'w' and resid 363 through 378 Processing helix chain 'w' and resid 400 through 421 removed outlier: 4.831A pdb=" N VAL w 404 " --> pdb=" O PRO w 400 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE w 405 " --> pdb=" O TYR w 401 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU w 406 " --> pdb=" O GLN w 402 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS w 407 " --> pdb=" O GLN w 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS w 409 " --> pdb=" O ILE w 405 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER w 412 " --> pdb=" O THR w 408 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG w 414 " --> pdb=" O SER w 410 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET w 417 " --> pdb=" O PHE w 413 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU w 418 " --> pdb=" O ARG w 414 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA w 419 " --> pdb=" O SER w 415 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 108 removed outlier: 3.731A pdb=" N LEU q 99 " --> pdb=" O HIS q 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER q 105 " --> pdb=" O SER q 101 " (cutoff:3.500A) Processing helix chain 'q' and resid 149 through 164 removed outlier: 3.797A pdb=" N ALA q 153 " --> pdb=" O ASP q 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS q 162 " --> pdb=" O GLU q 158 " (cutoff:3.500A) Processing helix chain 'q' and resid 180 through 194 removed outlier: 4.007A pdb=" N VAL q 184 " --> pdb=" O THR q 180 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU q 188 " --> pdb=" O VAL q 184 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU q 193 " --> pdb=" O TYR q 189 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 258 removed outlier: 3.997A pdb=" N ARG q 246 " --> pdb=" O TYR q 242 " (cutoff:3.500A) Processing helix chain 'q' and resid 264 through 293 removed outlier: 3.566A pdb=" N GLY q 273 " --> pdb=" O LEU q 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY q 274 " --> pdb=" O GLN q 270 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA q 275 " --> pdb=" O GLN q 271 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA q 277 " --> pdb=" O GLY q 273 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU q 291 " --> pdb=" O LEU q 287 " (cutoff:3.500A) Processing helix chain 'q' and resid 297 through 315 removed outlier: 3.563A pdb=" N ASP q 301 " --> pdb=" O LYS q 297 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN q 302 " --> pdb=" O VAL q 298 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR q 303 " --> pdb=" O SER q 299 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL q 304 " --> pdb=" O ALA q 300 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY q 305 " --> pdb=" O ASP q 301 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG q 306 " --> pdb=" O ASN q 302 " (cutoff:3.500A) Processing helix chain 'q' and resid 320 through 357 removed outlier: 4.578A pdb=" N GLU q 324 " --> pdb=" O PRO q 320 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU q 352 " --> pdb=" O ILE q 348 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL q 355 " --> pdb=" O ASN q 351 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN q 356 " --> pdb=" O GLU q 352 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 53 removed outlier: 3.597A pdb=" N VAL r 46 " --> pdb=" O ASP r 42 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS r 52 " --> pdb=" O LYS r 48 " (cutoff:3.500A) Processing helix chain 'r' and resid 97 through 111 removed outlier: 3.970A pdb=" N VAL r 110 " --> pdb=" O SER r 106 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 145 removed outlier: 3.607A pdb=" N ALA r 143 " --> pdb=" O SER r 139 " (cutoff:3.500A) Processing helix chain 'r' and resid 170 through 177 removed outlier: 3.815A pdb=" N MET r 174 " --> pdb=" O THR r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 184 through 193 removed outlier: 6.125A pdb=" N LYS r 188 " --> pdb=" O PRO r 184 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS r 189 " --> pdb=" O GLU r 185 " (cutoff:3.500A) Processing helix chain 'r' and resid 211 through 224 removed outlier: 3.566A pdb=" N TRP r 216 " --> pdb=" O ASN r 212 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU r 219 " --> pdb=" O MET r 215 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS r 220 " --> pdb=" O TRP r 216 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA r 223 " --> pdb=" O GLU r 219 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL r 224 " --> pdb=" O LYS r 220 " (cutoff:3.500A) Processing helix chain 'r' and resid 226 through 242 removed outlier: 3.641A pdb=" N SER r 232 " --> pdb=" O HIS r 228 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER r 235 " --> pdb=" O LEU r 231 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER r 236 " --> pdb=" O SER r 232 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN r 237 " --> pdb=" O LEU r 233 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS r 238 " --> pdb=" O ALA r 234 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY r 240 " --> pdb=" O SER r 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS r 241 " --> pdb=" O ASN r 237 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN r 242 " --> pdb=" O HIS r 238 " (cutoff:3.500A) Processing helix chain 'r' and resid 244 through 290 removed outlier: 4.172A pdb=" N VAL r 258 " --> pdb=" O SER r 254 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN r 278 " --> pdb=" O LYS r 274 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN r 279 " --> pdb=" O HIS r 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG r 281 " --> pdb=" O TYR r 277 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG r 288 " --> pdb=" O GLU r 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN r 289 " --> pdb=" O ASN r 285 " (cutoff:3.500A) Processing helix chain 'r' and resid 298 through 304 Processing helix chain 'r' and resid 314 through 352 removed outlier: 3.642A pdb=" N LEU r 318 " --> pdb=" O MET r 314 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN r 322 " --> pdb=" O LEU r 318 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN r 324 " --> pdb=" O ALA r 320 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN r 337 " --> pdb=" O PHE r 333 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU r 338 " --> pdb=" O THR r 334 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY r 339 " --> pdb=" O ALA r 335 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU r 347 " --> pdb=" O MET r 343 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 18 removed outlier: 3.870A pdb=" N GLN s 6 " --> pdb=" O ALA s 2 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN s 10 " --> pdb=" O GLN s 6 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS s 13 " --> pdb=" O ALA s 9 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS s 16 " --> pdb=" O GLY s 12 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE s 18 " --> pdb=" O LEU s 14 " (cutoff:3.500A) Processing helix chain 's' and resid 25 through 39 removed outlier: 3.514A pdb=" N GLU s 34 " --> pdb=" O GLU s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 43 through 58 removed outlier: 3.520A pdb=" N ASN s 47 " --> pdb=" O ASP s 43 " (cutoff:3.500A) Proline residue: s 58 - end of helix Processing helix chain 's' and resid 62 through 77 removed outlier: 3.969A pdb=" N LYS s 72 " --> pdb=" O GLN s 68 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN s 76 " --> pdb=" O LYS s 72 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU s 77 " --> pdb=" O ALA s 73 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 90 removed outlier: 3.733A pdb=" N LYS s 86 " --> pdb=" O PHE s 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS s 87 " --> pdb=" O THR s 83 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET s 88 " --> pdb=" O LEU s 84 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP s 90 " --> pdb=" O LYS s 86 " (cutoff:3.500A) Processing helix chain 's' and resid 91 through 96 removed outlier: 4.384A pdb=" N GLU s 95 " --> pdb=" O GLN s 91 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU s 96 " --> pdb=" O ALA s 92 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 91 through 96' Processing helix chain 's' and resid 97 through 112 removed outlier: 7.767A pdb=" N GLN s 101 " --> pdb=" O ARG s 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU s 108 " --> pdb=" O TYR s 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU s 109 " --> pdb=" O LEU s 105 " (cutoff:3.500A) Processing helix chain 's' and resid 113 through 121 Processing helix chain 's' and resid 125 through 131 removed outlier: 3.907A pdb=" N GLU s 129 " --> pdb=" O MET s 125 " (cutoff:3.500A) Processing helix chain 's' and resid 133 through 150 removed outlier: 3.984A pdb=" N ARG s 139 " --> pdb=" O GLU s 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE s 148 " --> pdb=" O HIS s 144 " (cutoff:3.500A) Processing helix chain 's' and resid 154 through 163 Processing helix chain 's' and resid 166 through 178 removed outlier: 3.837A pdb=" N LYS s 171 " --> pdb=" O ASP s 167 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET s 172 " --> pdb=" O SER s 168 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP s 173 " --> pdb=" O GLN s 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR s 177 " --> pdb=" O TRP s 173 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY s 178 " --> pdb=" O MET s 174 " (cutoff:3.500A) Processing helix chain 's' and resid 191 through 197 removed outlier: 3.732A pdb=" N ILE s 196 " --> pdb=" O GLN s 192 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS s 197 " --> pdb=" O GLU s 193 " (cutoff:3.500A) Processing helix chain 's' and resid 206 through 215 Processing helix chain 't' and resid 181 through 205 removed outlier: 3.586A pdb=" N GLU t 189 " --> pdb=" O ASP t 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE t 191 " --> pdb=" O ILE t 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN t 193 " --> pdb=" O GLU t 189 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN t 199 " --> pdb=" O GLN t 195 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR t 200 " --> pdb=" O SER t 196 " (cutoff:3.500A) Processing helix chain 't' and resid 208 through 219 removed outlier: 3.824A pdb=" N SER t 217 " --> pdb=" O ASP t 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN t 218 " --> pdb=" O PHE t 214 " (cutoff:3.500A) Proline residue: t 219 - end of helix Processing helix chain 't' and resid 221 through 248 removed outlier: 5.315A pdb=" N HIS t 225 " --> pdb=" O ILE t 221 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU t 228 " --> pdb=" O VAL t 224 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN t 229 " --> pdb=" O HIS t 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL t 230 " --> pdb=" O SER t 226 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU t 234 " --> pdb=" O VAL t 230 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR t 248 " --> pdb=" O LEU t 244 " (cutoff:3.500A) Processing helix chain 't' and resid 251 through 267 removed outlier: 5.064A pdb=" N SER t 255 " --> pdb=" O GLY t 251 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL t 256 " --> pdb=" O ASP t 252 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG t 262 " --> pdb=" O GLY t 258 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS t 263 " --> pdb=" O GLU t 259 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU t 265 " --> pdb=" O GLY t 261 " (cutoff:3.500A) Processing helix chain 't' and resid 273 through 291 removed outlier: 4.965A pdb=" N LEU t 277 " --> pdb=" O SER t 273 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN t 289 " --> pdb=" O GLY t 285 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA t 290 " --> pdb=" O ASP t 286 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE t 291 " --> pdb=" O TYR t 287 " (cutoff:3.500A) Processing helix chain 't' and resid 295 through 304 removed outlier: 3.514A pdb=" N ASN t 300 " --> pdb=" O ASN t 296 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N MET t 304 " --> pdb=" O ASN t 300 " (cutoff:3.500A) Processing helix chain 't' and resid 309 through 327 removed outlier: 3.922A pdb=" N THR t 314 " --> pdb=" O GLU t 310 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR t 318 " --> pdb=" O THR t 314 " (cutoff:3.500A) Processing helix chain 't' and resid 328 through 341 removed outlier: 4.252A pdb=" N ARG t 334 " --> pdb=" O GLN t 330 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN t 338 " --> pdb=" O ARG t 334 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE t 339 " --> pdb=" O VAL t 335 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU t 340 " --> pdb=" O PHE t 336 " (cutoff:3.500A) Processing helix chain 't' and resid 356 through 376 removed outlier: 3.620A pdb=" N ILE t 360 " --> pdb=" O LYS t 356 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN t 361 " --> pdb=" O TYR t 357 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN t 364 " --> pdb=" O ILE t 360 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU t 371 " --> pdb=" O MET t 367 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE t 373 " --> pdb=" O ALA t 369 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA t 374 " --> pdb=" O LEU t 370 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU t 375 " --> pdb=" O LEU t 371 " (cutoff:3.500A) Processing helix chain 't' and resid 381 through 386 removed outlier: 3.728A pdb=" N SER t 385 " --> pdb=" O ARG t 381 " (cutoff:3.500A) Processing helix chain 't' and resid 388 through 403 removed outlier: 4.619A pdb=" N LYS t 393 " --> pdb=" O GLN t 389 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU t 399 " --> pdb=" O GLY t 395 " (cutoff:3.500A) Processing helix chain 't' and resid 406 through 420 removed outlier: 3.876A pdb=" N GLU t 410 " --> pdb=" O PRO t 406 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE t 413 " --> pdb=" O TYR t 409 " (cutoff:3.500A) Proline residue: t 418 - end of helix Processing helix chain 't' and resid 434 through 463 removed outlier: 6.077A pdb=" N GLU t 438 " --> pdb=" O ASN t 434 " (cutoff:3.500A) Proline residue: t 439 - end of helix removed outlier: 4.001A pdb=" N GLN t 442 " --> pdb=" O GLU t 438 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE t 447 " --> pdb=" O GLN t 443 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP t 449 " --> pdb=" O LYS t 445 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU t 450 " --> pdb=" O VAL t 446 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL t 451 " --> pdb=" O PHE t 447 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN t 453 " --> pdb=" O ASP t 449 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN t 454 " --> pdb=" O GLU t 450 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN t 456 " --> pdb=" O GLN t 452 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER t 458 " --> pdb=" O GLN t 454 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR t 459 " --> pdb=" O ALA t 455 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE t 460 " --> pdb=" O GLN t 456 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG t 461 " --> pdb=" O LEU t 457 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE t 463 " --> pdb=" O THR t 459 " (cutoff:3.500A) Processing helix chain 't' and resid 471 through 483 removed outlier: 3.541A pdb=" N GLY t 477 " --> pdb=" O ALA t 473 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU t 481 " --> pdb=" O GLY t 477 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU t 483 " --> pdb=" O LEU t 479 " (cutoff:3.500A) Processing helix chain 't' and resid 488 through 500 removed outlier: 3.634A pdb=" N MET t 497 " --> pdb=" O PHE t 493 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS t 498 " --> pdb=" O LYS t 494 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN t 499 " --> pdb=" O HIS t 495 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU t 500 " --> pdb=" O LYS t 496 " (cutoff:3.500A) Processing helix chain 't' and resid 527 through 552 removed outlier: 4.913A pdb=" N ALA t 531 " --> pdb=" O MET t 527 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP t 532 " --> pdb=" O ILE t 528 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS t 534 " --> pdb=" O ILE t 530 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG t 545 " --> pdb=" O ASP t 541 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS t 549 " --> pdb=" O ARG t 545 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU t 552 " --> pdb=" O HIS t 548 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 27 removed outlier: 3.974A pdb=" N LEU u 22 " --> pdb=" O LEU u 18 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS u 23 " --> pdb=" O ARG u 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS u 25 " --> pdb=" O TYR u 21 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 41 removed outlier: 3.664A pdb=" N VAL u 40 " --> pdb=" O GLY u 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP u 41 " --> pdb=" O GLY u 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 53 removed outlier: 3.949A pdb=" N ASP u 50 " --> pdb=" O ILE u 46 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL u 51 " --> pdb=" O GLU u 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N CYS u 52 " --> pdb=" O ALA u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 62 through 77 removed outlier: 3.528A pdb=" N LEU u 71 " --> pdb=" O VAL u 67 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU u 72 " --> pdb=" O VAL u 68 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU u 74 " --> pdb=" O LEU u 70 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU u 75 " --> pdb=" O LEU u 71 " (cutoff:3.500A) Proline residue: u 76 - end of helix Processing helix chain 'u' and resid 78 through 94 removed outlier: 3.982A pdb=" N LEU u 82 " --> pdb=" O LYS u 78 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU u 84 " --> pdb=" O GLU u 80 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU u 86 " --> pdb=" O LEU u 82 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS u 87 " --> pdb=" O ILE u 83 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS u 89 " --> pdb=" O SER u 85 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU u 90 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL u 91 " --> pdb=" O CYS u 87 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 107 Proline residue: u 99 - end of helix removed outlier: 4.609A pdb=" N LEU u 106 " --> pdb=" O ARG u 102 " (cutoff:3.500A) Processing helix chain 'u' and resid 117 through 130 removed outlier: 4.450A pdb=" N TYR u 121 " --> pdb=" O THR u 117 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR u 124 " --> pdb=" O ARG u 120 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS u 129 " --> pdb=" O CYS u 125 " (cutoff:3.500A) Processing helix chain 'u' and resid 132 through 150 removed outlier: 3.774A pdb=" N ALA u 136 " --> pdb=" O ALA u 132 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN u 138 " --> pdb=" O CYS u 134 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR u 139 " --> pdb=" O GLY u 135 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE u 140 " --> pdb=" O ALA u 136 " (cutoff:3.500A) Proline residue: u 141 - end of helix Processing helix chain 'u' and resid 154 through 173 removed outlier: 3.731A pdb=" N THR u 158 " --> pdb=" O TRP u 154 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL u 173 " --> pdb=" O TYR u 169 " (cutoff:3.500A) Processing helix chain 'u' and resid 174 through 192 removed outlier: 3.752A pdb=" N GLU u 187 " --> pdb=" O LYS u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 198 through 215 removed outlier: 4.195A pdb=" N ASP u 203 " --> pdb=" O GLN u 199 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS u 205 " --> pdb=" O ARG u 201 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG u 206 " --> pdb=" O VAL u 202 " (cutoff:3.500A) Proline residue: u 215 - end of helix Processing helix chain 'u' and resid 220 through 227 removed outlier: 3.897A pdb=" N LEU u 226 " --> pdb=" O HIS u 222 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS u 227 " --> pdb=" O LEU u 223 " (cutoff:3.500A) Processing helix chain 'u' and resid 228 through 233 removed outlier: 4.283A pdb=" N GLU u 233 " --> pdb=" O VAL u 229 " (cutoff:3.500A) Processing helix chain 'u' and resid 239 through 250 removed outlier: 4.282A pdb=" N ILE u 243 " --> pdb=" O ASP u 239 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE u 244 " --> pdb=" O LEU u 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS u 248 " --> pdb=" O PHE u 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU u 249 " --> pdb=" O VAL u 245 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA u 250 " --> pdb=" O SER u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 251 through 259 removed outlier: 4.693A pdb=" N PHE u 255 " --> pdb=" O SER u 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR u 256 " --> pdb=" O TYR u 252 " (cutoff:3.500A) Processing helix chain 'u' and resid 260 through 267 removed outlier: 3.718A pdb=" N SER u 265 " --> pdb=" O ASP u 261 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU u 266 " --> pdb=" O PHE u 262 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY u 267 " --> pdb=" O ILE u 263 " (cutoff:3.500A) Processing helix chain 'u' and resid 269 through 289 removed outlier: 4.767A pdb=" N ASN u 273 " --> pdb=" O LEU u 269 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET u 274 " --> pdb=" O HIS u 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE u 282 " --> pdb=" O ARG u 278 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL u 287 " --> pdb=" O MET u 283 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN u 289 " --> pdb=" O MET u 285 " (cutoff:3.500A) Processing helix chain 'u' and resid 293 through 302 removed outlier: 3.729A pdb=" N MET u 297 " --> pdb=" O SER u 293 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN u 298 " --> pdb=" O PHE u 294 " (cutoff:3.500A) Processing helix chain 'u' and resid 304 through 319 removed outlier: 3.816A pdb=" N VAL u 308 " --> pdb=" O GLY u 304 " (cutoff:3.500A) Processing helix chain 'u' and resid 341 through 370 removed outlier: 3.779A pdb=" N ASP u 352 " --> pdb=" O GLN u 348 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR u 353 " --> pdb=" O GLN u 349 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP u 357 " --> pdb=" O THR u 353 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS u 358 " --> pdb=" O LEU u 354 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN u 362 " --> pdb=" O LYS u 358 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS u 363 " --> pdb=" O GLN u 359 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS u 365 " --> pdb=" O LEU u 361 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU u 368 " --> pdb=" O VAL u 364 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 24 through 28 removed outlier: 5.501A pdb=" N HIS C 24 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR C 28 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLY C 45 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 96 through 100 removed outlier: 3.701A pdb=" N THR C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 78 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 75 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 123 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 44 through 48 removed outlier: 3.828A pdb=" N GLY D 45 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR D 47 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 66 through 69 removed outlier: 7.365A pdb=" N HIS D 101 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 217 " --> pdb=" O HIS D 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 214 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 134 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D 123 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 143 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N THR D 119 " --> pdb=" O THR D 143 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 139 through 142 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'E' and resid 88 through 92 removed outlier: 3.708A pdb=" N LYS E 88 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE E 112 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 168 through 172 removed outlier: 3.646A pdb=" N GLY E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER E 210 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA E 183 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP E 206 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS E 207 " --> pdb=" O GLY E 188 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR E 209 " --> pdb=" O ILE E 190 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 109 through 116 Processing sheet with id= 9, first strand: chain 'F' and resid 45 through 53 removed outlier: 3.516A pdb=" N ILE F 48 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU F 89 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL F 91 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 148 through 155 removed outlier: 4.412A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 185 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY F 180 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 89 through 93 removed outlier: 3.804A pdb=" N ILE G 90 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 121 through 126 removed outlier: 4.586A pdb=" N ASP G 158 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR G 159 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.722A pdb=" N LYS G 128 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE G 130 " --> pdb=" O HIS G 138 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE G 136 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 180 through 184 removed outlier: 6.894A pdb=" N LEU G 180 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN G 224 " --> pdb=" O THR G 184 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 197 through 200 removed outlier: 4.661A pdb=" N ASN G 197 " --> pdb=" O HIS G 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS G 209 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL G 207 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 123 through 128 No H-bonds generated for sheet with id= 16 Processing sheet with id= 17, first strand: chain 'I' and resid 11 through 17 removed outlier: 3.593A pdb=" N ILE I 16 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU I 109 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN I 110 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 52 " --> pdb=" O THR I 34 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR I 34 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 159 through 163 removed outlier: 3.668A pdb=" N ARG I 170 " --> pdb=" O LEU I 162 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 54 through 57 removed outlier: 4.068A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 47 through 53 removed outlier: 4.619A pdb=" N ALA J 47 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG J 57 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL J 93 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 62 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL J 64 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 140 through 147 removed outlier: 4.363A pdb=" N SER J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP J 184 " --> pdb=" O ARG J 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 154 " --> pdb=" O ASP J 184 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= 23, first strand: chain 'K' and resid 71 through 75 removed outlier: 3.544A pdb=" N ARG K 74 " --> pdb=" O PHE K 65 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER K 66 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLY K 68 " --> pdb=" O VAL K 189 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP K 186 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU K 171 " --> pdb=" O ILE K 104 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS K 100 " --> pdb=" O ILE K 175 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.762A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 71 through 75 removed outlier: 5.772A pdb=" N ARG N 71 " --> pdb=" O GLU N 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 126 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR N 127 " --> pdb=" O LEU N 143 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 85 through 95 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.874A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 30 through 33 removed outlier: 5.735A pdb=" N GLY O 30 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS O 112 " --> pdb=" O GLY O 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL O 110 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER O 107 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN O 75 " --> pdb=" O HIS O 48 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS O 50 " --> pdb=" O ASN O 75 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER O 54 " --> pdb=" O VAL O 79 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 51 through 55 removed outlier: 6.760A pdb=" N GLU Q 51 " --> pdb=" O ASP Q 46 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL Q 44 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG Q 55 " --> pdb=" O VAL Q 42 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL Q 42 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE Q 41 " --> pdb=" O PHE Q 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS Q 43 " --> pdb=" O HIS Q 32 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS Q 32 " --> pdb=" O HIS Q 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL Q 30 " --> pdb=" O THR Q 45 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS Q 96 " --> pdb=" O CYS Q 31 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE Q 95 " --> pdb=" O GLY Q 127 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.629A pdb=" N GLU Q 130 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU Q 97 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL Q 132 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA Q 99 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 9 through 15 removed outlier: 3.730A pdb=" N ARG S 69 " --> pdb=" O HIS S 24 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU S 31 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE S 68 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL S 70 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'W' and resid 56 through 66 removed outlier: 5.628A pdb=" N LYS W 86 " --> pdb=" O PRO W 57 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS W 59 " --> pdb=" O ILE W 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 84 " --> pdb=" O LYS W 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR W 65 " --> pdb=" O ASP W 78 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 21 " --> pdb=" O THR W 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'X' and resid 32 through 37 removed outlier: 3.569A pdb=" N MET X 34 " --> pdb=" O TYR X 53 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Y' and resid 23 through 28 removed outlier: 5.337A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU Y 65 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL Y 25 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL Y 63 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU Y 49 " --> pdb=" O ASN Y 64 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Z' and resid 46 through 49 removed outlier: 3.776A pdb=" N ALA Z 47 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU Z 101 " --> pdb=" O VAL Z 123 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Z' and resid 53 through 59 removed outlier: 5.941A pdb=" N VAL Z 57 " --> pdb=" O ARG Z 67 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA Z 65 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS Z 79 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'a' and resid 5 through 8 Processing sheet with id= 38, first strand: chain 'a' and resid 20 through 29 removed outlier: 3.910A pdb=" N HIS a 29 " --> pdb=" O GLY a 67 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY a 67 " --> pdb=" O HIS a 29 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'b' and resid 20 through 24 removed outlier: 4.246A pdb=" N CYS b 28 " --> pdb=" O CYS b 23 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.783A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 32 through 35 removed outlier: 4.084A pdb=" N ARG c 81 " --> pdb=" O PHE c 32 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP c 34 " --> pdb=" O PHE c 79 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'd' and resid 9 through 14 removed outlier: 3.841A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP d 54 " --> pdb=" O VAL d 14 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'd' and resid 18 through 22 removed outlier: 3.674A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE d 34 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ARG d 40 " --> pdb=" O PHE d 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'f' and resid 137 through 140 removed outlier: 6.758A pdb=" N ASP f 137 " --> pdb=" O LYS f 152 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS f 152 " --> pdb=" O ASP f 137 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'g' and resid 5 through 12 removed outlier: 4.730A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR g 302 " --> pdb=" O LEU g 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG g 308 " --> pdb=" O ALA g 300 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN g 296 " --> pdb=" O VAL g 312 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR g 297 " --> pdb=" O SER g 292 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'g' and resid 20 through 23 removed outlier: 4.185A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP g 29 " --> pdb=" O LEU g 45 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU g 45 " --> pdb=" O ASP g 29 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR g 46 " --> pdb=" O TYR g 52 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR g 52 " --> pdb=" O THR g 46 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 67 through 72 removed outlier: 6.184A pdb=" N PHE g 77 " --> pdb=" O SER g 72 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG g 88 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU g 87 " --> pdb=" O PHE g 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 109 through 114 removed outlier: 3.862A pdb=" N ALA g 112 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN g 119 " --> pdb=" O SER g 114 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER g 124 " --> pdb=" O THR g 128 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 153 through 157 removed outlier: 5.368A pdb=" N ILE g 164 " --> pdb=" O SER g 157 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU g 179 " --> pdb=" O PRO g 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL g 176 " --> pdb=" O THR g 186 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 196 through 201 removed outlier: 3.553A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER g 201 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU g 206 " --> pdb=" O SER g 201 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY g 214 " --> pdb=" O GLY g 232 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR g 228 " --> pdb=" O LEU g 218 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 238 through 242 removed outlier: 4.493A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER g 242 " --> pdb=" O TRP g 247 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TRP g 247 " --> pdb=" O SER g 242 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER g 255 " --> pdb=" O THR g 252 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 39 through 42 removed outlier: 3.502A pdb=" N ILE g 40 " --> pdb=" O LEU g 59 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= 54, first strand: chain 'A' and resid 32 through 36 removed outlier: 5.089A pdb=" N ILE A 42 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'A' and resid 225 through 229 Processing sheet with id= 56, first strand: chain 'B' and resid 116 through 119 Processing sheet with id= 57, first strand: chain 'B' and resid 137 through 140 removed outlier: 7.292A pdb=" N ILE B 101 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS B 93 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 97 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 55 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 148 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLY B 61 " --> pdb=" O CYS B 148 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'B' and resid 268 through 272 removed outlier: 6.939A pdb=" N LEU B 269 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL B 370 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 271 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B' and resid 290 through 295 Processing sheet with id= 60, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.981A pdb=" N GLY B 299 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B' and resid 305 through 310 removed outlier: 4.711A pdb=" N GLN B 305 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N MET B 323 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.893A pdb=" N GLU B 379 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'B' and resid 424 through 429 removed outlier: 3.586A pdb=" N MET B 418 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 385 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR B 388 " --> pdb=" O ASP B 436 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP B 436 " --> pdb=" O TYR B 388 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'j' and resid 32 through 37 removed outlier: 6.515A pdb=" N GLY j 32 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU j 78 " --> pdb=" O ILE j 92 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN j 87 " --> pdb=" O LYS j 56 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL j 55 " --> pdb=" O CYS j 51 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG j 57 " --> pdb=" O ALA j 49 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA j 49 " --> pdb=" O ARG j 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'k' and resid 6 through 11 Processing sheet with id= 66, first strand: chain 'k' and resid 38 through 41 removed outlier: 7.434A pdb=" N CYS k 38 " --> pdb=" O SER k 51 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 92 through 95 removed outlier: 3.553A pdb=" N HIS k 95 " --> pdb=" O GLY k 297 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'k' and resid 166 through 169 removed outlier: 4.344A pdb=" N ILE k 167 " --> pdb=" O ILE k 237 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP k 241 " --> pdb=" O LYS k 169 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE k 238 " --> pdb=" O TYR k 268 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU k 104 " --> pdb=" O ARG k 267 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE k 269 " --> pdb=" O GLU k 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE k 285 " --> pdb=" O VAL k 105 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'k' and resid 351 through 356 removed outlier: 3.800A pdb=" N VAL k 365 " --> pdb=" O ALA k 545 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL k 534 " --> pdb=" O ASN k 546 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'k' and resid 374 through 377 removed outlier: 3.894A pdb=" N THR k 514 " --> pdb=" O ASP k 481 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP k 486 " --> pdb=" O LYS k 412 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 565 through 570 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'U' and resid 11 through 14 removed outlier: 6.345A pdb=" N HIS U 11 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY U 22 " --> pdb=" O HIS U 11 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'R' and resid 75 through 78 Processing sheet with id= 74, first strand: chain 'm' and resid 190 through 193 removed outlier: 4.341A pdb=" N GLN m 191 " --> pdb=" O ARG m 362 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR m 360 " --> pdb=" O ILE m 193 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'm' and resid 390 through 399 removed outlier: 3.871A pdb=" N ASN m 392 " --> pdb=" O TYR m 446 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS m 394 " --> pdb=" O LYS m 448 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR m 451 " --> pdb=" O LEU m 466 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 504 through 511 removed outlier: 4.157A pdb=" N TRP m 265 " --> pdb=" O LYS m 510 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA m 247 " --> pdb=" O ILE m 372 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'm' and resid 356 through 360 removed outlier: 3.968A pdb=" N ALA m 357 " --> pdb=" O HIS m 377 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS m 377 " --> pdb=" O ALA m 357 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'v' and resid 833 through 837 Processing sheet with id= 79, first strand: chain 'w' and resid 382 through 385 No H-bonds generated for sheet with id= 79 Processing sheet with id= 80, first strand: chain 'q' and resid 117 through 121 removed outlier: 4.351A pdb=" N LEU q 120 " --> pdb=" O GLY q 171 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY q 171 " --> pdb=" O LEU q 120 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE q 213 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL q 237 " --> pdb=" O ILE q 213 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA q 215 " --> pdb=" O LEU q 235 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU q 235 " --> pdb=" O ALA q 215 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL q 217 " --> pdb=" O THR q 233 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET q 231 " --> pdb=" O THR q 219 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL q 129 " --> pdb=" O VAL q 91 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'r' and resid 37 through 41 removed outlier: 3.689A pdb=" N GLN r 38 " --> pdb=" O ASP r 74 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'r' and resid 64 through 67 removed outlier: 3.546A pdb=" N GLY r 118 " --> pdb=" O LEU r 67 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP r 119 " --> pdb=" O VAL r 148 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN r 121 " --> pdb=" O LEU r 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR r 152 " --> pdb=" O GLN r 121 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR r 167 " --> pdb=" O VAL r 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER r 163 " --> pdb=" O ASP r 153 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 's' and resid 179 through 182 removed outlier: 4.242A pdb=" N SER s 180 " --> pdb=" O PHE s 188 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN s 186 " --> pdb=" O ASP s 182 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 't' and resid 503 through 508 removed outlier: 5.088A pdb=" N THR t 503 " --> pdb=" O ALA t 516 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU t 512 " --> pdb=" O SER t 507 " (cutoff:3.500A) 2914 hydrogen bonds defined for protein. 8673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1258 hydrogen bonds 2006 hydrogen bond angles 0 basepair planarities 504 basepair parallelities 888 stacking parallelities Total time for adding SS restraints: 66.50 Time building geometry restraints manager: 44.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.95: 7 0.95 - 1.46: 70151 1.46 - 1.97: 54442 1.97 - 2.48: 32 2.48 - 2.98: 4 Warning: very small bond lengths. Bond restraints: 124636 Sorted by residual: bond pdb=" C ASP k 521 " pdb=" N PHE k 522 " ideal model delta sigma weight residual 1.335 2.984 -1.649 1.25e-02 6.40e+03 1.74e+04 bond pdb=" C ARG U 142 " pdb=" N GLY U 143 " ideal model delta sigma weight residual 1.329 2.920 -1.591 1.40e-02 5.10e+03 1.29e+04 bond pdb=" C ILE k 451 " pdb=" N GLU k 452 " ideal model delta sigma weight residual 1.332 2.788 -1.456 1.40e-02 5.10e+03 1.08e+04 bond pdb=" C GLU k 373 " pdb=" N ILE k 374 " ideal model delta sigma weight residual 1.329 2.703 -1.374 1.63e-02 3.76e+03 7.11e+03 bond pdb=" C THR k 550 " pdb=" N LEU k 551 " ideal model delta sigma weight residual 1.335 2.350 -1.015 1.27e-02 6.20e+03 6.39e+03 ... (remaining 124631 not shown) Histogram of bond angle deviations from ideal: 35.70 - 64.31: 6 64.31 - 92.93: 57 92.93 - 121.54: 141801 121.54 - 150.15: 35369 150.15 - 178.77: 5 Bond angle restraints: 177238 Sorted by residual: angle pdb=" C ARG k 531 " pdb=" N VAL k 532 " pdb=" CA VAL k 532 " ideal model delta sigma weight residual 122.37 35.70 86.67 1.29e+00 6.01e-01 4.51e+03 angle pdb=" O LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 122.12 178.77 -56.65 1.06e+00 8.90e-01 2.86e+03 angle pdb=" CA ARG k 531 " pdb=" C ARG k 531 " pdb=" N VAL k 532 " ideal model delta sigma weight residual 116.37 43.39 72.98 1.45e+00 4.76e-01 2.53e+03 angle pdb=" CA LEU k 160 " pdb=" C LEU k 160 " pdb=" N GLU k 161 " ideal model delta sigma weight residual 117.30 61.23 56.07 1.16e+00 7.43e-01 2.34e+03 angle pdb=" CA ASN v 762 " pdb=" C ASN v 762 " pdb=" N GLY v 763 " ideal model delta sigma weight residual 117.30 64.77 52.53 1.16e+00 7.43e-01 2.05e+03 ... (remaining 177233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 73203 35.99 - 71.99: 4688 71.99 - 107.98: 605 107.98 - 143.97: 24 143.97 - 179.96: 30 Dihedral angle restraints: 78550 sinusoidal: 50011 harmonic: 28539 Sorted by residual: dihedral pdb=" CA SER r 122 " pdb=" C SER r 122 " pdb=" N THR r 123 " pdb=" CA THR r 123 " ideal model delta harmonic sigma weight residual -180.00 -48.38 -131.62 0 5.00e+00 4.00e-02 6.93e+02 dihedral pdb=" CA LEU B 322 " pdb=" C LEU B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 48.40 131.60 0 5.00e+00 4.00e-02 6.93e+02 dihedral pdb=" CA ASN j 19 " pdb=" C ASN j 19 " pdb=" N GLU j 20 " pdb=" CA GLU j 20 " ideal model delta harmonic sigma weight residual 180.00 53.27 126.73 0 5.00e+00 4.00e-02 6.42e+02 ... (remaining 78547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 21331 1.005 - 2.010: 6 2.010 - 3.015: 0 3.015 - 4.020: 1 4.020 - 5.025: 3 Chirality restraints: 21341 Sorted by residual: chirality pdb=" C4' C4J 21244 " pdb=" C5' C4J 21244 " pdb=" O4' C4J 21244 " pdb=" C3' C4J 21244 " both_signs ideal model delta sigma weight residual False 2.50 -2.53 5.02 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C2' C 1 17 " pdb=" C3' C 1 17 " pdb=" O2' C 1 17 " pdb=" C1' C 1 17 " both_signs ideal model delta sigma weight residual False -2.52 2.05 -4.57 2.00e-01 2.50e+01 5.22e+02 chirality pdb=" C3' G 1 18 " pdb=" C4' G 1 18 " pdb=" O3' G 1 18 " pdb=" C2' G 1 18 " both_signs ideal model delta sigma weight residual False -2.48 1.89 -4.37 2.00e-01 2.50e+01 4.77e+02 ... (remaining 21338 not shown) Planarity restraints: 15674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE k 451 " -0.184 2.00e-02 2.50e+03 2.66e-01 7.05e+02 pdb=" C ILE k 451 " 0.440 2.00e-02 2.50e+03 pdb=" O ILE k 451 " -0.232 2.00e-02 2.50e+03 pdb=" N GLU k 452 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU k 378 " -0.080 2.00e-02 2.50e+03 2.25e-01 5.08e+02 pdb=" C LEU k 378 " 0.379 2.00e-02 2.50e+03 pdb=" O LEU k 378 " -0.216 2.00e-02 2.50e+03 pdb=" N GLY k 379 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU y 245 " -0.099 2.00e-02 2.50e+03 1.92e-01 3.69e+02 pdb=" C LEU y 245 " 0.331 2.00e-02 2.50e+03 pdb=" O LEU y 245 " -0.136 2.00e-02 2.50e+03 pdb=" N TRP y 246 " -0.097 2.00e-02 2.50e+03 ... (remaining 15671 not shown) Histogram of nonbonded interaction distances: 0.63 - 1.49: 63 1.49 - 2.34: 485 2.34 - 3.19: 98990 3.19 - 4.05: 325698 4.05 - 4.90: 549186 Warning: very small nonbonded interaction distances. Nonbonded interactions: 974422 Sorted by model distance: nonbonded pdb=" NE2 HIS v 736 " pdb=" OE1 GLU v 759 " model vdw 0.634 2.520 nonbonded pdb=" CH2 TRP y 284 " pdb=" NE2 GLN y 426 " model vdw 0.727 3.420 nonbonded pdb=" C ILE k 451 " pdb=" N ASN k 453 " model vdw 0.805 3.350 nonbonded pdb=" CZ ARG y 367 " pdb=" CE1 HIS y 510 " model vdw 0.823 3.490 nonbonded pdb=" NH2 ARG y 367 " pdb=" CE1 HIS y 510 " model vdw 0.831 3.340 ... (remaining 974417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 15.620 Check model and map are aligned: 1.240 Set scattering table: 0.770 Process input model: 317.200 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 341.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5191 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 : 0.021 1.649 124636 Z= 1.361 Angle : 2.064 86.669 177238 Z= 1.288 Chirality : 0.118 5.025 21341 Planarity : 0.018 0.522 15674 Dihedral : 20.107 179.965 60087 Min Nonbonded Distance : 0.634 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 4.00 % Allowed : 10.80 % Favored : 85.20 % Rotamer: Outliers : 3.01 % Allowed : 5.49 % Favored : 91.50 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.47 % Twisted Proline : 4.89 % Twisted General : 1.52 % 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: -4.49 (0.07), residues: 9695 helix: -3.06 (0.06), residues: 3625 sheet: -2.46 (0.14), residues: 1114 loop : -3.06 (0.08), residues: 4956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.013 TRP s 173 HIS 0.013 0.001 HIS A 11 PHE 0.154 0.010 PHE k 535 TYR 0.253 0.016 TYR v 583 ARG 0.028 0.001 ARG k 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2367 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 2108 time to evaluate : 7.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6785 (m-40) REVERT: F 70 THR cc_start: 0.6943 (p) cc_final: 0.6612 (m) REVERT: F 148 LYS cc_start: 0.7003 (mttm) cc_final: 0.6788 (mtpt) REVERT: H 101 HIS cc_start: 0.6932 (t70) cc_final: 0.6619 (t70) REVERT: I 39 ASP cc_start: 0.2554 (m-30) cc_final: 0.2353 (t0) REVERT: J 171 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6883 (tm-30) REVERT: K 84 ASN cc_start: 0.4324 (OUTLIER) cc_final: 0.4092 (t0) REVERT: L 7 TRP cc_start: 0.3579 (m100) cc_final: 0.3003 (m100) REVERT: L 144 ILE cc_start: 0.8468 (mm) cc_final: 0.8179 (mm) REVERT: O 27 ILE cc_start: 0.5613 (mm) cc_final: 0.5180 (mt) REVERT: Q 93 LEU cc_start: 0.6881 (mt) cc_final: 0.6615 (mt) REVERT: V 75 MET cc_start: 0.6190 (mmm) cc_final: 0.5355 (mmm) REVERT: a 6 THR cc_start: 0.6333 (m) cc_final: 0.5676 (p) REVERT: a 97 TYR cc_start: 0.4132 (t80) cc_final: 0.3896 (t80) REVERT: b 73 TYR cc_start: 0.8111 (m-80) cc_final: 0.7779 (m-80) REVERT: c 73 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7335 (mm) REVERT: c 79 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5882 (m-10) REVERT: e 23 VAL cc_start: 0.2128 (OUTLIER) cc_final: 0.1554 (t) REVERT: e 34 TYR cc_start: 0.4429 (m-80) cc_final: 0.4085 (m-80) REVERT: A 58 SER cc_start: 0.4289 (t) cc_final: 0.3122 (t) REVERT: B 158 MET cc_start: -0.2262 (tmm) cc_final: -0.2612 (mtp) REVERT: B 204 LYS cc_start: 0.1121 (tppt) cc_final: 0.0355 (mmmt) REVERT: B 303 VAL cc_start: 0.0471 (p) cc_final: -0.0168 (t) REVERT: B 366 MET cc_start: 0.1501 (mtm) cc_final: 0.1299 (mtt) REVERT: B 402 ASP cc_start: 0.1440 (OUTLIER) cc_final: 0.0855 (p0) REVERT: B 430 VAL cc_start: 0.2038 (OUTLIER) cc_final: 0.1394 (m) REVERT: B 460 VAL cc_start: -0.3455 (p) cc_final: -0.3877 (m) REVERT: j 13 ARG cc_start: 0.2522 (OUTLIER) cc_final: 0.1705 (tpt90) REVERT: j 41 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: k 72 ILE cc_start: 0.6694 (tp) cc_final: 0.6257 (tp) REVERT: k 131 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5581 (tt) REVERT: k 317 VAL cc_start: 0.5363 (OUTLIER) cc_final: 0.5044 (t) REVERT: k 339 GLU cc_start: 0.2625 (OUTLIER) cc_final: 0.1488 (pt0) REVERT: k 419 LYS cc_start: 0.1821 (OUTLIER) cc_final: 0.1483 (mmmm) REVERT: m 182 MET cc_start: 0.4635 (mmm) cc_final: 0.3313 (mtt) REVERT: y 9 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5732 (pt0) REVERT: y 13 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5283 (ttmm) REVERT: y 35 MET cc_start: 0.6470 (mmm) cc_final: 0.6175 (mmm) REVERT: y 53 LYS cc_start: 0.7417 (tppp) cc_final: 0.6899 (tppt) REVERT: y 60 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.5532 (m-30) REVERT: y 65 HIS cc_start: 0.5889 (p-80) cc_final: 0.5427 (t-170) REVERT: y 88 ASP cc_start: 0.4615 (m-30) cc_final: 0.4356 (t0) REVERT: y 144 LEU cc_start: 0.5303 (tp) cc_final: 0.5001 (tp) REVERT: y 153 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.6017 (mt) REVERT: y 169 ARG cc_start: 0.4226 (ttp-110) cc_final: 0.3235 (mtp180) REVERT: y 195 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.5038 (mtt180) REVERT: y 198 CYS cc_start: 0.4516 (OUTLIER) cc_final: 0.3747 (t) REVERT: y 202 ARG cc_start: 0.5321 (ttp-170) cc_final: 0.4890 (mmp-170) REVERT: y 203 MET cc_start: 0.6316 (mtm) cc_final: 0.5808 (ttm) REVERT: y 248 GLU cc_start: 0.4957 (OUTLIER) cc_final: 0.4170 (mm-30) REVERT: y 254 GLU cc_start: 0.5121 (OUTLIER) cc_final: 0.4148 (mm-30) REVERT: v 351 ILE cc_start: 0.6581 (mt) cc_final: 0.6191 (mt) REVERT: v 405 ILE cc_start: 0.6241 (tp) cc_final: 0.6029 (tt) REVERT: v 406 ASN cc_start: 0.4280 (m-40) cc_final: 0.3909 (m110) REVERT: v 459 MET cc_start: 0.5218 (mmm) cc_final: 0.4663 (tpp) REVERT: v 748 ASP cc_start: 0.5394 (t0) cc_final: 0.4838 (m-30) REVERT: v 759 GLU cc_start: -0.0633 (mm-30) cc_final: -0.0982 (pt0) REVERT: w 7 THR cc_start: 0.0778 (OUTLIER) cc_final: 0.0259 (m) REVERT: w 91 ILE cc_start: 0.0924 (OUTLIER) cc_final: 0.0514 (mm) REVERT: s 7 MET cc_start: -0.1201 (mtm) cc_final: -0.1653 (tmm) REVERT: u 295 ASP cc_start: 0.5688 (m-30) cc_final: 0.5329 (m-30) outliers start: 259 outliers final: 46 residues processed: 2313 average time/residue: 1.1205 time to fit residues: 4265.6377 Evaluate side-chains 1205 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1136 time to evaluate : 7.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain K residue 84 ASN Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain c residue 70 LYS Chi-restraints excluded: chain c residue 73 LEU Chi-restraints excluded: chain c residue 79 PHE Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 378 PRO Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain j residue 13 ARG Chi-restraints excluded: chain j residue 41 MET Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 64 LYS Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 176 ILE Chi-restraints excluded: chain k residue 187 ILE Chi-restraints excluded: chain k residue 194 THR Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 329 LEU Chi-restraints excluded: chain k residue 332 LYS Chi-restraints excluded: chain k residue 339 GLU Chi-restraints excluded: chain k residue 419 LYS Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 533 ILE Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain y residue 13 LYS Chi-restraints excluded: chain y residue 28 LEU Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 60 ASP Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 113 LEU Chi-restraints excluded: chain y residue 126 SER Chi-restraints excluded: chain y residue 133 SER Chi-restraints excluded: chain y residue 149 TRP Chi-restraints excluded: chain y residue 153 LEU Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 179 GLN Chi-restraints excluded: chain y residue 195 ARG Chi-restraints excluded: chain y residue 198 CYS Chi-restraints excluded: chain y residue 237 LEU Chi-restraints excluded: chain y residue 242 SER Chi-restraints excluded: chain y residue 248 GLU Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 290 LEU Chi-restraints excluded: chain y residue 303 SER Chi-restraints excluded: chain y residue 324 LEU Chi-restraints excluded: chain y residue 327 LEU Chi-restraints excluded: chain y residue 347 ILE Chi-restraints excluded: chain y residue 355 LEU Chi-restraints excluded: chain v residue 396 GLU Chi-restraints excluded: chain v residue 418 ILE Chi-restraints excluded: chain v residue 521 ARG Chi-restraints excluded: chain v residue 542 GLU Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain q residue 187 HIS Chi-restraints excluded: chain u residue 9 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 0.9980 chunk 867 optimal weight: 6.9990 chunk 481 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 585 optimal weight: 5.9990 chunk 463 optimal weight: 5.9990 chunk 897 optimal weight: 0.0570 chunk 347 optimal weight: 6.9990 chunk 545 optimal weight: 0.8980 chunk 667 optimal weight: 9.9990 chunk 1039 optimal weight: 8.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 169 HIS ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 220 ASN E 257 HIS F 4 GLN F 74 GLN G 8 HIS G 17 HIS G 98 ASN H 74 ASN H 203 ASN J 91 HIS K 84 ASN K 181 GLN L 27 GLN M 84 HIS P 90 HIS Q 32 HIS T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 5 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 98 GLN Z 16 HIS Z 31 HIS Z 61 GLN b 72 HIS c 51 GLN c 65 GLN e 10 HIS f 111 ASN g 117 ASN g 159 ASN g 187 ASN g 196 ASN g 226 HIS ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN A 169 ASN j 37 GLN j 60 HIS ** k 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 154 ASN ** k 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 520 HIS k 546 ASN k 556 ASN k 588 GLN k 593 ASN U 85 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 296 ASN m 377 HIS m 479 GLN m 486 ASN m 515 GLN y 10 ASN y 73 GLN y 122 GLN y 179 GLN y 187 GLN ** y 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 301 HIS y 430 GLN ** y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 377 ASN v 399 GLN v 472 HIS v 819 HIS v 858 GLN w 80 GLN w 138 GLN w 252 HIS w 264 ASN w 348 HIS ** q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 182 HIS ** q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 288 GLN q 345 GLN r 40 GLN r 54 GLN r 58 GLN r 87 HIS ** r 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 141 GLN r 212 ASN r 237 ASN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN t 232 HIS t 281 HIS t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 389 GLN t 442 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 33 ASN u 298 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 124636 Z= 0.220 Angle : 0.791 15.237 177238 Z= 0.408 Chirality : 0.043 0.434 21341 Planarity : 0.006 0.150 15674 Dihedral : 21.290 178.692 40106 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.37 % Favored : 90.78 % Rotamer: Outliers : 3.53 % Allowed : 11.89 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 3.80 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.08), residues: 9717 helix: -1.30 (0.08), residues: 3800 sheet: -1.69 (0.14), residues: 1196 loop : -2.83 (0.08), residues: 4721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP v 766 HIS 0.044 0.002 HIS y 297 PHE 0.043 0.002 PHE v 755 TYR 0.035 0.002 TYR V 79 ARG 0.015 0.001 ARG J 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1618 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1314 time to evaluate : 7.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 MET cc_start: 0.7778 (mtm) cc_final: 0.7517 (mtm) REVERT: F 35 SER cc_start: 0.6844 (OUTLIER) cc_final: 0.6540 (t) REVERT: F 70 THR cc_start: 0.7167 (p) cc_final: 0.6959 (m) REVERT: F 142 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5111 (pp) REVERT: F 148 LYS cc_start: 0.6892 (mttm) cc_final: 0.6661 (mtpt) REVERT: G 166 THR cc_start: 0.7270 (p) cc_final: 0.6965 (p) REVERT: H 197 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: L 7 TRP cc_start: 0.3521 (m100) cc_final: 0.2785 (m100) REVERT: N 1 MET cc_start: 0.2242 (ttm) cc_final: 0.2003 (ttt) REVERT: O 27 ILE cc_start: 0.5234 (mm) cc_final: 0.4820 (mt) REVERT: O 36 ARG cc_start: 0.5253 (tpp-160) cc_final: 0.3866 (tpt90) REVERT: P 102 LEU cc_start: 0.8037 (mt) cc_final: 0.7737 (mp) REVERT: T 84 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.5553 (t80) REVERT: V 124 THR cc_start: 0.7574 (p) cc_final: 0.7162 (p) REVERT: W 56 MET cc_start: 0.6197 (mmt) cc_final: 0.5964 (mmt) REVERT: W 78 ASP cc_start: 0.6793 (t0) cc_final: 0.6592 (t0) REVERT: Z 37 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7660 (mttt) REVERT: a 97 TYR cc_start: 0.4347 (t80) cc_final: 0.3710 (t80) REVERT: c 27 SER cc_start: 0.8501 (m) cc_final: 0.8287 (m) REVERT: c 79 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: A 235 TYR cc_start: 0.2063 (OUTLIER) cc_final: 0.1773 (m-80) REVERT: A 255 MET cc_start: 0.0501 (tpt) cc_final: -0.0781 (mmt) REVERT: B 261 ARG cc_start: 0.2767 (mpt90) cc_final: 0.2489 (mtp180) REVERT: B 283 GLU cc_start: 0.2208 (OUTLIER) cc_final: 0.1561 (tt0) REVERT: B 323 MET cc_start: -0.1759 (tmm) cc_final: -0.2034 (tmm) REVERT: B 371 LEU cc_start: 0.0204 (mp) cc_final: -0.0039 (mp) REVERT: B 380 ILE cc_start: 0.2379 (OUTLIER) cc_final: 0.2092 (pt) REVERT: B 460 VAL cc_start: -0.4505 (OUTLIER) cc_final: -0.4757 (m) REVERT: j 66 ARG cc_start: 0.5899 (ttm-80) cc_final: 0.5646 (ttm170) REVERT: k 246 TYR cc_start: 0.4484 (OUTLIER) cc_final: 0.3655 (p90) REVERT: k 339 GLU cc_start: 0.2055 (OUTLIER) cc_final: 0.1202 (pt0) REVERT: k 347 MET cc_start: 0.5904 (tpp) cc_final: 0.5513 (tpt) REVERT: k 499 MET cc_start: 0.4120 (mmp) cc_final: 0.2188 (ppp) REVERT: U 118 ARG cc_start: 0.6162 (ptm160) cc_final: 0.5945 (ptp90) REVERT: R 24 GLN cc_start: 0.4830 (mt0) cc_final: 0.4628 (tm-30) REVERT: R 70 MET cc_start: 0.2859 (mpp) cc_final: 0.1774 (tmm) REVERT: m 182 MET cc_start: 0.4202 (mmm) cc_final: 0.2907 (mtt) REVERT: y 9 GLU cc_start: 0.5135 (OUTLIER) cc_final: 0.4891 (pm20) REVERT: y 53 LYS cc_start: 0.7825 (tppp) cc_final: 0.7201 (tppt) REVERT: y 65 HIS cc_start: 0.6049 (p-80) cc_final: 0.5623 (t-170) REVERT: y 88 ASP cc_start: 0.4670 (m-30) cc_final: 0.4443 (t0) REVERT: y 158 ARG cc_start: 0.4861 (tmm-80) cc_final: 0.4454 (mtp85) REVERT: y 161 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3965 (mt) REVERT: y 166 ASN cc_start: 0.4424 (m-40) cc_final: 0.3463 (p0) REVERT: y 179 GLN cc_start: 0.2666 (OUTLIER) cc_final: 0.1823 (mp10) REVERT: y 202 ARG cc_start: 0.4945 (ttp-110) cc_final: 0.4276 (mmp80) REVERT: y 231 GLU cc_start: 0.5815 (tt0) cc_final: 0.5581 (tt0) REVERT: y 248 GLU cc_start: 0.4793 (OUTLIER) cc_final: 0.4028 (mm-30) REVERT: y 268 LYS cc_start: 0.2626 (mmtm) cc_final: 0.1780 (mmmt) REVERT: y 290 LEU cc_start: 0.3837 (OUTLIER) cc_final: 0.3192 (pp) REVERT: y 520 ARG cc_start: 0.4890 (tpt170) cc_final: 0.3991 (tpm170) REVERT: y 522 GLN cc_start: 0.3541 (OUTLIER) cc_final: 0.2863 (mt0) REVERT: v 413 PHE cc_start: 0.2173 (m-80) cc_final: 0.1801 (m-80) REVERT: v 439 ARG cc_start: 0.4886 (mtp85) cc_final: 0.4449 (ppt170) REVERT: v 455 PHE cc_start: 0.5957 (t80) cc_final: 0.5401 (t80) REVERT: v 490 LEU cc_start: 0.2187 (tp) cc_final: 0.1828 (tt) REVERT: v 499 ILE cc_start: 0.2841 (tp) cc_final: 0.2597 (tp) REVERT: v 503 TYR cc_start: 0.5132 (m-80) cc_final: 0.4821 (m-10) REVERT: v 509 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5187 (m90) REVERT: w 4 TYR cc_start: 0.2834 (t80) cc_final: 0.2609 (t80) REVERT: w 7 THR cc_start: 0.0006 (OUTLIER) cc_final: -0.0224 (m) REVERT: w 91 ILE cc_start: 0.1312 (OUTLIER) cc_final: 0.0995 (mm) REVERT: q 150 MET cc_start: 0.1744 (OUTLIER) cc_final: 0.1310 (mtp) REVERT: r 174 MET cc_start: -0.1183 (ptp) cc_final: -0.2054 (mmt) REVERT: r 197 MET cc_start: 0.2888 (ppp) cc_final: 0.2452 (ppp) REVERT: r 343 MET cc_start: -0.0936 (mmm) cc_final: -0.1341 (tpp) REVERT: s 3 MET cc_start: 0.2192 (mpp) cc_final: -0.0686 (ttp) REVERT: t 268 MET cc_start: 0.4004 (ppp) cc_final: 0.3751 (ppp) REVERT: t 293 VAL cc_start: 0.2699 (OUTLIER) cc_final: 0.2461 (m) REVERT: t 349 MET cc_start: 0.2298 (tpt) cc_final: 0.1921 (tpp) REVERT: t 359 MET cc_start: 0.1924 (ttm) cc_final: 0.1376 (ttp) REVERT: u 64 MET cc_start: 0.1383 (OUTLIER) cc_final: 0.0895 (mmm) REVERT: u 206 ARG cc_start: 0.4856 (mtm110) cc_final: 0.4623 (mtm180) outliers start: 304 outliers final: 116 residues processed: 1522 average time/residue: 1.0658 time to fit residues: 2792.7483 Evaluate side-chains 1146 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1007 time to evaluate : 7.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 84 TYR Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain V residue 87 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 106 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain c residue 79 PHE Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 149 GLU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 196 ASN Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 213 ASP Chi-restraints excluded: chain g residue 235 ILE Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 176 ILE Chi-restraints excluded: chain k residue 205 ASP Chi-restraints excluded: chain k residue 206 LEU Chi-restraints excluded: chain k residue 246 TYR Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 339 GLU Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain m residue 174 MET Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 149 TRP Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 179 GLN Chi-restraints excluded: chain y residue 212 HIS Chi-restraints excluded: chain y residue 248 GLU Chi-restraints excluded: chain y residue 272 MET Chi-restraints excluded: chain y residue 290 LEU Chi-restraints excluded: chain y residue 327 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 522 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 397 MET Chi-restraints excluded: chain v residue 482 ILE Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 511 TYR Chi-restraints excluded: chain v residue 681 LEU Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 804 MET Chi-restraints excluded: chain w residue 7 THR Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 221 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain t residue 291 ILE Chi-restraints excluded: chain t residue 293 VAL Chi-restraints excluded: chain t residue 442 GLN Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 20.0000 chunk 322 optimal weight: 7.9990 chunk 865 optimal weight: 7.9990 chunk 708 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 1041 optimal weight: 5.9990 chunk 1125 optimal weight: 10.0000 chunk 927 optimal weight: 8.9990 chunk 1032 optimal weight: 7.9990 chunk 355 optimal weight: 3.9990 chunk 835 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS D 147 ASN E 98 GLN F 57 ASN G 50 ASN G 67 GLN G 142 HIS H 101 HIS H 203 ASN I 155 GLN J 76 GLN K 7 ASN K 64 ASN L 75 ASN L 113 GLN M 32 HIS N 13 GLN N 83 GLN N 94 HIS ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 48 HIS P 58 HIS S 48 GLN T 29 HIS T 118 GLN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 35 ASN Y 56 HIS Z 77 ASN ** Z 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 29 HIS a 112 ASN b 17 HIS b 80 HIS c 65 GLN d 29 GLN g 104 HIS g 147 HIS ** g 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 106 GLN n 112 ASN i 113 ASN j 85 GLN k 78 ASN k 85 HIS ** k 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 542 ASN U 87 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 GLN R 98 ASN R 114 HIS m 296 ASN ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 321 HIS m 322 ASN ** m 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 159 GLN ** y 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 292 HIS y 434 ASN y 477 HIS v 430 ASN v 595 GLN v 637 GLN ** v 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 716 HIS v 717 GLN v 753 HIS v 858 GLN ** q 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 199 HIS ** q 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 271 GLN ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 242 ASN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 489 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 222 HIS u 238 HIS u 345 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 124636 Z= 0.368 Angle : 0.929 18.193 177238 Z= 0.475 Chirality : 0.050 0.428 21341 Planarity : 0.008 0.143 15674 Dihedral : 21.393 179.783 39992 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.45 % Favored : 88.93 % Rotamer: Outliers : 4.71 % Allowed : 14.71 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 2.99 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.08), residues: 9717 helix: -0.96 (0.08), residues: 3819 sheet: -1.21 (0.14), residues: 1233 loop : -2.93 (0.08), residues: 4665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP m 363 HIS 0.061 0.003 HIS e 10 PHE 0.049 0.003 PHE g 113 TYR 0.045 0.003 TYR e 46 ARG 0.032 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1623 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1217 time to evaluate : 7.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 GLN cc_start: 0.7279 (mt0) cc_final: 0.6968 (mt0) REVERT: D 227 LYS cc_start: 0.6094 (tptp) cc_final: 0.5464 (ttmt) REVERT: E 157 ASN cc_start: 0.6624 (OUTLIER) cc_final: 0.5241 (m-40) REVERT: E 205 ASP cc_start: 0.6450 (m-30) cc_final: 0.6209 (m-30) REVERT: F 70 THR cc_start: 0.7393 (p) cc_final: 0.7080 (m) REVERT: G 97 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5310 (mt-10) REVERT: G 166 THR cc_start: 0.7284 (p) cc_final: 0.7037 (p) REVERT: H 49 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7086 (tp) REVERT: H 52 SER cc_start: 0.7580 (m) cc_final: 0.7334 (t) REVERT: H 92 ILE cc_start: 0.8398 (mt) cc_final: 0.8134 (mt) REVERT: K 7 ASN cc_start: 0.6981 (t160) cc_final: 0.6743 (t0) REVERT: L 7 TRP cc_start: 0.4622 (m100) cc_final: 0.3340 (m100) REVERT: M 29 MET cc_start: 0.7343 (mmm) cc_final: 0.6822 (mtm) REVERT: M 40 VAL cc_start: 0.5154 (t) cc_final: 0.4905 (t) REVERT: P 21 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.6148 (p) REVERT: Q 84 ARG cc_start: 0.6989 (ttt90) cc_final: 0.6587 (ttt90) REVERT: S 27 ARG cc_start: 0.6023 (ttt90) cc_final: 0.5651 (ttp-170) REVERT: T 84 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5932 (t80) REVERT: V 88 MET cc_start: 0.7766 (mmm) cc_final: 0.7223 (mpp) REVERT: a 16 ARG cc_start: 0.5263 (ttm-80) cc_final: 0.5058 (ttm-80) REVERT: a 97 TYR cc_start: 0.4638 (t80) cc_final: 0.3949 (t80) REVERT: a 107 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6485 (ttm170) REVERT: d 10 LYS cc_start: 0.7063 (tppt) cc_final: 0.6531 (tptp) REVERT: g 5 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4402 (mmm) REVERT: n 65 TYR cc_start: 0.3291 (m-10) cc_final: 0.2700 (m-80) REVERT: i 133 SER cc_start: 0.4008 (p) cc_final: 0.3660 (p) REVERT: A 64 ARG cc_start: 0.5422 (ptp-170) cc_final: 0.5066 (ttt180) REVERT: A 150 TYR cc_start: 0.3921 (t80) cc_final: 0.3225 (p90) REVERT: A 255 MET cc_start: 0.0319 (tpt) cc_final: -0.0444 (mmp) REVERT: B 250 GLU cc_start: -0.3823 (tt0) cc_final: -0.4079 (mt-10) REVERT: k 96 ARG cc_start: 0.6128 (mpp80) cc_final: 0.5914 (mtt180) REVERT: k 339 GLU cc_start: 0.1969 (OUTLIER) cc_final: 0.0944 (pt0) REVERT: k 493 ASP cc_start: 0.3765 (OUTLIER) cc_final: 0.3056 (m-30) REVERT: U 139 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6168 (p) REVERT: R 70 MET cc_start: 0.2803 (mpp) cc_final: 0.1687 (tmm) REVERT: R 112 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (pt) REVERT: R 137 HIS cc_start: 0.6302 (m90) cc_final: 0.6075 (m90) REVERT: m 182 MET cc_start: 0.4208 (mmm) cc_final: 0.3184 (mtm) REVERT: y 53 LYS cc_start: 0.8415 (tppp) cc_final: 0.7917 (tppt) REVERT: y 88 ASP cc_start: 0.4676 (m-30) cc_final: 0.4454 (t0) REVERT: y 98 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5798 (tm-30) REVERT: y 106 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4469 (mt-10) REVERT: y 141 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6682 (m) REVERT: y 149 TRP cc_start: 0.5042 (OUTLIER) cc_final: 0.4744 (m100) REVERT: y 163 LEU cc_start: 0.3692 (OUTLIER) cc_final: 0.3459 (tp) REVERT: y 166 ASN cc_start: 0.5497 (m-40) cc_final: 0.4021 (p0) REVERT: y 169 ARG cc_start: 0.5045 (ttm170) cc_final: 0.4541 (mtm180) REVERT: y 170 VAL cc_start: 0.6249 (m) cc_final: 0.5969 (m) REVERT: y 179 GLN cc_start: 0.3348 (OUTLIER) cc_final: 0.2344 (mp10) REVERT: y 202 ARG cc_start: 0.5557 (ttp-110) cc_final: 0.4621 (mmp80) REVERT: y 203 MET cc_start: 0.4893 (mtm) cc_final: 0.3735 (mmt) REVERT: y 254 GLU cc_start: 0.4220 (OUTLIER) cc_final: 0.3306 (mm-30) REVERT: y 272 MET cc_start: 0.3644 (mmm) cc_final: 0.3232 (mmm) REVERT: y 522 GLN cc_start: 0.4365 (OUTLIER) cc_final: 0.2885 (mm-40) REVERT: y 526 MET cc_start: 0.1278 (mmm) cc_final: 0.0968 (mmm) REVERT: v 347 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.3509 (tmt170) REVERT: v 368 GLU cc_start: 0.1398 (OUTLIER) cc_final: -0.0183 (tp30) REVERT: v 439 ARG cc_start: 0.4904 (mtp85) cc_final: 0.4379 (ppt170) REVERT: v 459 MET cc_start: 0.5390 (mmm) cc_final: 0.5114 (mmt) REVERT: v 469 TYR cc_start: 0.4944 (OUTLIER) cc_final: 0.4502 (m-80) REVERT: v 503 TYR cc_start: 0.5266 (m-80) cc_final: 0.4892 (m-80) REVERT: v 593 HIS cc_start: 0.4526 (OUTLIER) cc_final: 0.4138 (t-90) REVERT: w 242 TYR cc_start: 0.0319 (m-80) cc_final: 0.0076 (m-80) REVERT: w 249 MET cc_start: 0.3350 (ttt) cc_final: 0.3057 (ttt) REVERT: q 253 MET cc_start: 0.1728 (mmt) cc_final: 0.1246 (ttt) REVERT: q 311 LEU cc_start: 0.2507 (OUTLIER) cc_final: 0.2172 (mm) REVERT: r 174 MET cc_start: -0.0965 (ptp) cc_final: -0.1545 (mmt) REVERT: r 185 GLU cc_start: 0.1100 (mm-30) cc_final: 0.0066 (mt-10) REVERT: r 197 MET cc_start: 0.3156 (ppp) cc_final: 0.0412 (mpp) REVERT: r 343 MET cc_start: -0.0788 (mmm) cc_final: -0.1607 (tpp) REVERT: s 3 MET cc_start: 0.2974 (mpp) cc_final: 0.0325 (ttp) REVERT: s 62 GLN cc_start: 0.2498 (OUTLIER) cc_final: 0.1986 (tm-30) REVERT: t 192 TYR cc_start: 0.2145 (m-10) cc_final: 0.1446 (m-10) REVERT: t 326 MET cc_start: 0.2989 (ttp) cc_final: 0.2448 (tpt) REVERT: t 349 MET cc_start: 0.2492 (tpt) cc_final: 0.1765 (tpp) REVERT: t 359 MET cc_start: 0.1530 (ttm) cc_final: 0.1287 (ttt) REVERT: t 371 LEU cc_start: 0.0843 (OUTLIER) cc_final: 0.0546 (mp) REVERT: u 35 GLU cc_start: 0.5410 (mm-30) cc_final: 0.4641 (mt-10) REVERT: u 320 MET cc_start: 0.0122 (ttp) cc_final: -0.0789 (ptm) outliers start: 406 outliers final: 211 residues processed: 1512 average time/residue: 1.0173 time to fit residues: 2654.6850 Evaluate side-chains 1202 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 966 time to evaluate : 7.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 155 GLN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 84 TYR Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 51 ASN Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 85 GLN Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 339 GLU Chi-restraints excluded: chain k residue 353 MET Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 493 ASP Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 139 THR Chi-restraints excluded: chain R residue 112 ILE Chi-restraints excluded: chain m residue 353 ILE Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 141 THR Chi-restraints excluded: chain y residue 147 THR Chi-restraints excluded: chain y residue 149 TRP Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 163 LEU Chi-restraints excluded: chain y residue 179 GLN Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 282 VAL Chi-restraints excluded: chain y residue 327 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 410 VAL Chi-restraints excluded: chain y residue 488 SER Chi-restraints excluded: chain y residue 496 ASP Chi-restraints excluded: chain y residue 522 GLN Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 357 LEU Chi-restraints excluded: chain v residue 368 GLU Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 469 TYR Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 510 THR Chi-restraints excluded: chain v residue 546 VAL Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 593 HIS Chi-restraints excluded: chain v residue 681 LEU Chi-restraints excluded: chain v residue 701 HIS Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 220 PHE Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain w residue 372 VAL Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 311 LEU Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 219 GLU Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 125 MET Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 324 LEU Chi-restraints excluded: chain t residue 371 LEU Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 7 ILE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1029 optimal weight: 3.9990 chunk 783 optimal weight: 7.9990 chunk 540 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 699 optimal weight: 0.5980 chunk 1045 optimal weight: 0.9980 chunk 1106 optimal weight: 20.0000 chunk 546 optimal weight: 10.0000 chunk 990 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN D 76 ASN D 186 ASN E 98 GLN G 112 HIS G 201 HIS I 155 GLN J 76 GLN ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 HIS Q 103 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 HIS ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 65 GLN e 10 HIS g 285 GLN i 132 ASN j 85 GLN ** k 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 322 ASN m 377 HIS y 211 HIS y 257 HIS ** y 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 430 GLN ** y 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 143 ASN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 260 ASN q 271 GLN q 345 GLN ** r 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 121 GLN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 55 GLN t 344 GLN t 363 GLN t 364 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 402 GLN t 442 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 327 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 124636 Z= 0.225 Angle : 0.719 16.221 177238 Z= 0.371 Chirality : 0.042 0.286 21341 Planarity : 0.006 0.166 15674 Dihedral : 21.155 179.818 39969 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.00 % Favored : 90.44 % Rotamer: Outliers : 4.19 % Allowed : 17.14 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 1.90 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.08), residues: 9717 helix: -0.44 (0.08), residues: 3855 sheet: -0.93 (0.14), residues: 1241 loop : -2.83 (0.08), residues: 4621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP g 219 HIS 0.018 0.001 HIS y 297 PHE 0.030 0.002 PHE g 113 TYR 0.035 0.002 TYR y 174 ARG 0.010 0.001 ARG E 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1074 time to evaluate : 7.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.6855 (ttt180) cc_final: 0.6584 (ttt-90) REVERT: C 80 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7603 (mmm-85) REVERT: D 48 LEU cc_start: 0.8600 (pp) cc_final: 0.8386 (pp) REVERT: D 169 MET cc_start: 0.7849 (mtm) cc_final: 0.7545 (mtm) REVERT: D 227 LYS cc_start: 0.6389 (tptp) cc_final: 0.5636 (ttmt) REVERT: F 67 ARG cc_start: 0.5927 (tmm160) cc_final: 0.5679 (ttp-170) REVERT: F 70 THR cc_start: 0.7339 (p) cc_final: 0.7000 (m) REVERT: F 141 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6769 (mtmt) REVERT: F 145 GLN cc_start: 0.7227 (pt0) cc_final: 0.6939 (pt0) REVERT: F 224 SER cc_start: 0.7637 (m) cc_final: 0.7090 (p) REVERT: G 1 MET cc_start: 0.4957 (ttm) cc_final: 0.4454 (tpp) REVERT: G 118 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5821 (tt0) REVERT: H 52 SER cc_start: 0.7627 (m) cc_final: 0.7195 (t) REVERT: H 92 ILE cc_start: 0.8319 (mt) cc_final: 0.8094 (mt) REVERT: H 164 ARG cc_start: 0.6248 (ttt90) cc_final: 0.5946 (ttt90) REVERT: H 197 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: J 168 HIS cc_start: 0.5417 (p-80) cc_final: 0.5038 (p-80) REVERT: L 7 TRP cc_start: 0.4610 (m100) cc_final: 0.3543 (m100) REVERT: M 40 VAL cc_start: 0.4853 (t) cc_final: 0.4643 (t) REVERT: P 39 LYS cc_start: 0.6929 (tttm) cc_final: 0.6506 (tppt) REVERT: S 8 GLN cc_start: 0.7537 (mt0) cc_final: 0.7255 (mt0) REVERT: S 27 ARG cc_start: 0.6138 (ttt90) cc_final: 0.5593 (ttp-170) REVERT: S 48 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: T 84 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.6156 (t80) REVERT: V 88 MET cc_start: 0.7817 (mmm) cc_final: 0.7315 (mpp) REVERT: V 112 MET cc_start: 0.7225 (mmm) cc_final: 0.6632 (mmm) REVERT: V 134 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8425 (mt) REVERT: Y 23 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6317 (mtp-110) REVERT: a 97 TYR cc_start: 0.4823 (t80) cc_final: 0.4477 (t80) REVERT: d 10 LYS cc_start: 0.7201 (tppt) cc_final: 0.6568 (tptp) REVERT: g 5 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.4665 (mmm) REVERT: g 84 ASP cc_start: 0.7677 (p0) cc_final: 0.7464 (p0) REVERT: n 65 TYR cc_start: 0.3276 (m-10) cc_final: 0.3039 (m-80) REVERT: A 64 ARG cc_start: 0.5349 (ptp-170) cc_final: 0.5031 (ttt180) REVERT: A 150 TYR cc_start: 0.3946 (t80) cc_final: 0.3275 (p90) REVERT: A 235 TYR cc_start: 0.3366 (OUTLIER) cc_final: 0.2494 (m-80) REVERT: A 255 MET cc_start: -0.0261 (tpt) cc_final: -0.0628 (mmt) REVERT: B 155 MET cc_start: -0.0504 (tpt) cc_final: -0.0874 (tpt) REVERT: j 42 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4667 (mt) REVERT: k 142 GLU cc_start: 0.4840 (tt0) cc_final: 0.4403 (tp30) REVERT: k 153 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6309 (mt0) REVERT: k 339 GLU cc_start: 0.1977 (OUTLIER) cc_final: 0.0794 (pt0) REVERT: k 375 MET cc_start: 0.0948 (ttm) cc_final: 0.0373 (tpt) REVERT: k 391 MET cc_start: -0.0695 (tpp) cc_final: -0.1240 (tpp) REVERT: k 493 ASP cc_start: 0.3868 (OUTLIER) cc_final: 0.3273 (m-30) REVERT: k 563 GLU cc_start: 0.4882 (pt0) cc_final: 0.4441 (mm-30) REVERT: R 70 MET cc_start: 0.2727 (mpp) cc_final: 0.2043 (tmm) REVERT: m 182 MET cc_start: 0.4041 (mmm) cc_final: 0.3178 (mtm) REVERT: m 348 MET cc_start: 0.3266 (OUTLIER) cc_final: 0.3051 (ptm) REVERT: y 66 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.4962 (mm) REVERT: y 83 ILE cc_start: 0.4375 (mm) cc_final: 0.4118 (mm) REVERT: y 88 ASP cc_start: 0.4726 (m-30) cc_final: 0.4450 (t0) REVERT: y 98 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5823 (tm-30) REVERT: y 105 LYS cc_start: 0.4267 (tttt) cc_final: 0.4002 (tttt) REVERT: y 149 TRP cc_start: 0.5411 (OUTLIER) cc_final: 0.5141 (m100) REVERT: y 166 ASN cc_start: 0.5685 (m-40) cc_final: 0.3844 (p0) REVERT: y 169 ARG cc_start: 0.4888 (ttm170) cc_final: 0.4191 (mtp180) REVERT: y 170 VAL cc_start: 0.6135 (m) cc_final: 0.5819 (m) REVERT: y 202 ARG cc_start: 0.5720 (ttp-110) cc_final: 0.4606 (mmp80) REVERT: y 254 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4057 (mm-30) REVERT: y 488 SER cc_start: 0.1899 (OUTLIER) cc_final: 0.1544 (t) REVERT: y 522 GLN cc_start: 0.4529 (OUTLIER) cc_final: 0.2765 (tt0) REVERT: v 409 MET cc_start: 0.5089 (tpt) cc_final: 0.4652 (tpt) REVERT: v 439 ARG cc_start: 0.4575 (mtp85) cc_final: 0.4189 (ppt170) REVERT: v 446 THR cc_start: 0.5857 (p) cc_final: 0.5546 (t) REVERT: v 469 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: v 593 HIS cc_start: 0.4468 (OUTLIER) cc_final: 0.4086 (t-90) REVERT: v 670 GLN cc_start: 0.3704 (mp-120) cc_final: 0.2890 (pp30) REVERT: v 698 MET cc_start: 0.3372 (mmm) cc_final: 0.2974 (mmp) REVERT: w 56 ASP cc_start: 0.2030 (OUTLIER) cc_final: 0.1705 (m-30) REVERT: w 91 ILE cc_start: 0.2512 (OUTLIER) cc_final: 0.1617 (tp) REVERT: w 242 TYR cc_start: -0.0017 (m-80) cc_final: -0.0266 (m-80) REVERT: q 150 MET cc_start: 0.2154 (ttt) cc_final: 0.1694 (mtp) REVERT: q 228 MET cc_start: -0.0057 (mtm) cc_final: -0.1387 (tpt) REVERT: q 253 MET cc_start: 0.1462 (mmt) cc_final: 0.1233 (ttt) REVERT: r 174 MET cc_start: -0.1197 (ptp) cc_final: -0.1735 (mmt) REVERT: r 197 MET cc_start: 0.2813 (ppp) cc_final: 0.0541 (mmt) REVERT: r 343 MET cc_start: -0.0619 (mmm) cc_final: -0.1217 (tpp) REVERT: s 3 MET cc_start: 0.3196 (mpp) cc_final: 0.0557 (ttm) REVERT: t 192 TYR cc_start: 0.2127 (m-10) cc_final: 0.1383 (m-10) REVERT: t 326 MET cc_start: 0.3010 (ttp) cc_final: 0.2292 (tpt) REVERT: t 340 LEU cc_start: 0.2892 (mp) cc_final: 0.2491 (mp) REVERT: t 349 MET cc_start: 0.2523 (tpt) cc_final: 0.2273 (tpp) REVERT: t 359 MET cc_start: 0.1567 (ttm) cc_final: 0.1290 (ttt) REVERT: u 35 GLU cc_start: 0.5444 (mm-30) cc_final: 0.4569 (mt-10) REVERT: u 320 MET cc_start: 0.0217 (ttp) cc_final: -0.0953 (ptm) outliers start: 361 outliers final: 217 residues processed: 1334 average time/residue: 1.0579 time to fit residues: 2462.2591 Evaluate side-chains 1208 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 967 time to evaluate : 7.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 84 TYR Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 77 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 157 THR Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 339 GLU Chi-restraints excluded: chain k residue 353 MET Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 424 VAL Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 493 ASP Chi-restraints excluded: chain k residue 580 LEU Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 348 MET Chi-restraints excluded: chain m residue 389 SER Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 149 TRP Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 212 HIS Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 257 HIS Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 282 VAL Chi-restraints excluded: chain y residue 285 LYS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 327 LEU Chi-restraints excluded: chain y residue 355 LEU Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 428 VAL Chi-restraints excluded: chain y residue 488 SER Chi-restraints excluded: chain y residue 522 GLN Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 469 TYR Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 510 THR Chi-restraints excluded: chain v residue 546 VAL Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 593 HIS Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain w residue 28 VAL Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 220 PHE Chi-restraints excluded: chain w residue 241 GLN Chi-restraints excluded: chain w residue 280 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 327 LEU Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain s residue 125 MET Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 921 optimal weight: 20.0000 chunk 628 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 824 optimal weight: 30.0000 chunk 456 optimal weight: 5.9990 chunk 944 optimal weight: 8.9990 chunk 765 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 565 optimal weight: 10.0000 chunk 993 optimal weight: 7.9990 chunk 279 optimal weight: 0.0050 overall best weight: 6.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN E 98 GLN E 163 HIS I 65 GLN I 155 GLN K 7 ASN ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 GLN N 65 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 HIS a 89 HIS a 106 GLN a 124 ASN b 25 ASN c 65 GLN c 84 HIS i 111 GLN A 23 ASN A 68 ASN A 114 HIS j 85 GLN ** k 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 251 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 322 ASN m 428 ASN y 40 HIS y 270 GLN ** y 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 461 ASN ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 60 ASN ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 121 GLN r 272 GLN ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 324 ASN s 55 GLN s 76 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 442 GLN t 489 GLN ** t 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 33 ASN u 349 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 124636 Z= 0.307 Angle : 0.810 18.490 177238 Z= 0.414 Chirality : 0.045 0.362 21341 Planarity : 0.007 0.175 15674 Dihedral : 21.259 179.792 39964 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.75 % Favored : 88.68 % Rotamer: Outliers : 5.38 % Allowed : 17.62 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.36 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.08), residues: 9717 helix: -0.48 (0.08), residues: 3855 sheet: -0.97 (0.14), residues: 1231 loop : -2.91 (0.08), residues: 4631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP m 363 HIS 0.055 0.002 HIS y 257 PHE 0.038 0.003 PHE k 324 TYR 0.039 0.002 TYR v 799 ARG 0.013 0.001 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 463 poor density : 1066 time to evaluate : 7.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.7024 (ttt180) cc_final: 0.6765 (ttt-90) REVERT: l 21 ARG cc_start: 0.5581 (tmm-80) cc_final: 0.4552 (tpp80) REVERT: C 69 GLU cc_start: 0.6998 (mp0) cc_final: 0.6772 (mp0) REVERT: D 43 ASN cc_start: 0.6704 (t0) cc_final: 0.6416 (m110) REVERT: D 92 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: D 169 MET cc_start: 0.7816 (mtm) cc_final: 0.7506 (mtm) REVERT: D 227 LYS cc_start: 0.6550 (tptp) cc_final: 0.5965 (ttmt) REVERT: F 67 ARG cc_start: 0.5878 (tmm160) cc_final: 0.5609 (tmm160) REVERT: F 70 THR cc_start: 0.7336 (p) cc_final: 0.6944 (m) REVERT: F 145 GLN cc_start: 0.7377 (pt0) cc_final: 0.6993 (pt0) REVERT: F 224 SER cc_start: 0.7644 (m) cc_final: 0.7186 (p) REVERT: G 1 MET cc_start: 0.5146 (ttm) cc_final: 0.4882 (tpp) REVERT: G 118 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: H 15 PRO cc_start: 0.4405 (Cg_endo) cc_final: 0.3950 (Cg_exo) REVERT: H 18 LYS cc_start: 0.4340 (OUTLIER) cc_final: 0.3283 (mppt) REVERT: H 146 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7280 (mtp180) REVERT: H 197 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: J 60 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7413 (pt) REVERT: J 168 HIS cc_start: 0.5493 (p-80) cc_final: 0.5116 (p-80) REVERT: L 7 TRP cc_start: 0.4740 (m100) cc_final: 0.3645 (m100) REVERT: L 10 ARG cc_start: 0.7313 (ptp-170) cc_final: 0.6915 (ptt-90) REVERT: L 84 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7536 (mp) REVERT: L 92 MET cc_start: 0.7691 (tpp) cc_final: 0.7247 (tpt) REVERT: L 175 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5914 (mtp-110) REVERT: M 40 VAL cc_start: 0.5136 (t) cc_final: 0.4880 (t) REVERT: S 27 ARG cc_start: 0.6558 (ttt90) cc_final: 0.6094 (ptm160) REVERT: S 48 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: T 40 ILE cc_start: 0.6247 (OUTLIER) cc_final: 0.5981 (tt) REVERT: T 84 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.5904 (t80) REVERT: V 88 MET cc_start: 0.7744 (mmm) cc_final: 0.7273 (mpp) REVERT: V 112 MET cc_start: 0.7141 (mmm) cc_final: 0.6734 (mmm) REVERT: V 134 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (mt) REVERT: Y 23 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6886 (mtp-110) REVERT: Z 3 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.6355 (pptt) REVERT: a 97 TYR cc_start: 0.5058 (t80) cc_final: 0.4714 (t80) REVERT: e 31 ILE cc_start: 0.2104 (OUTLIER) cc_final: 0.1528 (tp) REVERT: g 5 MET cc_start: 0.4514 (OUTLIER) cc_final: 0.4122 (mmm) REVERT: g 84 ASP cc_start: 0.7635 (p0) cc_final: 0.7386 (p0) REVERT: g 217 MET cc_start: 0.5049 (ttm) cc_final: 0.4779 (ttm) REVERT: i 110 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6316 (ptm) REVERT: A 150 TYR cc_start: 0.4252 (t80) cc_final: 0.3156 (p90) REVERT: A 164 ASP cc_start: 0.1369 (OUTLIER) cc_final: -0.0549 (p0) REVERT: A 235 TYR cc_start: 0.3403 (OUTLIER) cc_final: 0.2615 (m-80) REVERT: A 255 MET cc_start: -0.0145 (OUTLIER) cc_final: -0.0892 (mmt) REVERT: j 42 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.4201 (mt) REVERT: k 153 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6616 (mt0) REVERT: k 375 MET cc_start: 0.0955 (ttm) cc_final: 0.0228 (tpt) REVERT: k 376 VAL cc_start: 0.5570 (OUTLIER) cc_final: 0.5305 (t) REVERT: k 391 MET cc_start: -0.0324 (tpp) cc_final: -0.0953 (tpp) REVERT: k 493 ASP cc_start: 0.3984 (OUTLIER) cc_final: 0.3545 (m-30) REVERT: U 144 ARG cc_start: 0.4478 (OUTLIER) cc_final: 0.3692 (mpt-90) REVERT: R 70 MET cc_start: 0.3129 (mpp) cc_final: 0.2047 (tmm) REVERT: m 182 MET cc_start: 0.3773 (mmm) cc_final: 0.3163 (mtm) REVERT: m 296 ASN cc_start: 0.1681 (OUTLIER) cc_final: 0.1241 (t0) REVERT: m 320 ASN cc_start: 0.2249 (p0) cc_final: 0.1977 (p0) REVERT: y 24 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5212 (mttp) REVERT: y 66 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4592 (mm) REVERT: y 83 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.3957 (mm) REVERT: y 88 ASP cc_start: 0.4696 (m-30) cc_final: 0.4372 (t0) REVERT: y 98 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5828 (tm-30) REVERT: y 106 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4741 (mt-10) REVERT: y 166 ASN cc_start: 0.6016 (m-40) cc_final: 0.3943 (p0) REVERT: y 169 ARG cc_start: 0.4568 (ttm170) cc_final: 0.4362 (ttm170) REVERT: y 170 VAL cc_start: 0.5909 (m) cc_final: 0.5307 (t) REVERT: y 191 LYS cc_start: 0.5859 (tptp) cc_final: 0.3827 (pttt) REVERT: y 199 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7565 (t0) REVERT: y 202 ARG cc_start: 0.6010 (ttp-110) cc_final: 0.4686 (tpt-90) REVERT: y 254 GLU cc_start: 0.4666 (OUTLIER) cc_final: 0.3977 (mm-30) REVERT: y 268 LYS cc_start: 0.3732 (OUTLIER) cc_final: 0.3008 (pttp) REVERT: y 522 GLN cc_start: 0.4235 (OUTLIER) cc_final: 0.2482 (mm-40) REVERT: v 347 ARG cc_start: 0.4751 (OUTLIER) cc_final: 0.3912 (ptt180) REVERT: v 355 GLN cc_start: 0.3557 (OUTLIER) cc_final: 0.2823 (tp40) REVERT: v 368 GLU cc_start: 0.0500 (OUTLIER) cc_final: -0.0547 (tp30) REVERT: v 409 MET cc_start: 0.5323 (tpt) cc_final: 0.4952 (tpp) REVERT: v 439 ARG cc_start: 0.4466 (mtp85) cc_final: 0.4123 (ppt170) REVERT: v 593 HIS cc_start: 0.4695 (OUTLIER) cc_final: 0.4313 (t-90) REVERT: v 744 MET cc_start: 0.2873 (mmm) cc_final: 0.1148 (ttm) REVERT: v 799 TYR cc_start: 0.1721 (OUTLIER) cc_final: 0.1147 (m-80) REVERT: w 4 TYR cc_start: 0.3050 (t80) cc_final: 0.2790 (t80) REVERT: w 94 MET cc_start: 0.2865 (ptt) cc_final: 0.2114 (ppp) REVERT: q 160 HIS cc_start: 0.2293 (OUTLIER) cc_final: 0.2012 (t-90) REVERT: r 141 GLN cc_start: 0.3666 (mm-40) cc_final: 0.2756 (pp30) REVERT: r 197 MET cc_start: 0.2644 (ppp) cc_final: 0.0369 (mmt) REVERT: r 228 HIS cc_start: 0.1926 (OUTLIER) cc_final: 0.1298 (m-70) REVERT: r 343 MET cc_start: -0.0545 (mmm) cc_final: -0.1407 (tpp) REVERT: s 3 MET cc_start: 0.3372 (mpp) cc_final: 0.0665 (ttm) REVERT: s 62 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1602 (mm-40) REVERT: t 192 TYR cc_start: 0.2354 (m-10) cc_final: 0.1684 (m-10) REVERT: t 326 MET cc_start: 0.3330 (ttp) cc_final: 0.2634 (tpt) REVERT: t 349 MET cc_start: 0.2917 (tpt) cc_final: 0.2345 (tpp) REVERT: u 35 GLU cc_start: 0.5873 (mm-30) cc_final: 0.4551 (mt-10) REVERT: u 219 LEU cc_start: 0.0853 (OUTLIER) cc_final: 0.0519 (mt) outliers start: 463 outliers final: 295 residues processed: 1407 average time/residue: 0.9769 time to fit residues: 2390.8078 Evaluate side-chains 1296 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 958 time to evaluate : 7.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 217 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 87 GLU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 40 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 84 TYR Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 29 HIS Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain c residue 79 PHE Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 219 TRP Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 85 GLN Chi-restraints excluded: chain j residue 91 VAL Chi-restraints excluded: chain j residue 98 ASP Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 157 THR Chi-restraints excluded: chain k residue 183 THR Chi-restraints excluded: chain k residue 264 ASN Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 321 ASN Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 326 ASP Chi-restraints excluded: chain k residue 376 VAL Chi-restraints excluded: chain k residue 409 VAL Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 493 ASP Chi-restraints excluded: chain k residue 540 SER Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain m residue 296 ASN Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 353 ILE Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain y residue 24 LYS Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 145 LEU Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 212 HIS Chi-restraints excluded: chain y residue 227 SER Chi-restraints excluded: chain y residue 232 THR Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 257 HIS Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 285 LYS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 355 LEU Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 392 ASN Chi-restraints excluded: chain y residue 428 VAL Chi-restraints excluded: chain y residue 496 ASP Chi-restraints excluded: chain y residue 522 GLN Chi-restraints excluded: chain y residue 542 ILE Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 360 ILE Chi-restraints excluded: chain v residue 368 GLU Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 510 THR Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 593 HIS Chi-restraints excluded: chain v residue 701 HIS Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 814 ASP Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 50 MET Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 220 PHE Chi-restraints excluded: chain w residue 241 GLN Chi-restraints excluded: chain w residue 280 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 160 HIS Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 46 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 228 HIS Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 125 MET Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 371 LEU Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 219 LEU Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 307 ASP Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 6.9990 chunk 996 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 649 optimal weight: 40.0000 chunk 273 optimal weight: 9.9990 chunk 1107 optimal weight: 20.0000 chunk 919 optimal weight: 9.9990 chunk 512 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 chunk 581 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN E 98 GLN F 207 HIS I 155 GLN K 167 GLN N 65 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN T 93 GLN V 12 GLN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 106 GLN a 124 ASN b 25 ASN c 65 GLN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 311 GLN j 85 GLN k 78 ASN k 593 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 436 GLN ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 869 ASN w 39 GLN ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 121 GLN r 228 HIS ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 239 ASN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 366 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 124636 Z= 0.332 Angle : 0.827 14.858 177238 Z= 0.421 Chirality : 0.046 0.263 21341 Planarity : 0.007 0.160 15674 Dihedral : 21.359 179.573 39957 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.67 % Favored : 88.82 % Rotamer: Outliers : 5.98 % Allowed : 18.94 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.36 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.08), residues: 9717 helix: -0.55 (0.08), residues: 3828 sheet: -1.08 (0.14), residues: 1265 loop : -2.95 (0.08), residues: 4624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 219 HIS 0.043 0.002 HIS y 257 PHE 0.034 0.003 PHE k 324 TYR 0.033 0.003 TYR j 84 ARG 0.048 0.001 ARG k 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 515 poor density : 1047 time to evaluate : 7.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 21 ARG cc_start: 0.5611 (tmm-80) cc_final: 0.4564 (tpp80) REVERT: D 43 ASN cc_start: 0.6739 (t0) cc_final: 0.6355 (m-40) REVERT: D 92 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6548 (pt0) REVERT: D 157 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: D 227 LYS cc_start: 0.6785 (tptp) cc_final: 0.5976 (ttpt) REVERT: E 157 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6418 (m-40) REVERT: F 5 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7452 (mt) REVERT: F 67 ARG cc_start: 0.5986 (tmm160) cc_final: 0.5680 (tmm160) REVERT: F 70 THR cc_start: 0.7314 (p) cc_final: 0.6818 (m) REVERT: F 145 GLN cc_start: 0.7413 (pt0) cc_final: 0.6919 (pt0) REVERT: F 223 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5798 (mt) REVERT: G 1 MET cc_start: 0.5084 (ttm) cc_final: 0.4540 (tpp) REVERT: G 118 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6241 (tt0) REVERT: H 15 PRO cc_start: 0.4828 (Cg_endo) cc_final: 0.4371 (Cg_exo) REVERT: H 146 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7228 (mtp180) REVERT: H 191 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7597 (tptm) REVERT: J 160 LYS cc_start: 0.6002 (mtpt) cc_final: 0.4863 (mmtt) REVERT: J 168 HIS cc_start: 0.5362 (p-80) cc_final: 0.5140 (p-80) REVERT: K 147 LYS cc_start: 0.4732 (mttp) cc_final: 0.3823 (tttt) REVERT: L 7 TRP cc_start: 0.4745 (m100) cc_final: 0.3646 (m100) REVERT: L 92 MET cc_start: 0.7648 (tpp) cc_final: 0.7165 (tpt) REVERT: L 175 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5970 (mtp-110) REVERT: M 40 VAL cc_start: 0.5373 (t) cc_final: 0.4955 (t) REVERT: N 96 ILE cc_start: 0.8598 (mm) cc_final: 0.8377 (mt) REVERT: S 48 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: S 50 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7645 (mmtt) REVERT: S 115 TYR cc_start: 0.5730 (p90) cc_final: 0.5055 (p90) REVERT: T 23 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7040 (mtt90) REVERT: T 84 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.6104 (t80) REVERT: V 88 MET cc_start: 0.7635 (mmm) cc_final: 0.7208 (mpp) REVERT: V 112 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6564 (mmm) REVERT: Y 23 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6772 (mtp-110) REVERT: Y 68 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6611 (mtp85) REVERT: Z 3 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.6320 (pptt) REVERT: Z 119 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7215 (mtt180) REVERT: a 107 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7624 (ttm110) REVERT: e 31 ILE cc_start: 0.2508 (OUTLIER) cc_final: 0.2045 (tp) REVERT: g 5 MET cc_start: 0.4766 (OUTLIER) cc_final: 0.4074 (mmm) REVERT: g 84 ASP cc_start: 0.7656 (p0) cc_final: 0.7438 (p0) REVERT: g 217 MET cc_start: 0.5181 (ttm) cc_final: 0.4972 (ttm) REVERT: n 58 LEU cc_start: 0.7644 (tp) cc_final: 0.7387 (tp) REVERT: i 110 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6378 (ptm) REVERT: A 150 TYR cc_start: 0.4620 (t80) cc_final: 0.3213 (p90) REVERT: A 235 TYR cc_start: 0.2896 (OUTLIER) cc_final: 0.2496 (m-80) REVERT: A 255 MET cc_start: -0.0060 (OUTLIER) cc_final: -0.1060 (mmt) REVERT: B 201 LEU cc_start: -0.1703 (tt) cc_final: -0.1921 (tt) REVERT: B 256 ILE cc_start: -0.1071 (mt) cc_final: -0.1373 (mt) REVERT: j 42 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4146 (mt) REVERT: j 101 ARG cc_start: 0.5349 (OUTLIER) cc_final: 0.5054 (ptp-170) REVERT: j 115 ILE cc_start: 0.5553 (tp) cc_final: 0.4955 (tp) REVERT: k 127 GLN cc_start: 0.6671 (tm-30) cc_final: 0.6248 (tt0) REVERT: k 153 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6618 (mt0) REVERT: k 246 TYR cc_start: 0.5771 (OUTLIER) cc_final: 0.5156 (p90) REVERT: k 357 MET cc_start: 0.2519 (ttm) cc_final: 0.1839 (ttp) REVERT: k 433 ARG cc_start: 0.0283 (OUTLIER) cc_final: 0.0061 (ptt90) REVERT: k 493 ASP cc_start: 0.4549 (OUTLIER) cc_final: 0.3974 (m-30) REVERT: R 70 MET cc_start: 0.2747 (mpp) cc_final: 0.1795 (tmm) REVERT: m 182 MET cc_start: 0.3738 (mmm) cc_final: 0.3336 (mtm) REVERT: m 296 ASN cc_start: 0.2695 (OUTLIER) cc_final: 0.1480 (t0) REVERT: m 503 GLU cc_start: -0.0289 (OUTLIER) cc_final: -0.2279 (pp20) REVERT: y 24 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.5435 (mttp) REVERT: y 66 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4977 (mm) REVERT: y 83 ILE cc_start: 0.4248 (OUTLIER) cc_final: 0.3682 (mm) REVERT: y 88 ASP cc_start: 0.4738 (m-30) cc_final: 0.4499 (t0) REVERT: y 98 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5801 (tm-30) REVERT: y 166 ASN cc_start: 0.6299 (m-40) cc_final: 0.3688 (p0) REVERT: y 170 VAL cc_start: 0.6178 (m) cc_final: 0.5514 (t) REVERT: y 172 ARG cc_start: 0.4667 (OUTLIER) cc_final: 0.3861 (tpp80) REVERT: y 191 LYS cc_start: 0.5877 (tptp) cc_final: 0.3900 (pttp) REVERT: y 199 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7505 (t0) REVERT: y 202 ARG cc_start: 0.5817 (ttp-110) cc_final: 0.4811 (mmp-170) REVERT: y 243 MET cc_start: 0.6137 (ttt) cc_final: 0.5814 (ttp) REVERT: y 254 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.4135 (mm-30) REVERT: y 268 LYS cc_start: 0.3856 (OUTLIER) cc_final: 0.3024 (pttt) REVERT: y 367 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.4335 (mtt90) REVERT: y 514 MET cc_start: 0.3196 (mpp) cc_final: 0.2854 (mpp) REVERT: v 347 ARG cc_start: 0.4893 (OUTLIER) cc_final: 0.3916 (ptt180) REVERT: v 355 GLN cc_start: 0.3197 (OUTLIER) cc_final: 0.2244 (tt0) REVERT: v 409 MET cc_start: 0.5101 (tpt) cc_final: 0.4621 (tpp) REVERT: v 439 ARG cc_start: 0.3588 (mtp85) cc_final: 0.3305 (ppt170) REVERT: v 459 MET cc_start: 0.4849 (mmt) cc_final: 0.4360 (tpt) REVERT: v 508 LEU cc_start: 0.5473 (mt) cc_final: 0.5250 (mp) REVERT: v 593 HIS cc_start: 0.4544 (OUTLIER) cc_final: 0.4264 (t-90) REVERT: v 622 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.4923 (ttp-170) REVERT: v 799 TYR cc_start: 0.2355 (OUTLIER) cc_final: 0.1319 (m-80) REVERT: w 4 TYR cc_start: 0.3144 (t80) cc_final: 0.2799 (t80) REVERT: w 91 ILE cc_start: 0.3419 (OUTLIER) cc_final: 0.2867 (tp) REVERT: w 275 LYS cc_start: 0.3437 (mttt) cc_final: 0.2968 (mttt) REVERT: q 150 MET cc_start: 0.2900 (OUTLIER) cc_final: 0.2494 (ttt) REVERT: r 141 GLN cc_start: 0.3583 (mm-40) cc_final: 0.2463 (pp30) REVERT: r 197 MET cc_start: 0.2572 (ppp) cc_final: 0.0572 (mmt) REVERT: r 228 HIS cc_start: 0.2836 (OUTLIER) cc_final: 0.2082 (m170) REVERT: r 343 MET cc_start: -0.0710 (mmm) cc_final: -0.1366 (tpp) REVERT: s 3 MET cc_start: 0.3503 (mpp) cc_final: 0.0969 (ttm) REVERT: s 62 GLN cc_start: 0.2178 (OUTLIER) cc_final: 0.1695 (mm-40) REVERT: s 172 MET cc_start: 0.3356 (ttt) cc_final: 0.2803 (mtm) REVERT: t 326 MET cc_start: 0.3596 (ttp) cc_final: 0.2897 (tpt) REVERT: u 35 GLU cc_start: 0.5922 (mm-30) cc_final: 0.4543 (mt-10) REVERT: u 219 LEU cc_start: 0.0790 (OUTLIER) cc_final: 0.0536 (mt) outliers start: 515 outliers final: 334 residues processed: 1425 average time/residue: 0.9837 time to fit residues: 2446.6403 Evaluate side-chains 1354 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 971 time to evaluate : 7.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 72 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 84 TYR Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 61 LEU Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 29 HIS Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 168 CYS Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain g residue 219 TRP Chi-restraints excluded: chain g residue 229 THR Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 101 ARG Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 77 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 157 THR Chi-restraints excluded: chain k residue 183 THR Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 246 TYR Chi-restraints excluded: chain k residue 264 ASN Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 271 VAL Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 321 ASN Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 326 ASP Chi-restraints excluded: chain k residue 424 VAL Chi-restraints excluded: chain k residue 433 ARG Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 443 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 449 LEU Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 493 ASP Chi-restraints excluded: chain k residue 540 SER Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain m residue 241 THR Chi-restraints excluded: chain m residue 296 ASN Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain m residue 495 ILE Chi-restraints excluded: chain m residue 503 GLU Chi-restraints excluded: chain m residue 519 VAL Chi-restraints excluded: chain y residue 24 LYS Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 147 THR Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 172 ARG Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 208 ILE Chi-restraints excluded: chain y residue 212 HIS Chi-restraints excluded: chain y residue 227 SER Chi-restraints excluded: chain y residue 232 THR Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 367 ARG Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 386 GLU Chi-restraints excluded: chain y residue 392 ASN Chi-restraints excluded: chain y residue 487 THR Chi-restraints excluded: chain y residue 507 ILE Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain v residue 433 ASN Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 444 ILE Chi-restraints excluded: chain v residue 446 THR Chi-restraints excluded: chain v residue 480 CYS Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 510 THR Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 593 HIS Chi-restraints excluded: chain v residue 605 VAL Chi-restraints excluded: chain v residue 622 ARG Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 798 VAL Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 814 ASP Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 134 TYR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 220 PHE Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 174 MET Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 228 HIS Chi-restraints excluded: chain r residue 302 SER Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 150 TYR Chi-restraints excluded: chain s residue 201 ILE Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 219 LEU Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 307 ASP Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1068 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 631 optimal weight: 10.0000 chunk 809 optimal weight: 6.9990 chunk 626 optimal weight: 20.0000 chunk 932 optimal weight: 40.0000 chunk 618 optimal weight: 20.0000 chunk 1103 optimal weight: 8.9990 chunk 690 optimal weight: 5.9990 chunk 672 optimal weight: 10.0000 chunk 509 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN K 167 GLN N 65 ASN N 141 ASN T 31 ASN T 93 GLN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 124 ASN b 25 ASN c 65 GLN e 5 GLN g 104 HIS ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS ** y 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 579 HIS v 610 ASN ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 309 GLN w 395 ASN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 124636 Z= 0.308 Angle : 0.801 21.231 177238 Z= 0.408 Chirality : 0.045 0.344 21341 Planarity : 0.006 0.183 15674 Dihedral : 21.374 179.248 39956 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.45 % Allowed : 11.29 % Favored : 88.26 % Rotamer: Outliers : 5.91 % Allowed : 19.73 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.50 % Twisted Proline : 1.36 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.08), residues: 9717 helix: -0.45 (0.08), residues: 3826 sheet: -1.01 (0.14), residues: 1225 loop : -2.98 (0.08), residues: 4666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 152 HIS 0.042 0.002 HIS r 228 PHE 0.045 0.002 PHE w 53 TYR 0.032 0.002 TYR v 799 ARG 0.011 0.001 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 509 poor density : 1019 time to evaluate : 7.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.6450 (ttt-90) cc_final: 0.6240 (ttt-90) REVERT: l 21 ARG cc_start: 0.5650 (tmm-80) cc_final: 0.4642 (tpp80) REVERT: D 43 ASN cc_start: 0.6768 (t0) cc_final: 0.6337 (m-40) REVERT: D 92 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6622 (pt0) REVERT: D 227 LYS cc_start: 0.6580 (tptp) cc_final: 0.5991 (ttpt) REVERT: E 157 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6321 (m-40) REVERT: F 70 THR cc_start: 0.7104 (p) cc_final: 0.6669 (m) REVERT: F 145 GLN cc_start: 0.7268 (pt0) cc_final: 0.6884 (pt0) REVERT: G 1 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.4499 (tpp) REVERT: G 118 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6280 (tt0) REVERT: H 15 PRO cc_start: 0.5322 (Cg_endo) cc_final: 0.4831 (Cg_exo) REVERT: H 18 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.3086 (mppt) REVERT: H 37 ASP cc_start: 0.6185 (OUTLIER) cc_final: 0.5956 (p0) REVERT: H 191 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (tptm) REVERT: I 84 TYR cc_start: 0.7899 (t80) cc_final: 0.7626 (t80) REVERT: J 75 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4847 (mp) REVERT: J 153 LEU cc_start: 0.6854 (tt) cc_final: 0.6223 (tp) REVERT: J 160 LYS cc_start: 0.5966 (mtpt) cc_final: 0.5072 (mmtt) REVERT: L 7 TRP cc_start: 0.4958 (m100) cc_final: 0.3790 (m100) REVERT: L 84 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7490 (mp) REVERT: L 92 MET cc_start: 0.7636 (tpp) cc_final: 0.7102 (tpt) REVERT: L 175 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.6032 (mtp-110) REVERT: M 40 VAL cc_start: 0.5333 (t) cc_final: 0.5011 (t) REVERT: N 35 ARG cc_start: 0.7803 (tpt170) cc_final: 0.7386 (mmm-85) REVERT: O 129 LYS cc_start: 0.4252 (mtmt) cc_final: 0.2395 (tttt) REVERT: P 119 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: S 48 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: S 50 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7665 (mmtt) REVERT: T 23 ARG cc_start: 0.7387 (mmm-85) cc_final: 0.7078 (mtt90) REVERT: V 88 MET cc_start: 0.7685 (mmm) cc_final: 0.7220 (mpp) REVERT: V 112 MET cc_start: 0.7007 (mmm) cc_final: 0.6390 (mmm) REVERT: X 1 MET cc_start: 0.7023 (ppp) cc_final: 0.6809 (ppp) REVERT: Y 23 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6847 (mtp-110) REVERT: Y 68 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6701 (mtp85) REVERT: Z 1 MET cc_start: 0.2303 (mpp) cc_final: 0.2101 (mpp) REVERT: Z 3 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.6293 (pptt) REVERT: Z 119 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7207 (mtt180) REVERT: a 107 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7565 (ttm110) REVERT: g 5 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4061 (mmm) REVERT: g 113 PHE cc_start: 0.4988 (OUTLIER) cc_final: 0.4478 (t80) REVERT: i 110 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6418 (ptm) REVERT: A 127 LEU cc_start: 0.1370 (OUTLIER) cc_final: 0.1073 (mm) REVERT: A 133 ARG cc_start: 0.3240 (ptm-80) cc_final: 0.1642 (ttm110) REVERT: A 150 TYR cc_start: 0.4823 (t80) cc_final: 0.3281 (p90) REVERT: A 164 ASP cc_start: 0.1484 (OUTLIER) cc_final: -0.0594 (p0) REVERT: B 86 LEU cc_start: 0.2112 (mt) cc_final: 0.1776 (mm) REVERT: j 42 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3950 (mt) REVERT: j 57 ARG cc_start: 0.5327 (mtt-85) cc_final: 0.4817 (ptp-110) REVERT: k 17 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5557 (mptt) REVERT: k 120 LEU cc_start: 0.7316 (tp) cc_final: 0.6838 (tp) REVERT: k 127 GLN cc_start: 0.6356 (tm-30) cc_final: 0.6122 (tt0) REVERT: k 153 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: k 246 TYR cc_start: 0.6296 (OUTLIER) cc_final: 0.5570 (p90) REVERT: k 345 MET cc_start: 0.3016 (tmm) cc_final: 0.1823 (mtm) REVERT: k 357 MET cc_start: 0.2687 (ttm) cc_final: 0.2026 (ttp) REVERT: k 375 MET cc_start: 0.1090 (tpp) cc_final: 0.0318 (mtp) REVERT: U 46 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6959 (mmt-90) REVERT: U 55 ARG cc_start: 0.5460 (OUTLIER) cc_final: 0.4117 (mmm-85) REVERT: U 144 ARG cc_start: 0.4369 (OUTLIER) cc_final: 0.3920 (mtt90) REVERT: R 127 LYS cc_start: 0.7127 (mtmm) cc_final: 0.6903 (tptp) REVERT: m 182 MET cc_start: 0.3674 (mmm) cc_final: 0.3174 (mtm) REVERT: m 296 ASN cc_start: 0.2821 (OUTLIER) cc_final: 0.0957 (t0) REVERT: m 503 GLU cc_start: -0.0305 (OUTLIER) cc_final: -0.2245 (pp20) REVERT: y 4 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6510 (t80) REVERT: y 6 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6405 (tp40) REVERT: y 66 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4977 (mm) REVERT: y 83 ILE cc_start: 0.4520 (OUTLIER) cc_final: 0.4254 (mm) REVERT: y 88 ASP cc_start: 0.4827 (m-30) cc_final: 0.4513 (t0) REVERT: y 106 GLU cc_start: 0.5067 (OUTLIER) cc_final: 0.4859 (mt-10) REVERT: y 172 ARG cc_start: 0.4863 (OUTLIER) cc_final: 0.3997 (tpp-160) REVERT: y 199 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7583 (t0) REVERT: y 202 ARG cc_start: 0.5668 (ttp-110) cc_final: 0.4840 (mmp-170) REVERT: y 254 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.4232 (mt-10) REVERT: y 268 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.2931 (pttt) REVERT: y 367 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.4376 (mtt90) REVERT: y 514 MET cc_start: 0.3169 (mpp) cc_final: 0.2798 (mpp) REVERT: v 324 ILE cc_start: 0.4937 (OUTLIER) cc_final: 0.4615 (tt) REVERT: v 347 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.3784 (ptt180) REVERT: v 355 GLN cc_start: 0.3254 (OUTLIER) cc_final: 0.2425 (tt0) REVERT: v 368 GLU cc_start: 0.0602 (OUTLIER) cc_final: -0.0579 (tp30) REVERT: v 409 MET cc_start: 0.5044 (tpt) cc_final: 0.4702 (tpp) REVERT: v 439 ARG cc_start: 0.3495 (mtp85) cc_final: 0.3289 (ppt170) REVERT: v 459 MET cc_start: 0.4901 (mmt) cc_final: 0.4409 (tpt) REVERT: v 548 MET cc_start: 0.5555 (mmm) cc_final: 0.5006 (mmm) REVERT: v 622 ARG cc_start: 0.5648 (OUTLIER) cc_final: 0.4656 (ttp-170) REVERT: v 744 MET cc_start: 0.3174 (mmm) cc_final: 0.2881 (tpp) REVERT: v 799 TYR cc_start: 0.2347 (OUTLIER) cc_final: 0.1574 (m-80) REVERT: v 858 GLN cc_start: 0.4814 (pp30) cc_final: 0.3087 (mt0) REVERT: w 94 MET cc_start: 0.3166 (tmm) cc_final: 0.2864 (mmp) REVERT: w 112 MET cc_start: 0.2360 (mtm) cc_final: -0.0289 (ttp) REVERT: w 275 LYS cc_start: 0.2512 (mttt) cc_final: 0.2300 (mttt) REVERT: q 150 MET cc_start: 0.2716 (OUTLIER) cc_final: 0.2291 (mtp) REVERT: q 231 MET cc_start: -0.1749 (mtm) cc_final: -0.2810 (mmt) REVERT: r 141 GLN cc_start: 0.3479 (mm-40) cc_final: 0.2430 (pp30) REVERT: r 343 MET cc_start: -0.0715 (mmm) cc_final: -0.1386 (tpp) REVERT: s 3 MET cc_start: 0.3497 (mpp) cc_final: 0.1055 (ttm) REVERT: s 62 GLN cc_start: 0.2005 (OUTLIER) cc_final: 0.1599 (mm-40) REVERT: s 214 MET cc_start: 0.3632 (pmm) cc_final: 0.0753 (mpp) REVERT: t 192 TYR cc_start: 0.2418 (m-10) cc_final: 0.1834 (m-10) REVERT: t 326 MET cc_start: 0.3497 (ttp) cc_final: 0.2932 (tpp) REVERT: t 366 GLN cc_start: 0.5947 (tm-30) cc_final: 0.5071 (tp40) REVERT: u 35 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5003 (tt0) REVERT: u 219 LEU cc_start: 0.0814 (OUTLIER) cc_final: 0.0486 (mt) REVERT: u 255 PHE cc_start: 0.2329 (OUTLIER) cc_final: 0.1958 (m-10) outliers start: 509 outliers final: 345 residues processed: 1394 average time/residue: 0.9849 time to fit residues: 2400.5694 Evaluate side-chains 1346 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 949 time to evaluate : 7.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 149 ASP Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 87 GLU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 48 GLN Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 16 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 112 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain Z residue 123 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 29 HIS Chi-restraints excluded: chain a residue 53 ASP Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 28 HIS Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 86 THR Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 187 ASN Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 206 LEU Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 102 SER Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 17 LYS Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 157 THR Chi-restraints excluded: chain k residue 183 THR Chi-restraints excluded: chain k residue 184 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 246 TYR Chi-restraints excluded: chain k residue 249 VAL Chi-restraints excluded: chain k residue 264 ASN Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 271 VAL Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 321 ASN Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 540 SER Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain m residue 241 THR Chi-restraints excluded: chain m residue 296 ASN Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain m residue 495 ILE Chi-restraints excluded: chain m residue 503 GLU Chi-restraints excluded: chain m residue 519 VAL Chi-restraints excluded: chain y residue 4 TYR Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 154 TRP Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 172 ARG Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 227 SER Chi-restraints excluded: chain y residue 232 THR Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 367 ARG Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 386 GLU Chi-restraints excluded: chain y residue 392 ASN Chi-restraints excluded: chain y residue 487 THR Chi-restraints excluded: chain y residue 496 ASP Chi-restraints excluded: chain y residue 507 ILE Chi-restraints excluded: chain y residue 542 ILE Chi-restraints excluded: chain v residue 324 ILE Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 368 GLU Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain v residue 433 ASN Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 446 THR Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 492 GLU Chi-restraints excluded: chain v residue 509 HIS Chi-restraints excluded: chain v residue 510 THR Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 605 VAL Chi-restraints excluded: chain v residue 622 ARG Chi-restraints excluded: chain v residue 677 ILE Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 814 ASP Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 134 TYR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 220 PHE Chi-restraints excluded: chain w residue 246 ILE Chi-restraints excluded: chain w residue 306 ASP Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 160 HIS Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 174 MET Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 228 HIS Chi-restraints excluded: chain r residue 302 SER Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 125 MET Chi-restraints excluded: chain s residue 150 TYR Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 349 MET Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 219 LEU Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 242 THR Chi-restraints excluded: chain u residue 255 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 307 ASP Chi-restraints excluded: chain u residue 328 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 659 optimal weight: 20.0000 chunk 332 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 701 optimal weight: 8.9990 chunk 751 optimal weight: 0.0060 chunk 545 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 867 optimal weight: 6.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 167 GLN N 65 ASN O 75 ASN T 31 ASN T 93 GLN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 GLN Z 97 ASN a 124 ASN b 25 ASN c 65 GLN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 208 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 225 HIS ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS ** y 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 392 ASN ** y 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 83 GLN ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 244 ASN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 313 ASN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 228 HIS r 271 GLN ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 489 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 124636 Z= 0.208 Angle : 0.701 17.237 177238 Z= 0.359 Chirality : 0.041 0.291 21341 Planarity : 0.005 0.169 15674 Dihedral : 21.237 179.398 39955 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.94 % Favored : 89.65 % Rotamer: Outliers : 4.62 % Allowed : 21.27 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.36 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.08), residues: 9717 helix: -0.14 (0.08), residues: 3840 sheet: -0.93 (0.15), residues: 1205 loop : -2.85 (0.08), residues: 4672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP g 219 HIS 0.016 0.001 HIS g 188 PHE 0.050 0.002 PHE w 53 TYR 0.023 0.002 TYR y 174 ARG 0.009 0.001 ARG k 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 1003 time to evaluate : 7.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.6344 (ttt-90) cc_final: 0.6125 (ttt-90) REVERT: l 21 ARG cc_start: 0.5596 (tmm-80) cc_final: 0.5307 (tpp80) REVERT: D 43 ASN cc_start: 0.6736 (t0) cc_final: 0.6307 (m-40) REVERT: D 157 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: D 227 LYS cc_start: 0.6447 (tptp) cc_final: 0.6068 (ttmt) REVERT: F 1 MET cc_start: 0.1591 (mmp) cc_final: 0.1381 (mmm) REVERT: F 67 ARG cc_start: 0.6128 (tmm160) cc_final: 0.5751 (tmm160) REVERT: F 70 THR cc_start: 0.6997 (p) cc_final: 0.6619 (m) REVERT: F 145 GLN cc_start: 0.7067 (pt0) cc_final: 0.6716 (pt0) REVERT: G 1 MET cc_start: 0.4250 (ttm) cc_final: 0.4013 (tpp) REVERT: G 118 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: H 15 PRO cc_start: 0.5194 (Cg_endo) cc_final: 0.4788 (Cg_exo) REVERT: H 18 LYS cc_start: 0.4324 (OUTLIER) cc_final: 0.2808 (mppt) REVERT: H 49 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7012 (tp) REVERT: J 75 ILE cc_start: 0.5095 (OUTLIER) cc_final: 0.4842 (mp) REVERT: J 153 LEU cc_start: 0.6682 (tt) cc_final: 0.6083 (tp) REVERT: J 160 LYS cc_start: 0.6027 (mtpt) cc_final: 0.5147 (mmtt) REVERT: K 123 ARG cc_start: 0.4925 (mmm-85) cc_final: 0.4578 (mmt180) REVERT: L 7 TRP cc_start: 0.4808 (m100) cc_final: 0.3739 (m100) REVERT: L 84 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7710 (mp) REVERT: L 131 ARG cc_start: 0.7639 (tpt170) cc_final: 0.7408 (tpt170) REVERT: L 175 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6173 (mtp-110) REVERT: M 25 LYS cc_start: 0.7125 (tttt) cc_final: 0.6809 (tttm) REVERT: M 40 VAL cc_start: 0.5090 (t) cc_final: 0.4847 (t) REVERT: O 129 LYS cc_start: 0.3834 (mtmt) cc_final: 0.2270 (tttt) REVERT: Q 121 ARG cc_start: 0.5721 (mtm180) cc_final: 0.5458 (mtp85) REVERT: S 50 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7713 (mmtt) REVERT: T 23 ARG cc_start: 0.7377 (mmm-85) cc_final: 0.7085 (mtt90) REVERT: V 88 MET cc_start: 0.7619 (mmm) cc_final: 0.7231 (mpp) REVERT: V 112 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6349 (mmm) REVERT: Y 23 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6556 (mtp-110) REVERT: Y 68 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6451 (mtp85) REVERT: Z 3 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.6109 (pptt) REVERT: Z 119 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7181 (mtt180) REVERT: a 107 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7713 (mtm180) REVERT: d 11 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8110 (mp) REVERT: g 113 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4347 (t80) REVERT: g 124 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7487 (p) REVERT: i 110 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6369 (ptm) REVERT: A 127 LEU cc_start: 0.1570 (OUTLIER) cc_final: 0.1306 (mm) REVERT: A 133 ARG cc_start: 0.3323 (ptm-80) cc_final: 0.1730 (ttm170) REVERT: A 150 TYR cc_start: 0.4745 (t80) cc_final: 0.3260 (p90) REVERT: A 162 ILE cc_start: 0.3994 (tt) cc_final: 0.3733 (tt) REVERT: A 255 MET cc_start: -0.0021 (tpt) cc_final: -0.2337 (tmm) REVERT: k 153 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6742 (mt0) REVERT: k 375 MET cc_start: 0.1374 (tpp) cc_final: 0.0699 (mtp) REVERT: k 499 MET cc_start: 0.5176 (mmp) cc_final: 0.2012 (ppp) REVERT: U 46 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6981 (mmt-90) REVERT: U 144 ARG cc_start: 0.4378 (OUTLIER) cc_final: 0.3460 (mpt-90) REVERT: R 70 MET cc_start: 0.2763 (mpp) cc_final: 0.1627 (tmm) REVERT: R 140 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.4988 (mtp180) REVERT: m 169 GLU cc_start: 0.4684 (tt0) cc_final: 0.4483 (tt0) REVERT: m 182 MET cc_start: 0.3483 (mmm) cc_final: 0.3015 (mtm) REVERT: m 503 GLU cc_start: -0.1162 (OUTLIER) cc_final: -0.2581 (pp20) REVERT: y 6 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6397 (tp40) REVERT: y 66 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4969 (mm) REVERT: y 83 ILE cc_start: 0.4543 (OUTLIER) cc_final: 0.4234 (mm) REVERT: y 88 ASP cc_start: 0.4736 (m-30) cc_final: 0.4474 (t0) REVERT: y 106 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4796 (mt-10) REVERT: y 172 ARG cc_start: 0.4695 (OUTLIER) cc_final: 0.3958 (tpp-160) REVERT: y 199 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7538 (t0) REVERT: y 202 ARG cc_start: 0.5654 (ttp-110) cc_final: 0.4852 (mmp-170) REVERT: y 254 GLU cc_start: 0.4899 (OUTLIER) cc_final: 0.4204 (mt-10) REVERT: y 268 LYS cc_start: 0.3447 (OUTLIER) cc_final: 0.2806 (pttt) REVERT: y 514 MET cc_start: 0.3430 (mpp) cc_final: 0.2941 (mpp) REVERT: v 347 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.3928 (ptt180) REVERT: v 355 GLN cc_start: 0.3113 (OUTLIER) cc_final: 0.2403 (tt0) REVERT: v 368 GLU cc_start: 0.0364 (OUTLIER) cc_final: -0.0742 (tp30) REVERT: v 409 MET cc_start: 0.5053 (tpt) cc_final: 0.4647 (tpp) REVERT: v 439 ARG cc_start: 0.3579 (mtp85) cc_final: 0.3357 (ppt170) REVERT: v 459 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4554 (tpt) REVERT: v 698 MET cc_start: 0.3396 (mmm) cc_final: 0.2584 (ttp) REVERT: v 799 TYR cc_start: 0.2490 (OUTLIER) cc_final: 0.1569 (m-80) REVERT: v 858 GLN cc_start: 0.4605 (pp30) cc_final: 0.2839 (mt0) REVERT: w 91 ILE cc_start: 0.3595 (OUTLIER) cc_final: 0.2930 (tp) REVERT: w 112 MET cc_start: 0.2335 (mtm) cc_final: -0.0309 (ttp) REVERT: q 121 LEU cc_start: 0.4495 (mm) cc_final: 0.3966 (mt) REVERT: q 150 MET cc_start: 0.2655 (OUTLIER) cc_final: 0.2321 (mtp) REVERT: q 228 MET cc_start: 0.0678 (mtm) cc_final: 0.0036 (ptp) REVERT: r 117 VAL cc_start: 0.3987 (t) cc_final: 0.3690 (p) REVERT: r 141 GLN cc_start: 0.3091 (mm-40) cc_final: 0.2233 (pp30) REVERT: r 343 MET cc_start: -0.0878 (mmm) cc_final: -0.1266 (tpp) REVERT: s 3 MET cc_start: 0.3451 (mpp) cc_final: 0.0972 (ttm) REVERT: s 214 MET cc_start: 0.3395 (pmm) cc_final: 0.0543 (mpp) REVERT: t 192 TYR cc_start: 0.2337 (m-10) cc_final: 0.1747 (m-10) REVERT: t 291 ILE cc_start: 0.0916 (tp) cc_final: -0.0051 (tp) REVERT: t 326 MET cc_start: 0.3445 (ttp) cc_final: 0.2822 (tpp) REVERT: t 366 GLN cc_start: 0.5933 (tm-30) cc_final: 0.5035 (tp40) REVERT: t 467 TYR cc_start: 0.0938 (OUTLIER) cc_final: 0.0314 (t80) REVERT: u 35 GLU cc_start: 0.5905 (mm-30) cc_final: 0.4919 (tt0) REVERT: u 212 LEU cc_start: 0.4398 (mt) cc_final: 0.3565 (pp) REVERT: u 255 PHE cc_start: 0.2240 (OUTLIER) cc_final: 0.1675 (m-10) outliers start: 398 outliers final: 262 residues processed: 1305 average time/residue: 0.9991 time to fit residues: 2271.1396 Evaluate side-chains 1245 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 942 time to evaluate : 7.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 57 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 97 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 103 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 184 VAL Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 249 VAL Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 271 VAL Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 445 VAL Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 540 SER Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain m residue 388 VAL Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain m residue 468 THR Chi-restraints excluded: chain m residue 495 ILE Chi-restraints excluded: chain m residue 503 GLU Chi-restraints excluded: chain m residue 508 ILE Chi-restraints excluded: chain m residue 519 VAL Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 172 ARG Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 227 SER Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 268 LYS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 392 ASN Chi-restraints excluded: chain y residue 507 ILE Chi-restraints excluded: chain y residue 542 ILE Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 368 GLU Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 459 MET Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 492 GLU Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 605 VAL Chi-restraints excluded: chain v residue 677 ILE Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 814 ASP Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 134 TYR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 246 ILE Chi-restraints excluded: chain w residue 301 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 160 HIS Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 174 MET Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain s residue 150 TYR Chi-restraints excluded: chain s residue 201 ILE Chi-restraints excluded: chain t residue 467 TYR Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 238 HIS Chi-restraints excluded: chain u residue 255 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1003 optimal weight: 5.9990 chunk 1057 optimal weight: 9.9990 chunk 964 optimal weight: 9.9990 chunk 1028 optimal weight: 30.0000 chunk 1056 optimal weight: 9.9990 chunk 618 optimal weight: 20.0000 chunk 448 optimal weight: 0.7980 chunk 807 optimal weight: 8.9990 chunk 315 optimal weight: 10.0000 chunk 929 optimal weight: 0.6980 chunk 972 optimal weight: 5.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN E 98 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 GLN N 65 ASN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 ASN b 25 ASN c 65 GLN g 187 ASN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 127 GLN k 468 GLN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS ** y 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 445 GLN v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 39 GLN ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 349 GLN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 166 ASN q 260 ASN q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 289 GLN ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.7748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 124636 Z= 0.245 Angle : 0.730 14.677 177238 Z= 0.372 Chirality : 0.042 0.394 21341 Planarity : 0.006 0.160 15674 Dihedral : 21.253 178.980 39955 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.10 % Favored : 88.46 % Rotamer: Outliers : 4.62 % Allowed : 21.15 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 1.36 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.08), residues: 9717 helix: -0.13 (0.08), residues: 3835 sheet: -0.98 (0.15), residues: 1226 loop : -2.85 (0.08), residues: 4656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP g 219 HIS 0.012 0.001 HIS g 188 PHE 0.040 0.002 PHE w 53 TYR 0.027 0.002 TYR v 791 ARG 0.007 0.001 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 978 time to evaluate : 7.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.6393 (ttt-90) cc_final: 0.6164 (ttt-90) REVERT: l 21 ARG cc_start: 0.5630 (tmm-80) cc_final: 0.5307 (tpp80) REVERT: D 43 ASN cc_start: 0.6737 (t0) cc_final: 0.6326 (m-40) REVERT: D 92 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6521 (pt0) REVERT: D 157 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: D 227 LYS cc_start: 0.6604 (tptp) cc_final: 0.6104 (ttpt) REVERT: F 70 THR cc_start: 0.6975 (p) cc_final: 0.6544 (m) REVERT: F 145 GLN cc_start: 0.7117 (pt0) cc_final: 0.6770 (pt0) REVERT: G 1 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3430 (ttt) REVERT: G 118 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5907 (tt0) REVERT: H 15 PRO cc_start: 0.5539 (Cg_endo) cc_final: 0.5078 (Cg_exo) REVERT: H 18 LYS cc_start: 0.4328 (OUTLIER) cc_final: 0.2798 (mppt) REVERT: H 49 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7032 (tp) REVERT: J 75 ILE cc_start: 0.5176 (OUTLIER) cc_final: 0.4925 (mp) REVERT: J 160 LYS cc_start: 0.6050 (mtpt) cc_final: 0.5410 (mmtt) REVERT: K 123 ARG cc_start: 0.4864 (mmm-85) cc_final: 0.4560 (mmt180) REVERT: K 196 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5229 (mt-10) REVERT: L 7 TRP cc_start: 0.4882 (m100) cc_final: 0.3932 (m100) REVERT: L 84 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (mp) REVERT: L 175 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.6106 (mtp-110) REVERT: M 3 MET cc_start: 0.6184 (ptp) cc_final: 0.5502 (mtp) REVERT: M 40 VAL cc_start: 0.5268 (t) cc_final: 0.4982 (t) REVERT: M 49 MET cc_start: 0.7381 (mmt) cc_final: 0.7145 (mmt) REVERT: N 35 ARG cc_start: 0.7844 (tpt170) cc_final: 0.7388 (mmm-85) REVERT: O 129 LYS cc_start: 0.4049 (mtmt) cc_final: 0.2484 (ptmt) REVERT: Q 121 ARG cc_start: 0.5962 (mtm180) cc_final: 0.5521 (mtp85) REVERT: S 50 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7690 (mmtt) REVERT: T 23 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6988 (mtt90) REVERT: T 126 MET cc_start: 0.4103 (OUTLIER) cc_final: 0.3656 (tpp) REVERT: V 88 MET cc_start: 0.7657 (mmm) cc_final: 0.7209 (mpp) REVERT: V 112 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6461 (mmm) REVERT: Y 23 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6462 (mtp85) REVERT: Y 68 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6529 (mtp85) REVERT: Z 3 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.6146 (pptt) REVERT: Z 119 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: a 107 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7550 (ttm110) REVERT: b 44 ILE cc_start: 0.7447 (mm) cc_final: 0.7056 (mt) REVERT: d 11 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8213 (mp) REVERT: g 113 PHE cc_start: 0.5040 (OUTLIER) cc_final: 0.4459 (t80) REVERT: g 124 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7494 (p) REVERT: i 110 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6406 (ptm) REVERT: A 127 LEU cc_start: 0.1609 (OUTLIER) cc_final: 0.1334 (mm) REVERT: A 150 TYR cc_start: 0.4793 (t80) cc_final: 0.3248 (p90) REVERT: A 255 MET cc_start: 0.0648 (tpt) cc_final: -0.1698 (tmm) REVERT: j 57 ARG cc_start: 0.6035 (mtt-85) cc_final: 0.5469 (ptp-110) REVERT: k 153 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: k 375 MET cc_start: 0.1455 (tpp) cc_final: 0.0653 (mtp) REVERT: k 499 MET cc_start: 0.5208 (mmp) cc_final: 0.1999 (ppp) REVERT: U 46 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6974 (mmt-90) REVERT: U 144 ARG cc_start: 0.4406 (OUTLIER) cc_final: 0.3924 (mpt-90) REVERT: R 127 LYS cc_start: 0.7231 (mtmm) cc_final: 0.6974 (tptp) REVERT: R 140 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5087 (mtp180) REVERT: m 182 MET cc_start: 0.3447 (mmm) cc_final: 0.2832 (mtm) REVERT: m 348 MET cc_start: 0.2809 (OUTLIER) cc_final: -0.0476 (mmm) REVERT: m 503 GLU cc_start: -0.1167 (OUTLIER) cc_final: -0.2569 (pp20) REVERT: y 6 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6378 (tp40) REVERT: y 66 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.5044 (mm) REVERT: y 80 GLN cc_start: 0.6194 (mm-40) cc_final: 0.4907 (pt0) REVERT: y 83 ILE cc_start: 0.4486 (OUTLIER) cc_final: 0.4138 (mm) REVERT: y 88 ASP cc_start: 0.4860 (m-30) cc_final: 0.4606 (t0) REVERT: y 106 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4807 (mt-10) REVERT: y 172 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.3855 (tpp-160) REVERT: y 199 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7447 (t0) REVERT: y 202 ARG cc_start: 0.5614 (ttp-110) cc_final: 0.4814 (mmp80) REVERT: y 243 MET cc_start: 0.5974 (ttp) cc_final: 0.5715 (ttt) REVERT: y 254 GLU cc_start: 0.4826 (OUTLIER) cc_final: 0.4080 (mt-10) REVERT: y 367 ARG cc_start: 0.4957 (OUTLIER) cc_final: 0.4225 (mtt90) REVERT: y 526 MET cc_start: 0.0641 (mmm) cc_final: 0.0253 (mmm) REVERT: v 347 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.3873 (ptt180) REVERT: v 355 GLN cc_start: 0.3106 (OUTLIER) cc_final: 0.2641 (tt0) REVERT: v 368 GLU cc_start: 0.0400 (OUTLIER) cc_final: -0.0706 (tp30) REVERT: v 409 MET cc_start: 0.4909 (tpt) cc_final: 0.4445 (tpp) REVERT: v 439 ARG cc_start: 0.3534 (mtp85) cc_final: 0.3289 (ppt170) REVERT: v 459 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4591 (tpt) REVERT: v 467 GLN cc_start: 0.6841 (tt0) cc_final: 0.5874 (tp-100) REVERT: v 492 GLU cc_start: 0.3313 (OUTLIER) cc_final: 0.1366 (mp0) REVERT: v 497 GLU cc_start: 0.5162 (pt0) cc_final: 0.4844 (pt0) REVERT: v 698 MET cc_start: 0.3541 (mmm) cc_final: 0.2576 (ttp) REVERT: v 744 MET cc_start: 0.3192 (mmm) cc_final: 0.2727 (tpp) REVERT: v 799 TYR cc_start: 0.2553 (OUTLIER) cc_final: 0.1534 (m-80) REVERT: w 91 ILE cc_start: 0.3677 (OUTLIER) cc_final: 0.3086 (tp) REVERT: w 94 MET cc_start: 0.2853 (tmm) cc_final: 0.2279 (ptt) REVERT: w 112 MET cc_start: 0.2215 (mtm) cc_final: -0.0260 (ttp) REVERT: q 121 LEU cc_start: 0.4463 (mm) cc_final: 0.3977 (mt) REVERT: q 150 MET cc_start: 0.2601 (OUTLIER) cc_final: 0.2267 (mtp) REVERT: q 228 MET cc_start: 0.1010 (mtm) cc_final: 0.0118 (ptp) REVERT: q 231 MET cc_start: -0.1536 (mtm) cc_final: -0.2945 (mmt) REVERT: r 141 GLN cc_start: 0.2956 (mm-40) cc_final: 0.2081 (pp30) REVERT: r 343 MET cc_start: -0.0836 (mmm) cc_final: -0.1315 (tpp) REVERT: s 62 GLN cc_start: 0.1954 (OUTLIER) cc_final: 0.1572 (mm-40) REVERT: s 214 MET cc_start: 0.3141 (pmm) cc_final: 0.0858 (mpp) REVERT: t 192 TYR cc_start: 0.2385 (m-10) cc_final: 0.1770 (m-10) REVERT: t 291 ILE cc_start: 0.0987 (tp) cc_final: 0.0209 (tp) REVERT: t 326 MET cc_start: 0.3339 (ttp) cc_final: 0.2811 (tpp) REVERT: t 366 GLN cc_start: 0.5952 (tm-30) cc_final: 0.5086 (tp40) REVERT: t 401 MET cc_start: 0.0774 (tpt) cc_final: 0.0049 (tmm) REVERT: t 467 TYR cc_start: 0.0977 (OUTLIER) cc_final: 0.0528 (t80) REVERT: u 35 GLU cc_start: 0.5953 (mm-30) cc_final: 0.4978 (tt0) REVERT: u 255 PHE cc_start: 0.2424 (OUTLIER) cc_final: 0.1935 (m-10) outliers start: 398 outliers final: 303 residues processed: 1284 average time/residue: 0.9935 time to fit residues: 2222.1690 Evaluate side-chains 1290 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 939 time to evaluate : 7.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 57 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 97 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 84 TYR Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 72 ILE Chi-restraints excluded: chain k residue 77 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 184 VAL Chi-restraints excluded: chain k residue 209 LEU Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 249 VAL Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 271 VAL Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 319 THR Chi-restraints excluded: chain k residue 321 ASN Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 407 LEU Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 116 LYS Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 34 MET Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain m residue 241 THR Chi-restraints excluded: chain m residue 296 ASN Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 348 MET Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain m residue 468 THR Chi-restraints excluded: chain m residue 495 ILE Chi-restraints excluded: chain m residue 503 GLU Chi-restraints excluded: chain m residue 508 ILE Chi-restraints excluded: chain m residue 519 VAL Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 172 ARG Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 257 HIS Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 367 ARG Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 507 ILE Chi-restraints excluded: chain y residue 542 ILE Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 368 GLU Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 459 MET Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 492 GLU Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 605 VAL Chi-restraints excluded: chain v residue 677 ILE Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 798 VAL Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 134 TYR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 246 ILE Chi-restraints excluded: chain w residue 301 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 160 HIS Chi-restraints excluded: chain q residue 166 ASN Chi-restraints excluded: chain q residue 304 VAL Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 174 MET Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 302 SER Chi-restraints excluded: chain r residue 314 MET Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 150 TYR Chi-restraints excluded: chain s residue 201 ILE Chi-restraints excluded: chain t residue 349 MET Chi-restraints excluded: chain t residue 467 TYR Chi-restraints excluded: chain t residue 488 ILE Chi-restraints excluded: chain t residue 544 ILE Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 242 THR Chi-restraints excluded: chain u residue 255 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 307 ASP Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1024 optimal weight: 9.9990 chunk 675 optimal weight: 9.9990 chunk 1087 optimal weight: 9.9990 chunk 663 optimal weight: 9.9990 chunk 515 optimal weight: 10.0000 chunk 755 optimal weight: 5.9990 chunk 1140 optimal weight: 7.9990 chunk 1049 optimal weight: 7.9990 chunk 908 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 701 optimal weight: 0.0170 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN E 98 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 GLN N 65 ASN S 11 GLN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN c 65 GLN ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 HIS ** k 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS y 466 GLN v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 159 GLN r 237 ASN ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 216 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 124636 Z= 0.303 Angle : 0.804 29.188 177238 Z= 0.407 Chirality : 0.045 0.407 21341 Planarity : 0.006 0.207 15674 Dihedral : 21.375 178.439 39955 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.46 % Favored : 88.09 % Rotamer: Outliers : 4.59 % Allowed : 21.21 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.36 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.08), residues: 9717 helix: -0.31 (0.08), residues: 3817 sheet: -1.08 (0.15), residues: 1211 loop : -2.92 (0.08), residues: 4689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP g 219 HIS 0.021 0.002 HIS y 257 PHE 0.040 0.002 PHE w 53 TYR 0.030 0.002 TYR v 791 ARG 0.010 0.001 ARG k 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19434 Ramachandran restraints generated. 9717 Oldfield, 0 Emsley, 9717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 991 time to evaluate : 7.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 15 ARG cc_start: 0.6442 (ttt-90) cc_final: 0.6221 (ttt-90) REVERT: l 21 ARG cc_start: 0.5737 (tmm-80) cc_final: 0.5421 (tpp80) REVERT: D 43 ASN cc_start: 0.6788 (t0) cc_final: 0.6347 (m-40) REVERT: D 92 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6557 (pt0) REVERT: D 157 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: D 227 LYS cc_start: 0.6615 (tptp) cc_final: 0.6303 (ttmt) REVERT: E 157 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6398 (t0) REVERT: F 70 THR cc_start: 0.7118 (p) cc_final: 0.6590 (m) REVERT: F 145 GLN cc_start: 0.7293 (pt0) cc_final: 0.6967 (pt0) REVERT: G 1 MET cc_start: 0.4451 (OUTLIER) cc_final: 0.3366 (ttt) REVERT: G 118 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: H 15 PRO cc_start: 0.5891 (Cg_endo) cc_final: 0.5443 (Cg_exo) REVERT: H 18 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.2966 (mppt) REVERT: H 49 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6913 (tp) REVERT: I 84 TYR cc_start: 0.7982 (t80) cc_final: 0.7727 (t80) REVERT: J 75 ILE cc_start: 0.5391 (OUTLIER) cc_final: 0.5138 (mp) REVERT: J 160 LYS cc_start: 0.6315 (mtpt) cc_final: 0.5667 (mmtt) REVERT: K 167 GLN cc_start: 0.7805 (tt0) cc_final: 0.7301 (tt0) REVERT: K 196 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5326 (mt-10) REVERT: L 7 TRP cc_start: 0.4962 (m100) cc_final: 0.3987 (m100) REVERT: L 175 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6337 (mtp-110) REVERT: M 3 MET cc_start: 0.6153 (ptp) cc_final: 0.5476 (mtp) REVERT: M 40 VAL cc_start: 0.5584 (t) cc_final: 0.5249 (t) REVERT: M 49 MET cc_start: 0.7245 (mmt) cc_final: 0.6990 (mmt) REVERT: O 129 LYS cc_start: 0.4174 (mtmt) cc_final: 0.2217 (ptmt) REVERT: T 23 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.7019 (mtt90) REVERT: T 126 MET cc_start: 0.4281 (OUTLIER) cc_final: 0.3856 (tpp) REVERT: V 88 MET cc_start: 0.7679 (mmm) cc_final: 0.7230 (mpp) REVERT: V 112 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6392 (mmm) REVERT: Y 23 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6581 (mtp85) REVERT: Y 68 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6627 (mtp85) REVERT: Z 3 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.6224 (pptt) REVERT: Z 119 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7241 (mtt180) REVERT: a 107 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7542 (ttm110) REVERT: b 44 ILE cc_start: 0.7360 (mm) cc_final: 0.6996 (mt) REVERT: g 5 MET cc_start: 0.4937 (OUTLIER) cc_final: 0.4697 (mmm) REVERT: g 113 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.4604 (t80) REVERT: g 124 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7465 (p) REVERT: g 146 SER cc_start: 0.6140 (m) cc_final: 0.5860 (p) REVERT: i 110 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6456 (ptm) REVERT: A 127 LEU cc_start: 0.1500 (OUTLIER) cc_final: 0.1164 (mm) REVERT: A 150 TYR cc_start: 0.4887 (t80) cc_final: 0.3154 (p90) REVERT: A 164 ASP cc_start: 0.1548 (OUTLIER) cc_final: -0.0456 (p0) REVERT: A 255 MET cc_start: 0.0337 (tpt) cc_final: -0.1731 (tmm) REVERT: B 183 THR cc_start: 0.2336 (p) cc_final: 0.2050 (m) REVERT: j 57 ARG cc_start: 0.6041 (mtt-85) cc_final: 0.5536 (ptp-110) REVERT: k 153 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: k 375 MET cc_start: 0.1486 (tpp) cc_final: 0.0629 (mtp) REVERT: U 144 ARG cc_start: 0.4384 (OUTLIER) cc_final: 0.3937 (mtt90) REVERT: R 127 LYS cc_start: 0.7362 (mtmm) cc_final: 0.7103 (tptp) REVERT: R 140 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5330 (mtp180) REVERT: m 182 MET cc_start: 0.3100 (mmm) cc_final: 0.2567 (mtm) REVERT: m 503 GLU cc_start: -0.0643 (OUTLIER) cc_final: -0.2467 (pp20) REVERT: y 6 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6469 (tp40) REVERT: y 66 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5104 (mm) REVERT: y 83 ILE cc_start: 0.4275 (OUTLIER) cc_final: 0.3831 (mm) REVERT: y 106 GLU cc_start: 0.4957 (OUTLIER) cc_final: 0.4754 (mt-10) REVERT: y 172 ARG cc_start: 0.4625 (OUTLIER) cc_final: 0.3811 (tpp-160) REVERT: y 191 LYS cc_start: 0.6068 (tptp) cc_final: 0.3790 (pttp) REVERT: y 199 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7298 (t0) REVERT: y 202 ARG cc_start: 0.5842 (ttp-110) cc_final: 0.5126 (mmp-170) REVERT: y 254 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.4107 (mt-10) REVERT: y 367 ARG cc_start: 0.4799 (OUTLIER) cc_final: 0.4222 (mtt90) REVERT: y 461 PHE cc_start: 0.1210 (OUTLIER) cc_final: -0.0589 (m-80) REVERT: v 347 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.3923 (ptt180) REVERT: v 355 GLN cc_start: 0.3356 (OUTLIER) cc_final: 0.2526 (tt0) REVERT: v 409 MET cc_start: 0.5304 (tpt) cc_final: 0.4728 (tpp) REVERT: v 459 MET cc_start: 0.4855 (OUTLIER) cc_final: 0.4452 (tpt) REVERT: v 467 GLN cc_start: 0.6873 (tt0) cc_final: 0.5932 (tp-100) REVERT: v 492 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.1772 (mp0) REVERT: v 698 MET cc_start: 0.3690 (mmm) cc_final: 0.3367 (ttp) REVERT: v 799 TYR cc_start: 0.2415 (OUTLIER) cc_final: 0.1504 (m-80) REVERT: w 91 ILE cc_start: 0.4102 (OUTLIER) cc_final: 0.3644 (tp) REVERT: w 94 MET cc_start: 0.2860 (tmm) cc_final: 0.2463 (ptt) REVERT: w 112 MET cc_start: 0.2287 (mtm) cc_final: -0.0101 (ttp) REVERT: q 121 LEU cc_start: 0.4235 (mm) cc_final: 0.3855 (mt) REVERT: q 150 MET cc_start: 0.2719 (OUTLIER) cc_final: 0.2479 (mtp) REVERT: r 141 GLN cc_start: 0.2993 (mm-40) cc_final: 0.2043 (pp30) REVERT: r 314 MET cc_start: 0.0436 (OUTLIER) cc_final: -0.1195 (ppp) REVERT: r 343 MET cc_start: -0.0609 (mmm) cc_final: -0.1273 (tpp) REVERT: s 3 MET cc_start: 0.4007 (mpp) cc_final: 0.2397 (mmm) REVERT: s 62 GLN cc_start: 0.1975 (OUTLIER) cc_final: 0.1619 (mm-40) REVERT: s 214 MET cc_start: 0.3502 (pmm) cc_final: 0.1370 (mpp) REVERT: t 289 GLN cc_start: 0.3719 (tt0) cc_final: 0.2901 (tp40) REVERT: t 291 ILE cc_start: 0.0920 (tp) cc_final: 0.0307 (tp) REVERT: t 326 MET cc_start: 0.3490 (ttp) cc_final: 0.2867 (tpp) REVERT: t 366 GLN cc_start: 0.5888 (tm-30) cc_final: 0.4971 (tp40) REVERT: u 35 GLU cc_start: 0.6033 (mm-30) cc_final: 0.4964 (tt0) REVERT: u 248 LYS cc_start: 0.1545 (mttt) cc_final: 0.1246 (pttt) REVERT: u 255 PHE cc_start: 0.2406 (OUTLIER) cc_final: 0.1160 (m-80) outliers start: 395 outliers final: 307 residues processed: 1286 average time/residue: 1.0160 time to fit residues: 2288.7381 Evaluate side-chains 1301 residues out of total 8613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 948 time to evaluate : 7.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 166 TYR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 ASP Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 118 ASN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 199 THR Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 91 LYS Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain L residue 175 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 16 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 60 CYS Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 106 HIS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 128 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 57 ASP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 110 VAL Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 105 ASN Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 87 GLU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 50 LYS Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 113 ILE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain T residue 41 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 126 MET Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 112 MET Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 68 ARG Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 3 LYS Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain a residue 14 THR Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 72 PHE Chi-restraints excluded: chain a residue 107 ARG Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 77 CYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 9 HIS Chi-restraints excluded: chain c residue 43 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 10 HIS Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain g residue 19 THR Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 66 VAL Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 TRP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 98 THR Chi-restraints excluded: chain g residue 105 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 121 VAL Chi-restraints excluded: chain g residue 124 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 207 CYS Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 79 ILE Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain i residue 117 VAL Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain j residue 27 VAL Chi-restraints excluded: chain j residue 103 LEU Chi-restraints excluded: chain k residue 5 LEU Chi-restraints excluded: chain k residue 25 CYS Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 77 SER Chi-restraints excluded: chain k residue 79 LEU Chi-restraints excluded: chain k residue 105 VAL Chi-restraints excluded: chain k residue 118 THR Chi-restraints excluded: chain k residue 139 ASP Chi-restraints excluded: chain k residue 147 PHE Chi-restraints excluded: chain k residue 153 GLN Chi-restraints excluded: chain k residue 184 VAL Chi-restraints excluded: chain k residue 236 ASP Chi-restraints excluded: chain k residue 249 VAL Chi-restraints excluded: chain k residue 268 TYR Chi-restraints excluded: chain k residue 270 ILE Chi-restraints excluded: chain k residue 271 VAL Chi-restraints excluded: chain k residue 305 VAL Chi-restraints excluded: chain k residue 310 ASN Chi-restraints excluded: chain k residue 316 TYR Chi-restraints excluded: chain k residue 317 VAL Chi-restraints excluded: chain k residue 321 ASN Chi-restraints excluded: chain k residue 324 PHE Chi-restraints excluded: chain k residue 404 VAL Chi-restraints excluded: chain k residue 407 LEU Chi-restraints excluded: chain k residue 437 THR Chi-restraints excluded: chain k residue 474 LEU Chi-restraints excluded: chain k residue 582 SER Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 46 ARG Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 53 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 136 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 38 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 140 ARG Chi-restraints excluded: chain m residue 241 THR Chi-restraints excluded: chain m residue 314 MET Chi-restraints excluded: chain m residue 452 VAL Chi-restraints excluded: chain m residue 464 VAL Chi-restraints excluded: chain m residue 468 THR Chi-restraints excluded: chain m residue 495 ILE Chi-restraints excluded: chain m residue 503 GLU Chi-restraints excluded: chain m residue 508 ILE Chi-restraints excluded: chain m residue 519 VAL Chi-restraints excluded: chain y residue 6 GLN Chi-restraints excluded: chain y residue 29 ASP Chi-restraints excluded: chain y residue 66 LEU Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 83 ILE Chi-restraints excluded: chain y residue 96 LEU Chi-restraints excluded: chain y residue 98 GLU Chi-restraints excluded: chain y residue 106 GLU Chi-restraints excluded: chain y residue 108 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 137 THR Chi-restraints excluded: chain y residue 150 VAL Chi-restraints excluded: chain y residue 161 LEU Chi-restraints excluded: chain y residue 172 ARG Chi-restraints excluded: chain y residue 199 ASP Chi-restraints excluded: chain y residue 208 ILE Chi-restraints excluded: chain y residue 254 GLU Chi-restraints excluded: chain y residue 299 LEU Chi-restraints excluded: chain y residue 323 LEU Chi-restraints excluded: chain y residue 336 THR Chi-restraints excluded: chain y residue 367 ARG Chi-restraints excluded: chain y residue 371 ILE Chi-restraints excluded: chain y residue 392 ASN Chi-restraints excluded: chain y residue 461 PHE Chi-restraints excluded: chain y residue 507 ILE Chi-restraints excluded: chain y residue 542 ILE Chi-restraints excluded: chain v residue 345 THR Chi-restraints excluded: chain v residue 347 ARG Chi-restraints excluded: chain v residue 355 GLN Chi-restraints excluded: chain v residue 357 LEU Chi-restraints excluded: chain v residue 434 VAL Chi-restraints excluded: chain v residue 445 LEU Chi-restraints excluded: chain v residue 459 MET Chi-restraints excluded: chain v residue 463 ASP Chi-restraints excluded: chain v residue 483 ILE Chi-restraints excluded: chain v residue 492 GLU Chi-restraints excluded: chain v residue 589 MET Chi-restraints excluded: chain v residue 605 VAL Chi-restraints excluded: chain v residue 677 ILE Chi-restraints excluded: chain v residue 718 LEU Chi-restraints excluded: chain v residue 767 ASP Chi-restraints excluded: chain v residue 797 SER Chi-restraints excluded: chain v residue 798 VAL Chi-restraints excluded: chain v residue 799 TYR Chi-restraints excluded: chain v residue 813 LEU Chi-restraints excluded: chain v residue 839 THR Chi-restraints excluded: chain v residue 841 THR Chi-restraints excluded: chain v residue 844 MET Chi-restraints excluded: chain w residue 91 ILE Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 134 TYR Chi-restraints excluded: chain w residue 199 ASN Chi-restraints excluded: chain w residue 246 ILE Chi-restraints excluded: chain w residue 301 VAL Chi-restraints excluded: chain w residue 325 LEU Chi-restraints excluded: chain q residue 131 VAL Chi-restraints excluded: chain q residue 150 MET Chi-restraints excluded: chain q residue 156 MET Chi-restraints excluded: chain q residue 160 HIS Chi-restraints excluded: chain q residue 304 VAL Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 139 SER Chi-restraints excluded: chain r residue 174 MET Chi-restraints excluded: chain r residue 204 VAL Chi-restraints excluded: chain r residue 302 SER Chi-restraints excluded: chain r residue 314 MET Chi-restraints excluded: chain s residue 62 GLN Chi-restraints excluded: chain s residue 150 TYR Chi-restraints excluded: chain s residue 201 ILE Chi-restraints excluded: chain t residue 349 MET Chi-restraints excluded: chain u residue 45 ILE Chi-restraints excluded: chain u residue 91 VAL Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 158 THR Chi-restraints excluded: chain u residue 220 PHE Chi-restraints excluded: chain u residue 242 THR Chi-restraints excluded: chain u residue 255 PHE Chi-restraints excluded: chain u residue 303 ILE Chi-restraints excluded: chain u residue 307 ASP Chi-restraints excluded: chain u residue 328 THR Chi-restraints excluded: chain u residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 9.9990 chunk 721 optimal weight: 8.9990 chunk 967 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 837 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 909 optimal weight: 4.9990 chunk 380 optimal weight: 6.9990 chunk 934 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN F 74 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 ASN P 62 GLN T 31 ASN ** W 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN c 65 GLN g 15 ASN ** g 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 78 ASN ** k 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 257 HIS y 430 GLN v 509 HIS ** v 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 396 ASN ** q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 166 ASN q 345 GLN ** r 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 79 HIS ** s 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 366 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.204470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197371 restraints weight = 202592.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.194816 restraints weight = 397193.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.191990 restraints weight = 304762.128| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 124636 Z= 0.269 Angle : 0.758 24.617 177238 Z= 0.385 Chirality : 0.043 0.357 21341 Planarity : 0.006 0.192 15674 Dihedral : 21.338 178.990 39955 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.09 % Favored : 88.51 % Rotamer: Outliers : 4.53 % Allowed : 21.53 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.49 % Twisted Proline : 1.63 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.08), residues: 9717 helix: -0.27 (0.08), residues: 3825 sheet: -1.08 (0.15), residues: 1206 loop : -2.93 (0.08), residues: 4686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP g 219 HIS 0.013 0.001 HIS k 85 PHE 0.038 0.002 PHE H 20 TYR 0.028 0.002 TYR v 791 ARG 0.008 0.001 ARG J 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33574.18 seconds wall clock time: 585 minutes 2.74 seconds (35102.74 seconds total)