Starting phenix.real_space_refine on Tue Apr 9 12:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h4p_9569/04_2024/5h4p_9569_neut.pdb" } resolution = 3.07 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= 0.021 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: 5 Type Number sf(0) Gaussians P 3370 5.49 5 S 100 5.16 5 C 64362 2.51 5 N 22646 2.21 5 O 32451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "Q ARG 178": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "Z PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "f TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 18": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 303": "NH1" <-> "NH2" Residue "w PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 330": "NH1" <-> "NH2" Residue "w ARG 333": "NH1" <-> "NH2" Residue "w ARG 356": "NH1" <-> "NH2" Residue "w TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 419": "NH1" <-> "NH2" Residue "z ARG 427": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 122929 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 66124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3091, 66124 Classifications: {'RNA': 3091} Modifications used: {'rna2p_pur': 323, 'rna2p_pyr': 213, 'rna3p_pur': 1393, 'rna3p_pyr': 1162} Link IDs: {'rna2p': 536, 'rna3p': 2554} Chain breaks: 4 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "4" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "A" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "B" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2375 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "G" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "M" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "N" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "P" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1442 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain: "Q" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "R" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "S" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1445 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "T" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "U" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "X" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "b" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "j" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 84} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "o" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 765 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "w" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1894 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 238} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "y" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1699 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 218} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "z" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 469 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Time building chain proxies: 46.40, per 1000 atoms: 0.38 Number of scatterers: 122929 At special positions: 0 Unit cell: (205.2, 234.36, 264.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 3370 15.00 O 32451 8.00 N 22646 7.00 C 64362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 48.52 Conformation dependent library (CDL) restraints added in 7.1 seconds 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11984 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 72 sheets defined 34.9% alpha, 15.8% beta 718 base pairs and 1762 stacking pairs defined. Time for finding SS restraints: 37.45 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.732A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.659A pdb=" N TYR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.667A pdb=" N MET A 204 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.830A pdb=" N TYR B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.635A pdb=" N GLU B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.810A pdb=" N LYS B 168 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 169' Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.681A pdb=" N VAL B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 114 through 123 removed outlier: 3.531A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 131 through 137 removed outlier: 3.866A pdb=" N VAL C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.547A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.513A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.673A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.455A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.567A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.516A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.509A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 21 through 26 Processing helix chain 'D' and resid 29 through 38 removed outlier: 4.554A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.777A pdb=" N TYR D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 removed outlier: 3.877A pdb=" N GLN D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.667A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.638A pdb=" N TYR D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.892A pdb=" N TYR D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.658A pdb=" N PHE D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 235 through 248 removed outlier: 3.549A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 4.417A pdb=" N ALA D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 291 removed outlier: 4.058A pdb=" N ARG D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.812A pdb=" N ASP E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 29 through 71 removed outlier: 3.560A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.701A pdb=" N GLN F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.804A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.512A pdb=" N VAL F 148 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.970A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.586A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 235 through 243 removed outlier: 3.692A pdb=" N LEU F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 69 removed outlier: 3.724A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 removed outlier: 3.724A pdb=" N LEU G 93 " --> pdb=" O GLU G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.705A pdb=" N THR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 removed outlier: 3.725A pdb=" N VAL G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.680A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.459A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA G 212 " --> pdb=" O GLU G 208 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 239 through 255 removed outlier: 3.646A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 83 removed outlier: 3.552A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.728A pdb=" N LEU H 161 " --> pdb=" O ASN H 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 42 removed outlier: 3.688A pdb=" N ALA J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS J 35 " --> pdb=" O THR J 31 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 86 removed outlier: 3.800A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.512A pdb=" N LEU J 112 " --> pdb=" O HIS J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 140 removed outlier: 3.528A pdb=" N VAL J 138 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Processing helix chain 'L' and resid 29 through 46 removed outlier: 4.005A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.508A pdb=" N ARG L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 94 No H-bonds generated for 'chain 'L' and resid 92 through 94' Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.564A pdb=" N ALA L 111 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU L 118 " --> pdb=" O GLN L 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 179 removed outlier: 3.640A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 192 removed outlier: 3.657A pdb=" N GLU L 184 " --> pdb=" O ARG L 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS L 185 " --> pdb=" O GLY L 181 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 52 removed outlier: 3.730A pdb=" N GLY M 52 " --> pdb=" O PRO M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.618A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.562A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 109 removed outlier: 3.823A pdb=" N LYS M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE M 103 " --> pdb=" O TRP M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.784A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 removed outlier: 3.710A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 33 removed outlier: 3.866A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 removed outlier: 3.739A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.516A pdb=" N ARG N 109 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 removed outlier: 3.636A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.505A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 167 through 172 removed outlier: 3.626A pdb=" N SER N 171 " --> pdb=" O THR N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.753A pdb=" N ASN N 181 " --> pdb=" O HIS N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.527A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.573A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.509A pdb=" N GLY O 69 " --> pdb=" O LYS O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.554A pdb=" N GLY O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 109 through 113 removed outlier: 3.735A pdb=" N TYR O 112 " --> pdb=" O PRO O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 removed outlier: 3.624A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER O 144 " --> pdb=" O LYS O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 185 removed outlier: 3.715A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS O 176 " --> pdb=" O ARG O 172 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 197 removed outlier: 3.872A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 31 removed outlier: 3.752A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.687A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.585A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.753A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS P 105 " --> pdb=" O ASN P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 182 Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.587A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 52 removed outlier: 3.963A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 73 Processing helix chain 'Q' and resid 75 through 79 removed outlier: 4.382A pdb=" N ASN Q 78 " --> pdb=" O GLY Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 117 removed outlier: 3.553A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.570A pdb=" N LEU Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.519A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 71 Processing helix chain 'R' and resid 77 through 81 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.660A pdb=" N VAL R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 127 removed outlier: 3.543A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'S' and resid 33 through 46 removed outlier: 4.056A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 removed outlier: 3.633A pdb=" N THR S 105 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 99 through 120 removed outlier: 4.395A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 40 removed outlier: 3.597A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 removed outlier: 3.700A pdb=" N LEU U 79 " --> pdb=" O TYR U 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 70 Processing helix chain 'V' and resid 119 through 124 removed outlier: 3.655A pdb=" N ASP V 124 " --> pdb=" O LYS V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 Processing helix chain 'W' and resid 33 through 41 removed outlier: 3.638A pdb=" N LYS W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 49 Processing helix chain 'W' and resid 52 through 59 Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 77 removed outlier: 3.597A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.743A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 137 removed outlier: 3.676A pdb=" N ASN X 137 " --> pdb=" O LEU X 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 4.549A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 43 removed outlier: 3.816A pdb=" N ALA Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 removed outlier: 3.696A pdb=" N LYS Y 122 " --> pdb=" O LEU Y 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 104 through 111 removed outlier: 3.656A pdb=" N GLU Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 123 removed outlier: 3.537A pdb=" N ALA Z 117 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN Z 123 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 10 removed outlier: 3.551A pdb=" N ARG a 9 " --> pdb=" O THR a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 46 Processing helix chain 'a' and resid 83 through 92 removed outlier: 4.373A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR a 90 " --> pdb=" O LYS a 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 141 removed outlier: 3.844A pdb=" N GLU a 136 " --> pdb=" O LYS a 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 removed outlier: 3.520A pdb=" N HIS b 17 " --> pdb=" O THR b 13 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 58 removed outlier: 3.509A pdb=" N HIS b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS b 52 " --> pdb=" O HIS b 48 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU b 54 " --> pdb=" O THR b 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA b 57 " --> pdb=" O ALA b 53 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 21 removed outlier: 3.561A pdb=" N VAL c 17 " --> pdb=" O LYS c 13 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE c 18 " --> pdb=" O LEU c 14 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER c 20 " --> pdb=" O LEU c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 35 removed outlier: 3.523A pdb=" N THR c 30 " --> pdb=" O GLY c 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 81 removed outlier: 3.547A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 44 removed outlier: 3.705A pdb=" N LEU d 42 " --> pdb=" O LYS d 38 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 removed outlier: 3.588A pdb=" N GLN d 57 " --> pdb=" O PRO d 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 removed outlier: 3.505A pdb=" N GLY e 58 " --> pdb=" O ILE e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.547A pdb=" N ARG e 105 " --> pdb=" O SER e 101 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'g' and resid 58 through 63 removed outlier: 3.543A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 113 removed outlier: 3.634A pdb=" N GLU g 87 " --> pdb=" O ASN g 83 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS g 103 " --> pdb=" O LYS g 99 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL g 105 " --> pdb=" O VAL g 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU g 107 " --> pdb=" O LYS g 103 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS g 113 " --> pdb=" O THR g 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.588A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 32 removed outlier: 3.510A pdb=" N LEU h 28 " --> pdb=" O LEU h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 70 removed outlier: 3.851A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG h 48 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA h 52 " --> pdb=" O ARG h 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS h 53 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL h 57 " --> pdb=" O CYS h 53 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 85 through 89 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 56 through 64 removed outlier: 3.641A pdb=" N LEU i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 removed outlier: 3.561A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 99 removed outlier: 3.947A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 10 removed outlier: 3.508A pdb=" N GLY j 9 " --> pdb=" O PRO j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.509A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.762A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY j 77 " --> pdb=" O ARG j 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 15 removed outlier: 3.605A pdb=" N PHE k 11 " --> pdb=" O ASP k 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 68 removed outlier: 3.685A pdb=" N ALA k 62 " --> pdb=" O ASP k 58 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS k 63 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS k 64 " --> pdb=" O GLY k 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER k 68 " --> pdb=" O LYS k 64 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 18 removed outlier: 3.544A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA l 16 " --> pdb=" O LYS l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 28 Processing helix chain 'o' and resid 37 through 47 Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.714A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 34 removed outlier: 3.886A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE p 31 " --> pdb=" O LYS p 27 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 78 removed outlier: 3.918A pdb=" N THR p 78 " --> pdb=" O ALA p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 78 through 92 Processing helix chain 'w' and resid 167 through 171 removed outlier: 3.975A pdb=" N PHE w 171 " --> pdb=" O LYS w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 172 through 183 removed outlier: 4.247A pdb=" N ALA w 183 " --> pdb=" O LEU w 179 " (cutoff:3.500A) Processing helix chain 'w' and resid 204 through 218 removed outlier: 3.578A pdb=" N VAL w 208 " --> pdb=" O LYS w 204 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE w 211 " --> pdb=" O ALA w 207 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA w 216 " --> pdb=" O ASP w 212 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL w 217 " --> pdb=" O PHE w 213 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 265 Processing helix chain 'w' and resid 297 through 304 removed outlier: 3.697A pdb=" N TRP w 302 " --> pdb=" O PRO w 298 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG w 303 " --> pdb=" O SER w 299 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA w 304 " --> pdb=" O VAL w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 311 through 315 removed outlier: 3.810A pdb=" N LEU w 315 " --> pdb=" O VAL w 312 " (cutoff:3.500A) Processing helix chain 'w' and resid 344 through 349 removed outlier: 4.589A pdb=" N VAL w 348 " --> pdb=" O SER w 344 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN w 349 " --> pdb=" O ASP w 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 344 through 349' Processing helix chain 'w' and resid 381 through 387 removed outlier: 3.653A pdb=" N ASP w 385 " --> pdb=" O SER w 381 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU w 387 " --> pdb=" O LEU w 383 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.331A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 34 through 43 removed outlier: 3.898A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU y 39 " --> pdb=" O TYR y 35 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.689A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 removed outlier: 4.415A pdb=" N HIS y 83 " --> pdb=" O GLN y 79 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 107 removed outlier: 3.932A pdb=" N VAL y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 103 through 107' Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.504A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU y 127 " --> pdb=" O ARG y 123 " (cutoff:3.500A) Processing helix chain 'y' and resid 141 through 145 removed outlier: 4.249A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 151 removed outlier: 3.743A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 147 through 151' Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.918A pdb=" N SER y 175 " --> pdb=" O GLU y 171 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'z' and resid 380 through 387 Processing helix chain 'z' and resid 392 through 405 removed outlier: 3.649A pdb=" N LYS z 400 " --> pdb=" O LYS z 396 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU z 405 " --> pdb=" O MET z 401 " (cutoff:3.500A) Processing helix chain 'z' and resid 405 through 420 removed outlier: 3.674A pdb=" N THR z 411 " --> pdb=" O ASN z 407 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG z 414 " --> pdb=" O ASN z 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG z 415 " --> pdb=" O THR z 411 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS z 418 " --> pdb=" O ARG z 414 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG z 419 " --> pdb=" O ARG z 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 6.316A pdb=" N LEU A 58 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 48 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 44 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG A 64 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG A 42 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.443A pdb=" N ILE A 136 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG A 149 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 140 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.511A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 279 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 282 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.293A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.293A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 20 removed outlier: 8.097A pdb=" N THR C 16 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER C 10 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 removed outlier: 3.637A pdb=" N GLU C 63 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'D' and resid 73 through 79 removed outlier: 5.851A pdb=" N VAL D 74 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER D 66 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 76 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.513A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 77 removed outlier: 3.713A pdb=" N TYR F 75 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 77 " --> pdb=" O ARG T 139 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG T 139 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 116 through 118 removed outlier: 6.826A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG F 232 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N TYR F 136 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'G' and resid 178 through 180 removed outlier: 6.404A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.812A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL H 57 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AC3, first strand: chain 'H' and resid 132 through 136 Processing sheet with id=AC4, first strand: chain 'H' and resid 132 through 136 Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.597A pdb=" N ASN H 102 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 104 " --> pdb=" O PHE H 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.648A pdb=" N VAL J 67 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE J 14 " --> pdb=" O ASN J 132 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN J 132 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.565A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AC9, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD1, first strand: chain 'L' and resid 156 through 157 Processing sheet with id=AD2, first strand: chain 'M' and resid 56 through 59 removed outlier: 6.706A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.498A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.020A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AD6, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.632A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD8, first strand: chain 'P' and resid 125 through 131 removed outlier: 3.527A pdb=" N ARG P 131 " --> pdb=" O ARG P 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.674A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL Q 87 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE2, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AE3, first strand: chain 'S' and resid 60 through 63 removed outlier: 3.545A pdb=" N GLY S 11 " --> pdb=" O PHE S 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE S 25 " --> pdb=" O GLY S 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 87 through 96 removed outlier: 7.099A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 61 through 63 Processing sheet with id=AE6, first strand: chain 'T' and resid 71 through 80 Processing sheet with id=AE7, first strand: chain 'U' and resid 54 through 58 removed outlier: 7.815A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR U 98 " --> pdb=" O GLU U 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 42 through 43 removed outlier: 3.573A pdb=" N VAL U 43 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA U 46 " --> pdb=" O VAL U 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'V' and resid 17 through 18 removed outlier: 3.622A pdb=" N LEU V 17 " --> pdb=" O ALA V 52 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.301A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 85 through 86 removed outlier: 6.505A pdb=" N PHE V 92 " --> pdb=" O LEU W 20 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL W 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR V 94 " --> pdb=" O VAL W 22 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 4 through 5 removed outlier: 3.767A pdb=" N GLU W 4 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.947A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AF6, first strand: chain 'Y' and resid 94 through 99 removed outlier: 3.671A pdb=" N ILE Y 97 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.474A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS Z 27 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL Z 23 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 72 through 74 Processing sheet with id=AF9, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.789A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER c 91 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 13 through 15 removed outlier: 7.001A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 13 through 15 Processing sheet with id=AG3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.026A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'f' and resid 8 through 18 removed outlier: 6.508A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR f 16 " --> pdb=" O VAL f 27 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL f 27 " --> pdb=" O TYR f 16 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ARG f 18 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG6, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AG7, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.658A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA k 23 " --> pdb=" O LYS k 74 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'o' and resid 7 through 12 removed outlier: 3.557A pdb=" N ARG o 8 " --> pdb=" O HIS o 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL o 68 " --> pdb=" O LEU o 85 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'p' and resid 48 through 51 removed outlier: 7.110A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'w' and resid 189 through 190 removed outlier: 3.660A pdb=" N SER w 189 " --> pdb=" O PHE w 200 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR w 239 " --> pdb=" O ILE w 229 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER w 243 " --> pdb=" O SER w 225 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'w' and resid 256 through 258 Processing sheet with id=AH3, first strand: chain 'w' and resid 283 through 286 Processing sheet with id=AH4, first strand: chain 'w' and resid 353 through 357 removed outlier: 6.900A pdb=" N LEU w 335 " --> pdb=" O THR w 326 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR w 326 " --> pdb=" O LEU w 335 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP w 322 " --> pdb=" O THR w 339 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA w 341 " --> pdb=" O VAL w 320 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL w 320 " --> pdb=" O ALA w 341 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR w 372 " --> pdb=" O LEU w 397 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU w 397 " --> pdb=" O TYR w 372 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'y' and resid 2 through 4 removed outlier: 5.969A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 18 through 19 Processing sheet with id=AH7, first strand: chain 'y' and resid 64 through 66 Processing sheet with id=AH8, first strand: chain 'y' and resid 108 through 111 Processing sheet with id=AH9, first strand: chain 'y' and resid 152 through 153 1634 hydrogen bonds defined for protein. 4515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1657 hydrogen bonds 2552 hydrogen bond angles 0 basepair planarities 718 basepair parallelities 1762 stacking parallelities Total time for adding SS restraints: 167.73 Time building geometry restraints manager: 52.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 14295 1.32 - 1.44: 54534 1.44 - 1.57: 56696 1.57 - 1.69: 6735 1.69 - 1.82: 161 Bond restraints: 132421 Sorted by residual: bond pdb=" C ASP w 186 " pdb=" N THR w 187 " ideal model delta sigma weight residual 1.331 1.591 -0.260 1.30e-02 5.92e+03 4.01e+02 bond pdb=" C VAL w 165 " pdb=" N PRO w 166 " ideal model delta sigma weight residual 1.334 1.475 -0.141 2.34e-02 1.83e+03 3.61e+01 bond pdb=" C ARG O 74 " pdb=" N ALA O 75 " ideal model delta sigma weight residual 1.331 1.218 0.113 2.07e-02 2.33e+03 2.97e+01 bond pdb=" C ARG Z 48 " pdb=" N TYR Z 49 " ideal model delta sigma weight residual 1.331 1.227 0.104 2.07e-02 2.33e+03 2.51e+01 bond pdb=" CA ILE y 146 " pdb=" CB ILE y 146 " ideal model delta sigma weight residual 1.540 1.579 -0.039 1.36e-02 5.41e+03 8.03e+00 ... (remaining 132416 not shown) Histogram of bond angle deviations from ideal: 96.82 - 104.82: 15532 104.82 - 112.83: 77891 112.83 - 120.84: 61705 120.84 - 128.85: 36095 128.85 - 136.85: 4058 Bond angle restraints: 195281 Sorted by residual: angle pdb=" O VAL w 165 " pdb=" C VAL w 165 " pdb=" N PRO w 166 " ideal model delta sigma weight residual 121.10 136.85 -15.75 1.14e+00 7.69e-01 1.91e+02 angle pdb=" CA VAL w 165 " pdb=" C VAL w 165 " pdb=" N PRO w 166 " ideal model delta sigma weight residual 118.88 103.61 15.27 1.54e+00 4.22e-01 9.84e+01 angle pdb=" O ASP w 186 " pdb=" C ASP w 186 " pdb=" N THR w 187 " ideal model delta sigma weight residual 123.27 113.44 9.83 1.16e+00 7.43e-01 7.18e+01 angle pdb=" CA ASP w 186 " pdb=" C ASP w 186 " pdb=" N THR w 187 " ideal model delta sigma weight residual 115.60 125.13 -9.53 1.47e+00 4.63e-01 4.20e+01 angle pdb=" O3' U 11607 " pdb=" C3' U 11607 " pdb=" C2' U 11607 " ideal model delta sigma weight residual 109.50 118.73 -9.23 1.50e+00 4.44e-01 3.78e+01 ... (remaining 195276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 75613 35.93 - 71.86: 7456 71.86 - 107.79: 833 107.79 - 143.72: 31 143.72 - 179.64: 51 Dihedral angle restraints: 83984 sinusoidal: 65393 harmonic: 18591 Sorted by residual: dihedral pdb=" CA THR G 30 " pdb=" C THR G 30 " pdb=" N PRO G 31 " pdb=" CA PRO G 31 " ideal model delta harmonic sigma weight residual -180.00 -118.20 -61.80 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ASN y 145 " pdb=" C ASN y 145 " pdb=" N ILE y 146 " pdb=" CA ILE y 146 " ideal model delta harmonic sigma weight residual 180.00 126.69 53.31 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" O4' U 13306 " pdb=" C1' U 13306 " pdb=" N1 U 13306 " pdb=" C2 U 13306 " ideal model delta sinusoidal sigma weight residual 200.00 21.59 178.41 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 83981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 21603 0.073 - 0.146: 2700 0.146 - 0.219: 229 0.219 - 0.293: 26 0.293 - 0.366: 4 Chirality restraints: 24562 Sorted by residual: chirality pdb=" CB ILE O 108 " pdb=" CA ILE O 108 " pdb=" CG1 ILE O 108 " pdb=" CG2 ILE O 108 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C3' U 11607 " pdb=" C4' U 11607 " pdb=" O3' U 11607 " pdb=" C2' U 11607 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' G 1 282 " pdb=" C4' G 1 282 " pdb=" O3' G 1 282 " pdb=" C2' G 1 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.48e+00 ... (remaining 24559 not shown) Planarity restraints: 12214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 255 " -0.031 2.00e-02 2.50e+03 2.45e-02 1.49e+01 pdb=" CG TRP B 255 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 255 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 255 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 255 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 255 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 255 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 255 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 255 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12437 " -0.051 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G 12437 " 0.051 2.00e-02 2.50e+03 pdb=" C8 G 12437 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 12437 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 12437 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 12437 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 12437 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G 12437 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G 12437 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 12437 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 12437 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G 12437 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP w 186 " 0.021 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASP w 186 " -0.064 2.00e-02 2.50e+03 pdb=" O ASP w 186 " 0.024 2.00e-02 2.50e+03 pdb=" N THR w 187 " 0.019 2.00e-02 2.50e+03 ... (remaining 12211 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 425 2.35 - 2.99: 61226 2.99 - 3.62: 194689 3.62 - 4.26: 352914 4.26 - 4.90: 496724 Nonbonded interactions: 1105978 Sorted by model distance: nonbonded pdb=" OP2 U 13151 " pdb=" NZ LYS B 132 " model vdw 1.709 2.520 nonbonded pdb=" OP2 G 1 912 " pdb=" NH2 ARG A 9 " model vdw 1.743 2.520 nonbonded pdb=" OP2 U 11724 " pdb=" NZ LYS R 128 " model vdw 1.780 2.520 nonbonded pdb=" OP2 A 11135 " pdb=" NZ LYS b 5 " model vdw 1.780 2.520 nonbonded pdb=" OD1 ASP S 109 " pdb=" NH1 ARG S 113 " model vdw 1.811 2.520 ... (remaining 1105973 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 14.230 Check model and map are aligned: 1.310 Set scattering table: 0.840 Process input model: 386.970 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.260 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:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 409.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.008 0.260 132421 Z= 0.510 Angle : 0.861 15.753 195281 Z= 0.455 Chirality : 0.049 0.366 24562 Planarity : 0.006 0.078 12214 Dihedral : 22.128 179.644 72000 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.85 % Allowed : 6.21 % Favored : 92.94 % Rotamer: Outliers : 0.15 % Allowed : 1.29 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 1.71 % Twisted General : 0.28 % 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: -4.11 (0.08), residues: 6348 helix: -4.36 (0.06), residues: 1925 sheet: -1.60 (0.15), residues: 841 loop : -2.04 (0.08), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP B 255 HIS 0.017 0.003 HIS S 154 PHE 0.051 0.004 PHE F 229 TYR 0.036 0.004 TYR C 194 ARG 0.017 0.002 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1873 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1865 time to evaluate : 5.883 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: A 15 ILE cc_start: 0.8023 (pt) cc_final: 0.7822 (pt) REVERT: C 211 GLU cc_start: 0.8093 (tt0) cc_final: 0.7749 (tt0) REVERT: E 57 HIS cc_start: 0.7749 (t-170) cc_final: 0.7248 (p90) REVERT: F 64 GLN cc_start: 0.7336 (tp40) cc_final: 0.7133 (tp40) REVERT: G 208 GLU cc_start: 0.7864 (tp30) cc_final: 0.7540 (mt-10) REVERT: G 231 LYS cc_start: 0.8556 (mttt) cc_final: 0.8161 (ttpt) REVERT: H 94 TYR cc_start: 0.7607 (p90) cc_final: 0.7322 (p90) REVERT: J 13 LYS cc_start: 0.6533 (ptmt) cc_final: 0.6307 (pptt) REVERT: J 53 THR cc_start: 0.7397 (m) cc_final: 0.7142 (p) REVERT: L 104 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7201 (mtm180) REVERT: N 26 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6914 (mtt180) REVERT: S 7 TYR cc_start: 0.8756 (m-80) cc_final: 0.8438 (m-80) REVERT: S 131 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8974 (mtmm) REVERT: T 112 ASN cc_start: 0.8845 (m-40) cc_final: 0.8274 (m110) REVERT: U 86 LYS cc_start: 0.8396 (tptt) cc_final: 0.7552 (ttpt) REVERT: V 86 ARG cc_start: 0.6404 (ttt-90) cc_final: 0.6133 (ttt-90) REVERT: W 51 TRP cc_start: 0.8029 (p-90) cc_final: 0.7807 (p-90) REVERT: X 25 LYS cc_start: 0.7994 (mttp) cc_final: 0.7614 (tttt) REVERT: X 63 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7423 (mt) REVERT: Y 95 VAL cc_start: 0.9076 (t) cc_final: 0.8813 (m) REVERT: Z 66 THR cc_start: 0.8910 (p) cc_final: 0.8616 (t) REVERT: b 29 TYR cc_start: 0.8590 (m-80) cc_final: 0.8304 (m-10) REVERT: b 48 HIS cc_start: 0.7687 (t-90) cc_final: 0.7398 (t-170) REVERT: c 35 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7152 (ptp-110) REVERT: f 65 ARG cc_start: 0.8350 (mtt180) cc_final: 0.8107 (mtt180) REVERT: g 55 SER cc_start: 0.8619 (m) cc_final: 0.8413 (p) REVERT: g 102 LYS cc_start: 0.5805 (mmtt) cc_final: 0.5211 (ttpt) REVERT: h 70 TYR cc_start: 0.8680 (m-80) cc_final: 0.8470 (m-80) REVERT: h 109 ILE cc_start: 0.8641 (mt) cc_final: 0.8434 (mt) REVERT: i 67 LYS cc_start: 0.8129 (tttm) cc_final: 0.7907 (mmtm) REVERT: j 76 ASN cc_start: 0.7461 (m-40) cc_final: 0.7235 (m110) REVERT: j 82 SER cc_start: 0.8435 (p) cc_final: 0.8235 (m) REVERT: k 74 LYS cc_start: 0.7387 (mttm) cc_final: 0.6950 (ptmm) REVERT: o 6 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7856 (mtmm) REVERT: o 92 GLU cc_start: 0.7912 (pt0) cc_final: 0.7432 (mt-10) REVERT: w 209 LYS cc_start: 0.3872 (mmtt) cc_final: 0.3648 (mptt) REVERT: w 239 THR cc_start: 0.6918 (t) cc_final: 0.6317 (p) REVERT: w 253 LYS cc_start: 0.6488 (ttpt) cc_final: 0.6257 (tttm) REVERT: w 255 ASP cc_start: 0.6171 (p0) cc_final: 0.5876 (p0) REVERT: w 286 MET cc_start: 0.7386 (ttm) cc_final: 0.6996 (tpp) REVERT: w 287 ASP cc_start: 0.6280 (m-30) cc_final: 0.5723 (m-30) REVERT: w 293 THR cc_start: 0.8070 (p) cc_final: 0.7802 (t) REVERT: w 297 SER cc_start: 0.4715 (m) cc_final: 0.4266 (t) REVERT: w 330 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7120 (mtt90) REVERT: w 350 ASP cc_start: 0.6796 (t70) cc_final: 0.6441 (t70) REVERT: w 362 ILE cc_start: 0.7353 (mt) cc_final: 0.6962 (mt) REVERT: w 390 ASP cc_start: 0.8549 (m-30) cc_final: 0.7814 (p0) REVERT: y 57 ARG cc_start: 0.6748 (mtm180) cc_final: 0.6364 (mtm180) REVERT: y 123 ARG cc_start: 0.7443 (ttt-90) cc_final: 0.6553 (mmm-85) REVERT: y 171 GLU cc_start: 0.8397 (tp30) cc_final: 0.8179 (pp20) outliers start: 8 outliers final: 3 residues processed: 1871 average time/residue: 1.2128 time to fit residues: 3725.5801 Evaluate side-chains 1146 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1141 time to evaluate : 5.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 330 ARG Chi-restraints excluded: chain w residue 374 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 808 optimal weight: 0.7980 chunk 726 optimal weight: 4.9990 chunk 402 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 489 optimal weight: 0.9980 chunk 387 optimal weight: 5.9990 chunk 750 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 456 optimal weight: 2.9990 chunk 558 optimal weight: 5.9990 chunk 869 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 83 HIS A 97 ASN A 209 HIS B 109 HIS B 269 GLN B 377 HIS C 43 ASN C 48 GLN C 114 ASN C 116 ASN C 260 GLN C 296 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 81 HIS D 151 GLN E 167 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN G 61 GLN G 138 HIS ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN H 156 GLN H 157 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 28 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS N 95 GLN O 90 HIS O 122 GLN P 54 HIS P 133 HIS R 66 HIS S 89 ASN T 5 HIS T 58 GLN T 112 ASN T 127 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN W 59 HIS X 65 GLN X 94 GLN ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 HIS Z 106 GLN a 40 HIS ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 65 GLN a 74 ASN b 42 ASN d 87 ASN e 71 HIS f 87 ASN f 106 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 HIS g 52 GLN h 113 GLN ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 23 HIS o 27 GLN o 82 GLN p 25 GLN p 33 GLN p 34 HIS w 272 GLN y 21 ASN y 106 ASN y 140 GLN y 145 ASN y 156 ASN y 157 GLN ** y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 132421 Z= 0.205 Angle : 0.643 11.845 195281 Z= 0.338 Chirality : 0.039 0.344 24562 Planarity : 0.005 0.085 12214 Dihedral : 23.268 179.796 59292 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.58 % Allowed : 5.17 % Favored : 94.25 % Rotamer: Outliers : 2.79 % Allowed : 11.72 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.85 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.09), residues: 6348 helix: -2.38 (0.09), residues: 2009 sheet: -1.03 (0.16), residues: 857 loop : -1.62 (0.09), residues: 3482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 147 HIS 0.009 0.001 HIS D 244 PHE 0.024 0.002 PHE D 160 TYR 0.043 0.002 TYR i 28 ARG 0.010 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1329 time to evaluate : 5.815 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: A 89 TYR cc_start: 0.8881 (m-80) cc_final: 0.8659 (m-80) REVERT: B 94 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 187 SER cc_start: 0.7936 (t) cc_final: 0.7565 (t) REVERT: B 227 GLU cc_start: 0.6960 (tp30) cc_final: 0.6647 (tp30) REVERT: B 380 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7241 (mtt) REVERT: C 260 GLN cc_start: 0.7410 (mp-120) cc_final: 0.7064 (mp10) REVERT: D 94 ASN cc_start: 0.7340 (p0) cc_final: 0.7124 (p0) REVERT: D 120 LYS cc_start: 0.7888 (mttt) cc_final: 0.7575 (mmtt) REVERT: D 208 MET cc_start: 0.6548 (mtp) cc_final: 0.6308 (mtp) REVERT: E 57 HIS cc_start: 0.7750 (t-170) cc_final: 0.7254 (p-80) REVERT: E 143 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8670 (ttpp) REVERT: F 68 ASP cc_start: 0.7541 (m-30) cc_final: 0.7308 (m-30) REVERT: F 203 TRP cc_start: 0.8633 (t-100) cc_final: 0.8343 (t-100) REVERT: G 204 ARG cc_start: 0.7838 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: G 208 GLU cc_start: 0.7880 (tp30) cc_final: 0.7605 (mt-10) REVERT: H 94 TYR cc_start: 0.7582 (p90) cc_final: 0.7381 (p90) REVERT: H 111 PHE cc_start: 0.7909 (m-80) cc_final: 0.7694 (m-10) REVERT: H 171 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6172 (t70) REVERT: J 13 LYS cc_start: 0.6543 (ptmt) cc_final: 0.6150 (pptt) REVERT: J 53 THR cc_start: 0.7288 (m) cc_final: 0.7059 (p) REVERT: J 78 GLU cc_start: 0.8146 (tp30) cc_final: 0.7887 (tp30) REVERT: L 68 LYS cc_start: 0.7318 (mmtp) cc_final: 0.6970 (ptmt) REVERT: L 117 LYS cc_start: 0.7380 (mmtp) cc_final: 0.6985 (ttpp) REVERT: L 126 PHE cc_start: 0.7706 (m-10) cc_final: 0.7355 (m-10) REVERT: L 176 GLU cc_start: 0.7501 (tp30) cc_final: 0.7236 (mm-30) REVERT: M 93 LYS cc_start: 0.7888 (mttp) cc_final: 0.7639 (mttp) REVERT: Q 44 PHE cc_start: 0.8159 (t80) cc_final: 0.7848 (t80) REVERT: Q 180 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6916 (mtm180) REVERT: R 111 ASP cc_start: 0.8777 (m-30) cc_final: 0.8568 (m-30) REVERT: S 7 TYR cc_start: 0.8689 (m-80) cc_final: 0.8390 (m-80) REVERT: T 128 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6274 (pp) REVERT: X 104 GLU cc_start: 0.8103 (mp0) cc_final: 0.7885 (mp0) REVERT: Z 66 THR cc_start: 0.8973 (p) cc_final: 0.8715 (m) REVERT: a 131 SER cc_start: 0.8081 (t) cc_final: 0.7591 (p) REVERT: a 135 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7223 (tp30) REVERT: b 29 TYR cc_start: 0.8346 (m-80) cc_final: 0.8049 (m-10) REVERT: b 48 HIS cc_start: 0.7739 (t-90) cc_final: 0.7493 (t-170) REVERT: e 60 ASN cc_start: 0.8282 (t0) cc_final: 0.8034 (t0) REVERT: g 55 SER cc_start: 0.8654 (m) cc_final: 0.8442 (p) REVERT: h 105 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7451 (ttp80) REVERT: i 67 LYS cc_start: 0.8181 (tttm) cc_final: 0.7926 (mmtm) REVERT: j 76 ASN cc_start: 0.7226 (m-40) cc_final: 0.6990 (m110) REVERT: j 82 SER cc_start: 0.8475 (p) cc_final: 0.8229 (m) REVERT: k 31 LEU cc_start: 0.8360 (pp) cc_final: 0.8064 (tt) REVERT: k 74 LYS cc_start: 0.7301 (mttm) cc_final: 0.6965 (ptmm) REVERT: o 6 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7876 (mtmm) REVERT: o 66 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8232 (mttt) REVERT: o 92 GLU cc_start: 0.7837 (pt0) cc_final: 0.7412 (mt-10) REVERT: p 45 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8303 (ptmm) REVERT: w 284 GLN cc_start: 0.5407 (tt0) cc_final: 0.5079 (tt0) REVERT: w 286 MET cc_start: 0.7379 (ttm) cc_final: 0.7036 (tpp) REVERT: w 293 THR cc_start: 0.8222 (p) cc_final: 0.7888 (t) REVERT: y 80 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7057 (mt-10) REVERT: y 171 GLU cc_start: 0.8413 (tp30) cc_final: 0.8041 (tt0) REVERT: y 220 SER cc_start: 0.9252 (t) cc_final: 0.8996 (p) REVERT: z 418 LYS cc_start: 0.8027 (mttt) cc_final: 0.7825 (mttp) outliers start: 149 outliers final: 90 residues processed: 1397 average time/residue: 1.1013 time to fit residues: 2598.2003 Evaluate side-chains 1200 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1105 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 25 SER Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 45 LYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 325 SER Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 483 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 724 optimal weight: 5.9990 chunk 592 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 871 optimal weight: 9.9990 chunk 941 optimal weight: 9.9990 chunk 776 optimal weight: 7.9990 chunk 864 optimal weight: 0.9990 chunk 297 optimal weight: 30.0000 chunk 699 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 HIS ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS C 48 GLN C 311 HIS D 32 GLN D 63 GLN E 57 HIS E 80 ASN E 138 GLN F 37 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN G 28 HIS ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN H 156 GLN J 47 GLN L 19 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN N 175 ASN O 72 HIS O 122 GLN P 97 ASN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN W 32 GLN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN c 75 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 59 ASN ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN z 393 GLN z 402 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 132421 Z= 0.312 Angle : 0.678 13.883 195281 Z= 0.351 Chirality : 0.041 0.341 24562 Planarity : 0.006 0.072 12214 Dihedral : 23.143 179.739 59282 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.41 % Favored : 93.12 % Rotamer: Outliers : 4.53 % Allowed : 13.59 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.08 % 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 (0.09), residues: 6348 helix: -1.48 (0.10), residues: 2012 sheet: -0.78 (0.16), residues: 896 loop : -1.62 (0.10), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 12 HIS 0.012 0.002 HIS a 40 PHE 0.027 0.002 PHE F 229 TYR 0.035 0.002 TYR C 194 ARG 0.012 0.001 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1151 time to evaluate : 5.936 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: B 87 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8745 (t) REVERT: B 94 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 187 SER cc_start: 0.8217 (t) cc_final: 0.7817 (t) REVERT: B 227 GLU cc_start: 0.6952 (tp30) cc_final: 0.6610 (tp30) REVERT: B 333 LYS cc_start: 0.8399 (mtmt) cc_final: 0.8137 (mttt) REVERT: C 14 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: C 260 GLN cc_start: 0.7542 (mp-120) cc_final: 0.7158 (mp10) REVERT: D 120 LYS cc_start: 0.8050 (mttt) cc_final: 0.7708 (mmtt) REVERT: E 57 HIS cc_start: 0.7761 (t70) cc_final: 0.7194 (p-80) REVERT: F 203 TRP cc_start: 0.8611 (t-100) cc_final: 0.8357 (t-100) REVERT: G 28 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7425 (m90) REVERT: G 38 GLN cc_start: 0.7528 (pm20) cc_final: 0.7265 (pm20) REVERT: G 84 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7620 (mtm180) REVERT: G 204 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7401 (mtm-85) REVERT: G 208 GLU cc_start: 0.7886 (tp30) cc_final: 0.7563 (mt-10) REVERT: H 171 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6246 (t70) REVERT: J 29 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7639 (tpt-90) REVERT: J 53 THR cc_start: 0.7303 (m) cc_final: 0.7059 (p) REVERT: J 78 GLU cc_start: 0.8278 (tp30) cc_final: 0.7989 (tp30) REVERT: J 170 ASP cc_start: 0.7454 (t0) cc_final: 0.6827 (p0) REVERT: L 68 LYS cc_start: 0.7368 (mmtp) cc_final: 0.6877 (ptmt) REVERT: L 117 LYS cc_start: 0.7596 (mmtp) cc_final: 0.6988 (ttpp) REVERT: L 176 GLU cc_start: 0.7448 (tp30) cc_final: 0.7190 (mm-30) REVERT: M 41 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8336 (mm-40) REVERT: N 119 TYR cc_start: 0.8359 (p90) cc_final: 0.8145 (p90) REVERT: R 72 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: R 111 ASP cc_start: 0.8775 (m-30) cc_final: 0.8515 (m-30) REVERT: R 140 GLU cc_start: 0.8116 (tp30) cc_final: 0.7911 (tm-30) REVERT: S 7 TYR cc_start: 0.8705 (m-80) cc_final: 0.8503 (m-80) REVERT: S 24 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8608 (mp) REVERT: S 89 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6929 (m110) REVERT: T 92 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.5984 (mtp180) REVERT: T 112 ASN cc_start: 0.8438 (m-40) cc_final: 0.8210 (m-40) REVERT: T 128 LEU cc_start: 0.7019 (pp) cc_final: 0.6730 (pp) REVERT: V 108 GLU cc_start: 0.7457 (mp0) cc_final: 0.7204 (mp0) REVERT: V 128 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7696 (mmt90) REVERT: X 33 ARG cc_start: 0.7842 (mtp-110) cc_final: 0.7269 (mtp-110) REVERT: X 63 ILE cc_start: 0.7559 (pt) cc_final: 0.7272 (mp) REVERT: X 74 LYS cc_start: 0.7848 (tptm) cc_final: 0.7499 (tptm) REVERT: Z 115 LYS cc_start: 0.8366 (tttm) cc_final: 0.8141 (tttt) REVERT: a 135 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7526 (tm-30) REVERT: b 29 TYR cc_start: 0.8389 (m-80) cc_final: 0.8007 (m-10) REVERT: b 48 HIS cc_start: 0.7668 (t-90) cc_final: 0.7378 (t-170) REVERT: e 60 ASN cc_start: 0.8350 (t0) cc_final: 0.8114 (t0) REVERT: f 20 LYS cc_start: 0.7947 (mttp) cc_final: 0.7650 (mtpt) REVERT: g 55 SER cc_start: 0.8716 (m) cc_final: 0.8492 (p) REVERT: h 109 ILE cc_start: 0.8712 (mt) cc_final: 0.8439 (mt) REVERT: i 67 LYS cc_start: 0.8237 (tttm) cc_final: 0.7946 (mptt) REVERT: j 76 ASN cc_start: 0.7425 (m-40) cc_final: 0.7163 (m110) REVERT: j 82 SER cc_start: 0.8368 (p) cc_final: 0.8151 (m) REVERT: k 74 LYS cc_start: 0.7336 (mttm) cc_final: 0.6936 (ptmm) REVERT: o 66 LYS cc_start: 0.8562 (mtpp) cc_final: 0.8335 (mttt) REVERT: p 45 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8300 (ptmm) REVERT: p 89 MET cc_start: 0.7711 (ttm) cc_final: 0.7157 (tmm) REVERT: w 284 GLN cc_start: 0.5297 (tt0) cc_final: 0.4970 (tt0) REVERT: w 286 MET cc_start: 0.7465 (ttm) cc_final: 0.6945 (tpp) REVERT: w 293 THR cc_start: 0.8077 (p) cc_final: 0.7779 (t) REVERT: y 1 MET cc_start: 0.5945 (tpp) cc_final: 0.5729 (tpp) REVERT: y 80 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7038 (mt-10) REVERT: y 127 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7552 (mp0) REVERT: y 168 GLN cc_start: 0.6821 (pm20) cc_final: 0.5809 (pp30) REVERT: y 171 GLU cc_start: 0.8286 (tp30) cc_final: 0.8008 (pp20) REVERT: y 220 SER cc_start: 0.9253 (t) cc_final: 0.8957 (p) REVERT: z 393 GLN cc_start: 0.6806 (tt0) cc_final: 0.6599 (tt0) outliers start: 242 outliers final: 163 residues processed: 1282 average time/residue: 1.1704 time to fit residues: 2579.5273 Evaluate side-chains 1231 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1060 time to evaluate : 5.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 28 HIS Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 98 THR Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 325 SER Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 861 optimal weight: 10.0000 chunk 655 optimal weight: 3.9990 chunk 452 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 415 optimal weight: 5.9990 chunk 585 optimal weight: 7.9990 chunk 874 optimal weight: 10.0000 chunk 926 optimal weight: 20.0000 chunk 456 optimal weight: 10.0000 chunk 828 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 109 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN F 37 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN G 28 HIS H 50 ASN H 156 GLN J 109 HIS ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 ASN O 122 GLN Q 45 ASN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 65 GLN a 120 ASN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 22 GLN p 33 GLN y 11 ASN ** y 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 412 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 132421 Z= 0.383 Angle : 0.717 13.011 195281 Z= 0.370 Chirality : 0.043 0.369 24562 Planarity : 0.006 0.103 12214 Dihedral : 23.109 179.782 59282 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.28 % Favored : 92.27 % Rotamer: Outliers : 5.72 % Allowed : 14.87 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.06 % 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: -2.17 (0.10), residues: 6348 helix: -1.26 (0.11), residues: 2014 sheet: -0.88 (0.16), residues: 957 loop : -1.71 (0.10), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP O 147 HIS 0.030 0.002 HIS G 28 PHE 0.031 0.002 PHE D 160 TYR 0.040 0.002 TYR C 194 ARG 0.011 0.001 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1098 time to evaluate : 5.985 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: B 167 ARG cc_start: 0.8194 (ptt-90) cc_final: 0.7961 (ptt-90) REVERT: B 187 SER cc_start: 0.8212 (t) cc_final: 0.7807 (t) REVERT: B 227 GLU cc_start: 0.6934 (tp30) cc_final: 0.6635 (tp30) REVERT: C 14 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: C 260 GLN cc_start: 0.7639 (mp-120) cc_final: 0.7196 (mp10) REVERT: D 208 MET cc_start: 0.7097 (mtp) cc_final: 0.6667 (mtp) REVERT: D 273 ARG cc_start: 0.6770 (ptm-80) cc_final: 0.5214 (tpp80) REVERT: E 57 HIS cc_start: 0.7904 (t70) cc_final: 0.7154 (p-80) REVERT: G 38 GLN cc_start: 0.7765 (pm20) cc_final: 0.7402 (pm20) REVERT: G 84 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7652 (mtm180) REVERT: G 202 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7118 (mm-30) REVERT: G 208 GLU cc_start: 0.7820 (tp30) cc_final: 0.7515 (mt-10) REVERT: H 171 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.6297 (t70) REVERT: J 53 THR cc_start: 0.7217 (m) cc_final: 0.7016 (p) REVERT: J 131 MET cc_start: 0.8486 (mmm) cc_final: 0.8152 (mmm) REVERT: L 19 GLN cc_start: 0.8359 (mt0) cc_final: 0.8085 (mt0) REVERT: L 117 LYS cc_start: 0.7615 (mmtp) cc_final: 0.7018 (ttpp) REVERT: L 176 GLU cc_start: 0.7414 (tp30) cc_final: 0.7157 (mm-30) REVERT: O 193 GLN cc_start: 0.8522 (mt0) cc_final: 0.8298 (mt0) REVERT: P 120 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7771 (p0) REVERT: P 126 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: R 72 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: R 111 ASP cc_start: 0.8724 (m-30) cc_final: 0.8469 (m-30) REVERT: R 140 GLU cc_start: 0.8091 (tp30) cc_final: 0.7868 (tm-30) REVERT: S 89 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6829 (m110) REVERT: S 161 LYS cc_start: 0.8276 (tttp) cc_final: 0.7806 (mtpt) REVERT: T 32 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7981 (mmmt) REVERT: T 92 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.5987 (mtp180) REVERT: V 56 ASP cc_start: 0.7857 (t70) cc_final: 0.7169 (t0) REVERT: V 86 ARG cc_start: 0.6221 (ttt90) cc_final: 0.5960 (ttp80) REVERT: V 108 GLU cc_start: 0.7502 (mp0) cc_final: 0.7263 (mp0) REVERT: V 128 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7827 (mmt90) REVERT: X 33 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7289 (mtp-110) REVERT: X 74 LYS cc_start: 0.7873 (tptm) cc_final: 0.7551 (tptm) REVERT: X 135 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8646 (mp) REVERT: a 21 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7430 (mtt180) REVERT: b 48 HIS cc_start: 0.7693 (t-90) cc_final: 0.7337 (t-170) REVERT: e 60 ASN cc_start: 0.8471 (t0) cc_final: 0.8232 (t0) REVERT: i 67 LYS cc_start: 0.8288 (tttm) cc_final: 0.8050 (mptt) REVERT: j 76 ASN cc_start: 0.7510 (m-40) cc_final: 0.7275 (m110) REVERT: j 82 SER cc_start: 0.8473 (p) cc_final: 0.8227 (m) REVERT: k 74 LYS cc_start: 0.7270 (mttm) cc_final: 0.6953 (ptmm) REVERT: o 38 GLN cc_start: 0.8731 (tp40) cc_final: 0.8491 (tp-100) REVERT: o 45 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6386 (ttm-80) REVERT: o 71 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7015 (tmm160) REVERT: o 78 LYS cc_start: 0.8097 (tppt) cc_final: 0.7553 (tptt) REVERT: p 45 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8354 (ptmm) REVERT: p 89 MET cc_start: 0.7554 (ttm) cc_final: 0.7337 (mtt) REVERT: w 284 GLN cc_start: 0.5304 (tt0) cc_final: 0.5003 (tt0) REVERT: w 286 MET cc_start: 0.7658 (ttm) cc_final: 0.6994 (tpp) REVERT: w 293 THR cc_start: 0.8131 (p) cc_final: 0.7837 (t) REVERT: y 1 MET cc_start: 0.6038 (tpp) cc_final: 0.5708 (tpp) REVERT: y 4 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6577 (mtt-85) REVERT: y 12 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7883 (mp0) REVERT: y 80 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6895 (mt-10) outliers start: 306 outliers final: 220 residues processed: 1269 average time/residue: 1.0751 time to fit residues: 2348.4473 Evaluate side-chains 1277 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1045 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 98 THR Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 7 THR Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 45 LYS Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 217 VAL Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 109 CYS Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 128 LEU Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 199 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 412 GLN Chi-restraints excluded: chain z residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 771 optimal weight: 7.9990 chunk 525 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 689 optimal weight: 6.9990 chunk 382 optimal weight: 5.9990 chunk 790 optimal weight: 0.0980 chunk 640 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 472 optimal weight: 8.9990 chunk 831 optimal weight: 0.0070 chunk 233 optimal weight: 10.0000 overall best weight: 3.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 109 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS D 63 GLN E 80 ASN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN O 42 ASN O 122 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 13 ASN l 19 GLN w 231 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 170 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 132421 Z= 0.245 Angle : 0.614 13.980 195281 Z= 0.320 Chirality : 0.039 0.570 24562 Planarity : 0.005 0.093 12214 Dihedral : 22.989 179.910 59282 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.95 % Favored : 92.60 % Rotamer: Outliers : 4.82 % Allowed : 16.77 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.10), residues: 6348 helix: -0.86 (0.11), residues: 2014 sheet: -0.82 (0.16), residues: 935 loop : -1.57 (0.10), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 12 HIS 0.014 0.001 HIS W 59 PHE 0.029 0.002 PHE D 260 TYR 0.031 0.002 TYR C 194 ARG 0.009 0.001 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1122 time to evaluate : 5.927 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: B 167 ARG cc_start: 0.8176 (ptt-90) cc_final: 0.7969 (ptt-90) REVERT: B 187 SER cc_start: 0.8156 (t) cc_final: 0.7783 (t) REVERT: B 227 GLU cc_start: 0.6926 (tp30) cc_final: 0.6665 (tp30) REVERT: C 14 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: C 260 GLN cc_start: 0.7621 (mp-120) cc_final: 0.7217 (mp10) REVERT: D 35 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7858 (mtm-85) REVERT: D 120 LYS cc_start: 0.8028 (mttt) cc_final: 0.7640 (mmtt) REVERT: D 208 MET cc_start: 0.7105 (mtp) cc_final: 0.6814 (mtp) REVERT: D 273 ARG cc_start: 0.6679 (ptm-80) cc_final: 0.5217 (tpp80) REVERT: E 57 HIS cc_start: 0.7878 (t70) cc_final: 0.7101 (p-80) REVERT: G 38 GLN cc_start: 0.7609 (pm20) cc_final: 0.6382 (pm20) REVERT: G 84 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7675 (mtm180) REVERT: G 202 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6924 (mm-30) REVERT: G 208 GLU cc_start: 0.7792 (tp30) cc_final: 0.7495 (mt-10) REVERT: H 171 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6259 (t70) REVERT: J 53 THR cc_start: 0.7201 (m) cc_final: 0.6968 (p) REVERT: L 117 LYS cc_start: 0.7585 (mmtp) cc_final: 0.6970 (ttpp) REVERT: L 176 GLU cc_start: 0.7341 (tp30) cc_final: 0.7089 (mm-30) REVERT: N 119 TYR cc_start: 0.8435 (p90) cc_final: 0.8157 (p90) REVERT: P 120 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7573 (p0) REVERT: P 126 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7400 (mtm-85) REVERT: P 154 GLU cc_start: 0.7718 (pp20) cc_final: 0.7235 (pp20) REVERT: Q 44 PHE cc_start: 0.8342 (t80) cc_final: 0.7949 (t80) REVERT: R 72 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: R 111 ASP cc_start: 0.8710 (m-30) cc_final: 0.8461 (m-30) REVERT: R 140 GLU cc_start: 0.8058 (tp30) cc_final: 0.7809 (tm-30) REVERT: V 56 ASP cc_start: 0.7984 (t70) cc_final: 0.7320 (t0) REVERT: V 108 GLU cc_start: 0.7525 (mp0) cc_final: 0.7259 (mp0) REVERT: V 128 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7738 (mmt90) REVERT: X 33 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7112 (mtp-110) REVERT: X 74 LYS cc_start: 0.7787 (tptm) cc_final: 0.7495 (tptm) REVERT: X 135 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8654 (mp) REVERT: a 135 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7293 (tm-30) REVERT: b 29 TYR cc_start: 0.8306 (m-80) cc_final: 0.7927 (m-10) REVERT: e 60 ASN cc_start: 0.8496 (t0) cc_final: 0.8255 (t0) REVERT: g 55 SER cc_start: 0.8891 (m) cc_final: 0.8542 (p) REVERT: i 67 LYS cc_start: 0.8374 (tttm) cc_final: 0.8114 (mptt) REVERT: j 76 ASN cc_start: 0.7410 (m-40) cc_final: 0.7166 (m110) REVERT: j 82 SER cc_start: 0.8451 (p) cc_final: 0.8218 (m) REVERT: k 74 LYS cc_start: 0.7227 (mttm) cc_final: 0.6958 (ptmm) REVERT: l 30 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8439 (mtp85) REVERT: o 38 GLN cc_start: 0.8705 (tp40) cc_final: 0.8437 (tp-100) REVERT: o 45 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6397 (ttm-80) REVERT: o 71 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6947 (tmm160) REVERT: p 45 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8340 (ptmm) REVERT: p 89 MET cc_start: 0.7751 (ttm) cc_final: 0.7280 (ttp) REVERT: w 220 ILE cc_start: 0.4468 (OUTLIER) cc_final: 0.4223 (pt) REVERT: w 267 MET cc_start: 0.6765 (ptp) cc_final: 0.6508 (pmm) REVERT: w 286 MET cc_start: 0.7463 (ttm) cc_final: 0.6912 (tpp) REVERT: w 293 THR cc_start: 0.8210 (p) cc_final: 0.7965 (t) REVERT: w 358 HIS cc_start: 0.6314 (t70) cc_final: 0.6033 (t70) REVERT: y 1 MET cc_start: 0.5944 (tpp) cc_final: 0.5716 (tpp) REVERT: y 4 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6567 (mtt-85) REVERT: y 12 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7841 (mp0) outliers start: 258 outliers final: 205 residues processed: 1258 average time/residue: 1.0806 time to fit residues: 2326.0822 Evaluate side-chains 1286 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1070 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 45 LYS Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 217 VAL Chi-restraints excluded: chain w residue 220 ILE Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 342 ARG Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 377 SER Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 311 optimal weight: 10.0000 chunk 833 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 543 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 926 optimal weight: 20.0000 chunk 769 optimal weight: 1.9990 chunk 429 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 109 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS D 63 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN L 19 GLN L 120 GLN O 42 ASN O 122 GLN S 142 GLN T 112 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN ** j 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 132421 Z= 0.266 Angle : 0.619 13.865 195281 Z= 0.322 Chirality : 0.038 0.500 24562 Planarity : 0.005 0.090 12214 Dihedral : 22.944 179.777 59282 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.28 % Favored : 92.30 % Rotamer: Outliers : 5.42 % Allowed : 17.15 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.10), residues: 6348 helix: -0.68 (0.11), residues: 2010 sheet: -0.82 (0.16), residues: 929 loop : -1.57 (0.10), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 147 HIS 0.013 0.001 HIS W 59 PHE 0.027 0.002 PHE F 229 TYR 0.033 0.002 TYR C 194 ARG 0.008 0.001 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1114 time to evaluate : 5.990 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: B 187 SER cc_start: 0.8155 (t) cc_final: 0.7799 (t) REVERT: B 227 GLU cc_start: 0.6847 (tp30) cc_final: 0.6564 (tp30) REVERT: C 260 GLN cc_start: 0.7648 (mp-120) cc_final: 0.7247 (mp10) REVERT: D 35 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7865 (mtm-85) REVERT: D 120 LYS cc_start: 0.8017 (mttt) cc_final: 0.7662 (mmtt) REVERT: D 273 ARG cc_start: 0.6758 (ptm-80) cc_final: 0.5219 (tpp80) REVERT: E 57 HIS cc_start: 0.7838 (t70) cc_final: 0.7091 (p-80) REVERT: F 145 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7999 (ttt-90) REVERT: G 38 GLN cc_start: 0.7633 (pm20) cc_final: 0.6407 (pm20) REVERT: G 84 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7688 (mtm180) REVERT: G 202 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6870 (mm-30) REVERT: H 171 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6267 (t70) REVERT: J 53 THR cc_start: 0.7193 (m) cc_final: 0.6962 (p) REVERT: L 117 LYS cc_start: 0.7550 (mmtp) cc_final: 0.6919 (ttpp) REVERT: L 176 GLU cc_start: 0.7386 (tp30) cc_final: 0.7149 (mm-30) REVERT: N 119 TYR cc_start: 0.8425 (p90) cc_final: 0.8185 (p90) REVERT: P 120 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7538 (p0) REVERT: P 126 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7388 (mtm-85) REVERT: R 72 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: R 111 ASP cc_start: 0.8680 (m-30) cc_final: 0.8433 (m-30) REVERT: R 140 GLU cc_start: 0.8044 (tp30) cc_final: 0.7794 (tm-30) REVERT: S 13 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8030 (tpt90) REVERT: S 61 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7618 (tp) REVERT: S 89 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6852 (m110) REVERT: T 92 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.5921 (mtp180) REVERT: V 56 ASP cc_start: 0.8049 (t70) cc_final: 0.7375 (t0) REVERT: X 33 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7123 (mtp-110) REVERT: X 74 LYS cc_start: 0.7788 (tptm) cc_final: 0.7478 (tptm) REVERT: X 104 GLU cc_start: 0.8294 (mp0) cc_final: 0.7726 (mp0) REVERT: Z 6 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8101 (mtpp) REVERT: b 29 TYR cc_start: 0.8323 (m-80) cc_final: 0.7932 (m-10) REVERT: e 60 ASN cc_start: 0.8522 (t0) cc_final: 0.8267 (t0) REVERT: f 92 LYS cc_start: 0.7987 (pttp) cc_final: 0.7756 (pttp) REVERT: g 55 SER cc_start: 0.8902 (m) cc_final: 0.8452 (p) REVERT: h 109 ILE cc_start: 0.8780 (mt) cc_final: 0.8509 (mt) REVERT: i 67 LYS cc_start: 0.8360 (tttm) cc_final: 0.8117 (mmtm) REVERT: j 76 ASN cc_start: 0.7428 (m-40) cc_final: 0.7195 (m110) REVERT: j 82 SER cc_start: 0.8435 (p) cc_final: 0.8219 (m) REVERT: k 74 LYS cc_start: 0.7297 (mttm) cc_final: 0.7096 (ptmm) REVERT: o 38 GLN cc_start: 0.8768 (tp40) cc_final: 0.8494 (tp-100) REVERT: o 45 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6394 (ttm-80) REVERT: o 71 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7013 (tmm160) REVERT: p 89 MET cc_start: 0.7778 (ttm) cc_final: 0.7327 (ttp) REVERT: w 220 ILE cc_start: 0.4384 (OUTLIER) cc_final: 0.4118 (pt) REVERT: w 284 GLN cc_start: 0.5508 (tt0) cc_final: 0.5265 (tt0) REVERT: w 286 MET cc_start: 0.7583 (ttm) cc_final: 0.6805 (tpp) REVERT: w 293 THR cc_start: 0.8258 (p) cc_final: 0.8011 (t) REVERT: w 358 HIS cc_start: 0.6270 (t70) cc_final: 0.6022 (t-90) REVERT: y 4 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6559 (mtt-85) REVERT: y 12 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7976 (mp0) REVERT: y 80 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6974 (mt-10) outliers start: 290 outliers final: 232 residues processed: 1275 average time/residue: 1.1482 time to fit residues: 2506.7596 Evaluate side-chains 1303 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1059 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 66 LYS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 217 VAL Chi-restraints excluded: chain w residue 220 ILE Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 340 VAL Chi-restraints excluded: chain w residue 342 ARG Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 377 SER Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 403 GLN Chi-restraints excluded: chain z residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 893 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 528 optimal weight: 2.9990 chunk 676 optimal weight: 5.9990 chunk 524 optimal weight: 1.9990 chunk 780 optimal weight: 4.9990 chunk 517 optimal weight: 7.9990 chunk 923 optimal weight: 10.0000 chunk 577 optimal weight: 10.0000 chunk 562 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN O 122 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN c 11 ASN d 57 GLN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 132421 Z= 0.275 Angle : 0.625 15.676 195281 Z= 0.324 Chirality : 0.039 0.453 24562 Planarity : 0.005 0.089 12214 Dihedral : 22.910 179.652 59282 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.31 % Favored : 92.28 % Rotamer: Outliers : 5.20 % Allowed : 17.97 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.10), residues: 6348 helix: -0.61 (0.11), residues: 2014 sheet: -0.86 (0.16), residues: 936 loop : -1.58 (0.10), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 12 HIS 0.017 0.001 HIS W 59 PHE 0.030 0.002 PHE W 55 TYR 0.046 0.002 TYR w 379 ARG 0.008 0.001 ARG o 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1098 time to evaluate : 5.978 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: B 187 SER cc_start: 0.8148 (t) cc_final: 0.7791 (t) REVERT: B 227 GLU cc_start: 0.6838 (tp30) cc_final: 0.6574 (tp30) REVERT: B 232 ARG cc_start: 0.7832 (ttt-90) cc_final: 0.7567 (ttt-90) REVERT: B 261 MET cc_start: 0.8546 (mmm) cc_final: 0.8258 (mmp) REVERT: B 333 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8218 (mttt) REVERT: B 352 GLU cc_start: 0.7021 (mp0) cc_final: 0.6818 (mp0) REVERT: C 260 GLN cc_start: 0.7565 (mp-120) cc_final: 0.7176 (mp10) REVERT: D 35 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7792 (mtm-85) REVERT: D 120 LYS cc_start: 0.7958 (mttt) cc_final: 0.7624 (mmtt) REVERT: D 208 MET cc_start: 0.6935 (mtp) cc_final: 0.6660 (mtp) REVERT: D 273 ARG cc_start: 0.6890 (ptm-80) cc_final: 0.5351 (tpp80) REVERT: F 145 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7908 (ttt-90) REVERT: G 38 GLN cc_start: 0.7600 (pm20) cc_final: 0.6364 (pm20) REVERT: G 84 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7737 (mtm180) REVERT: G 202 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6950 (mm-30) REVERT: G 231 LYS cc_start: 0.8297 (mttt) cc_final: 0.7959 (ttpt) REVERT: H 171 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6384 (t70) REVERT: J 53 THR cc_start: 0.7121 (m) cc_final: 0.6905 (p) REVERT: L 117 LYS cc_start: 0.7527 (mmtp) cc_final: 0.6902 (ttpp) REVERT: L 176 GLU cc_start: 0.7406 (tp30) cc_final: 0.7177 (mm-30) REVERT: P 120 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7559 (p0) REVERT: P 126 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7385 (mtm-85) REVERT: R 111 ASP cc_start: 0.8684 (m-30) cc_final: 0.8441 (m-30) REVERT: R 140 GLU cc_start: 0.8055 (tp30) cc_final: 0.7787 (tm-30) REVERT: S 13 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8073 (tpt90) REVERT: S 61 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7642 (tp) REVERT: S 89 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6904 (m110) REVERT: V 56 ASP cc_start: 0.8036 (t70) cc_final: 0.7361 (t0) REVERT: X 33 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7110 (mtp-110) REVERT: X 74 LYS cc_start: 0.7780 (tptm) cc_final: 0.7015 (mtmt) REVERT: X 104 GLU cc_start: 0.8367 (mp0) cc_final: 0.7874 (mp0) REVERT: X 115 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8555 (mtm180) REVERT: e 60 ASN cc_start: 0.8521 (t0) cc_final: 0.8280 (t0) REVERT: g 55 SER cc_start: 0.8915 (m) cc_final: 0.8455 (p) REVERT: i 67 LYS cc_start: 0.8310 (tttm) cc_final: 0.8099 (mmtm) REVERT: i 90 MET cc_start: 0.6741 (mmp) cc_final: 0.6313 (mmp) REVERT: j 76 ASN cc_start: 0.7061 (m-40) cc_final: 0.6849 (m110) REVERT: j 82 SER cc_start: 0.8432 (p) cc_final: 0.8207 (m) REVERT: k 74 LYS cc_start: 0.7423 (mttm) cc_final: 0.7140 (ptmm) REVERT: o 38 GLN cc_start: 0.8752 (tp40) cc_final: 0.8453 (tp-100) REVERT: o 45 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6390 (ttm-80) REVERT: o 71 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7050 (tmm160) REVERT: p 89 MET cc_start: 0.7726 (ttm) cc_final: 0.7337 (ttp) REVERT: w 270 ILE cc_start: 0.7334 (tt) cc_final: 0.7003 (tt) REVERT: w 284 GLN cc_start: 0.5396 (tt0) cc_final: 0.5123 (tt0) REVERT: w 286 MET cc_start: 0.7613 (ttm) cc_final: 0.6815 (tpp) REVERT: w 293 THR cc_start: 0.8323 (p) cc_final: 0.8108 (t) REVERT: y 1 MET cc_start: 0.5985 (tpp) cc_final: 0.5746 (tpp) REVERT: y 4 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6580 (mtt-85) REVERT: y 80 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6921 (mt-10) REVERT: y 123 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7398 (mmm-85) outliers start: 278 outliers final: 233 residues processed: 1254 average time/residue: 1.2374 time to fit residues: 2682.3469 Evaluate side-chains 1311 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1069 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain X residue 105 VAL Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 66 LYS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain w residue 217 VAL Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 340 VAL Chi-restraints excluded: chain w residue 342 ARG Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 357 SER Chi-restraints excluded: chain w residue 377 SER Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 571 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 551 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 587 optimal weight: 2.9990 chunk 629 optimal weight: 0.0570 chunk 456 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 725 optimal weight: 10.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 109 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN J 150 ASN N 122 ASN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN S 142 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN d 57 GLN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 225 GLN ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 412 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 132421 Z= 0.334 Angle : 0.674 14.394 195281 Z= 0.348 Chirality : 0.041 0.466 24562 Planarity : 0.005 0.090 12214 Dihedral : 22.948 179.770 59282 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.97 % Favored : 91.60 % Rotamer: Outliers : 5.74 % Allowed : 17.86 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.10), residues: 6348 helix: -0.71 (0.11), residues: 2027 sheet: -0.92 (0.16), residues: 941 loop : -1.64 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 12 HIS 0.014 0.002 HIS B 109 PHE 0.032 0.002 PHE i 39 TYR 0.054 0.002 TYR w 379 ARG 0.010 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1088 time to evaluate : 6.102 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: B 5 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8115 (tptt) REVERT: B 227 GLU cc_start: 0.6889 (tp30) cc_final: 0.6594 (tp30) REVERT: D 35 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7783 (mtm-85) REVERT: D 120 LYS cc_start: 0.7996 (mttt) cc_final: 0.7666 (mmtt) REVERT: D 273 ARG cc_start: 0.6955 (ptm-80) cc_final: 0.5406 (tpp80) REVERT: F 59 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7213 (mt-10) REVERT: F 145 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7984 (ttt-90) REVERT: G 33 ASN cc_start: 0.7744 (t0) cc_final: 0.7414 (t0) REVERT: G 38 GLN cc_start: 0.7779 (pm20) cc_final: 0.6505 (pm20) REVERT: G 84 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7891 (mtm180) REVERT: G 202 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6907 (mm-30) REVERT: G 226 TYR cc_start: 0.8525 (t80) cc_final: 0.8174 (t80) REVERT: H 171 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6444 (t70) REVERT: J 53 THR cc_start: 0.7152 (m) cc_final: 0.6922 (p) REVERT: J 78 GLU cc_start: 0.8354 (tp30) cc_final: 0.8073 (mp0) REVERT: L 117 LYS cc_start: 0.7528 (mmtp) cc_final: 0.6864 (ttpp) REVERT: L 127 PRO cc_start: 0.8432 (Cg_exo) cc_final: 0.8225 (Cg_endo) REVERT: L 176 GLU cc_start: 0.7474 (tp30) cc_final: 0.7258 (mm-30) REVERT: P 120 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7678 (p0) REVERT: P 126 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7405 (mtm-85) REVERT: Q 95 GLU cc_start: 0.6557 (tm-30) cc_final: 0.5955 (tm-30) REVERT: R 72 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: R 111 ASP cc_start: 0.8693 (m-30) cc_final: 0.8433 (m-30) REVERT: R 140 GLU cc_start: 0.8095 (tp30) cc_final: 0.7805 (tm-30) REVERT: S 13 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8111 (tpt90) REVERT: S 61 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7624 (tp) REVERT: T 58 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7818 (tp-100) REVERT: T 92 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.5960 (mtp180) REVERT: T 106 LEU cc_start: 0.8317 (mm) cc_final: 0.8111 (mm) REVERT: U 61 THR cc_start: 0.7897 (m) cc_final: 0.7618 (p) REVERT: V 56 ASP cc_start: 0.8024 (t70) cc_final: 0.7369 (t0) REVERT: W 30 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7815 (ttm110) REVERT: X 33 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7281 (mtp-110) REVERT: X 74 LYS cc_start: 0.7826 (tptm) cc_final: 0.7066 (mtmt) REVERT: X 104 GLU cc_start: 0.8365 (mp0) cc_final: 0.7861 (mp0) REVERT: X 115 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8552 (mtm180) REVERT: X 138 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8386 (ttp80) REVERT: a 21 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7467 (mtt180) REVERT: b 29 TYR cc_start: 0.8411 (m-80) cc_final: 0.8032 (m-10) REVERT: e 60 ASN cc_start: 0.8520 (t0) cc_final: 0.8268 (t0) REVERT: f 21 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7579 (mtm-85) REVERT: g 55 SER cc_start: 0.8927 (m) cc_final: 0.8463 (p) REVERT: h 109 ILE cc_start: 0.8801 (mt) cc_final: 0.8530 (mt) REVERT: i 67 LYS cc_start: 0.8299 (tttm) cc_final: 0.8035 (mptt) REVERT: j 82 SER cc_start: 0.8397 (p) cc_final: 0.8193 (m) REVERT: o 36 PHE cc_start: 0.7372 (m-80) cc_final: 0.7148 (m-80) REVERT: o 38 GLN cc_start: 0.8821 (tp40) cc_final: 0.8551 (tp-100) REVERT: o 45 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6412 (ttm-80) REVERT: o 71 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7067 (tmm160) REVERT: p 89 MET cc_start: 0.7623 (ttm) cc_final: 0.7235 (ttp) REVERT: w 286 MET cc_start: 0.7603 (ttm) cc_final: 0.6830 (tpp) REVERT: y 1 MET cc_start: 0.5982 (tpp) cc_final: 0.5706 (tpp) REVERT: y 4 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6606 (mtt-85) REVERT: y 80 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6911 (mt-10) REVERT: z 393 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6817 (tm-30) outliers start: 307 outliers final: 258 residues processed: 1265 average time/residue: 1.1391 time to fit residues: 2482.0246 Evaluate side-chains 1324 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1054 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 121 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 122 ASN Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 180 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain T residue 58 GLN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 66 LYS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain w residue 217 VAL Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 340 VAL Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 357 SER Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 4 ARG Chi-restraints excluded: chain y residue 51 THR Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 147 LEU Chi-restraints excluded: chain y residue 187 ASN Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 403 GLN Chi-restraints excluded: chain z residue 412 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 839 optimal weight: 5.9990 chunk 884 optimal weight: 0.9980 chunk 807 optimal weight: 7.9990 chunk 860 optimal weight: 4.9990 chunk 517 optimal weight: 8.9990 chunk 374 optimal weight: 0.8980 chunk 675 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 777 optimal weight: 2.9990 chunk 813 optimal weight: 7.9990 chunk 857 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN N 122 ASN O 122 GLN S 142 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN d 57 GLN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 132421 Z= 0.223 Angle : 0.608 13.911 195281 Z= 0.318 Chirality : 0.038 0.451 24562 Planarity : 0.005 0.087 12214 Dihedral : 22.917 179.451 59282 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.28 % Favored : 92.36 % Rotamer: Outliers : 4.82 % Allowed : 19.24 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.10), residues: 6348 helix: -0.50 (0.11), residues: 2014 sheet: -0.91 (0.16), residues: 948 loop : -1.57 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 12 HIS 0.007 0.001 HIS a 40 PHE 0.034 0.002 PHE D 260 TYR 0.055 0.002 TYR w 379 ARG 0.011 0.001 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1088 time to evaluate : 5.996 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: B 5 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8091 (tptt) REVERT: B 227 GLU cc_start: 0.6750 (tp30) cc_final: 0.6496 (tp30) REVERT: C 260 GLN cc_start: 0.7571 (mp-120) cc_final: 0.7205 (mp10) REVERT: D 120 LYS cc_start: 0.7986 (mttt) cc_final: 0.7657 (mmtt) REVERT: F 59 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7214 (mt-10) REVERT: F 145 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7878 (ttt-90) REVERT: G 33 ASN cc_start: 0.7724 (t0) cc_final: 0.7415 (t0) REVERT: G 38 GLN cc_start: 0.7693 (pm20) cc_final: 0.6391 (pm20) REVERT: G 84 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7876 (mtm180) REVERT: G 157 VAL cc_start: 0.7936 (t) cc_final: 0.7492 (t) REVERT: G 202 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6934 (mm-30) REVERT: G 226 TYR cc_start: 0.8450 (t80) cc_final: 0.8090 (t80) REVERT: G 231 LYS cc_start: 0.8253 (mttt) cc_final: 0.7890 (ttpt) REVERT: H 171 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6357 (t70) REVERT: J 53 THR cc_start: 0.7136 (m) cc_final: 0.6905 (p) REVERT: J 78 GLU cc_start: 0.8300 (tp30) cc_final: 0.8067 (mp0) REVERT: L 117 LYS cc_start: 0.7567 (mmtp) cc_final: 0.6874 (ttpp) REVERT: L 127 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8194 (Cg_endo) REVERT: L 176 GLU cc_start: 0.7450 (tp30) cc_final: 0.7234 (mm-30) REVERT: N 38 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7961 (tpt90) REVERT: P 120 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7605 (p0) REVERT: P 126 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7313 (mtm-85) REVERT: Q 95 GLU cc_start: 0.6523 (tm-30) cc_final: 0.5919 (tm-30) REVERT: R 72 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: R 111 ASP cc_start: 0.8688 (m-30) cc_final: 0.8451 (m-30) REVERT: R 140 GLU cc_start: 0.8066 (tp30) cc_final: 0.7798 (tm-30) REVERT: S 13 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (tpt90) REVERT: W 30 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7853 (ttm110) REVERT: X 33 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7195 (mtp-110) REVERT: X 74 LYS cc_start: 0.7790 (tptm) cc_final: 0.7017 (mtmt) REVERT: X 104 GLU cc_start: 0.8427 (mp0) cc_final: 0.7943 (mp0) REVERT: X 115 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8518 (mtm180) REVERT: X 138 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8339 (ttp80) REVERT: b 29 TYR cc_start: 0.8330 (m-80) cc_final: 0.8010 (m-10) REVERT: e 60 ASN cc_start: 0.8505 (t0) cc_final: 0.8251 (t0) REVERT: g 55 SER cc_start: 0.8892 (m) cc_final: 0.8447 (p) REVERT: h 109 ILE cc_start: 0.8767 (mt) cc_final: 0.8485 (mt) REVERT: i 67 LYS cc_start: 0.8268 (tttm) cc_final: 0.8031 (mptt) REVERT: j 82 SER cc_start: 0.8413 (p) cc_final: 0.8189 (m) REVERT: k 74 LYS cc_start: 0.7467 (mttm) cc_final: 0.7122 (ptmm) REVERT: l 41 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: o 38 GLN cc_start: 0.8764 (tp40) cc_final: 0.8469 (tp-100) REVERT: o 45 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6411 (ttm-80) REVERT: o 71 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7015 (tmm160) REVERT: p 89 MET cc_start: 0.7716 (ttm) cc_final: 0.7342 (ttp) REVERT: w 247 GLU cc_start: 0.4616 (pm20) cc_final: 0.4286 (tp30) REVERT: w 284 GLN cc_start: 0.5409 (tt0) cc_final: 0.5109 (tt0) REVERT: w 286 MET cc_start: 0.7567 (ttm) cc_final: 0.6838 (tpp) REVERT: w 351 GLN cc_start: 0.5040 (mm-40) cc_final: 0.4791 (mm-40) REVERT: y 1 MET cc_start: 0.5975 (tpp) cc_final: 0.5723 (tpp) REVERT: z 393 GLN cc_start: 0.7162 (tm-30) cc_final: 0.6820 (tm-30) REVERT: z 401 MET cc_start: 0.7488 (mtt) cc_final: 0.7126 (mtp) outliers start: 258 outliers final: 222 residues processed: 1236 average time/residue: 1.0907 time to fit residues: 2310.1766 Evaluate side-chains 1295 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1065 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 127 LEU Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 66 LYS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 340 VAL Chi-restraints excluded: chain w residue 342 ARG Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 357 SER Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 403 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 565 optimal weight: 4.9990 chunk 909 optimal weight: 0.9980 chunk 555 optimal weight: 5.9990 chunk 431 optimal weight: 9.9990 chunk 632 optimal weight: 6.9990 chunk 954 optimal weight: 10.0000 chunk 878 optimal weight: 9.9990 chunk 760 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 587 optimal weight: 10.0000 chunk 466 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN S 122 HIS S 142 GLN ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 412 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 132421 Z= 0.309 Angle : 0.651 13.928 195281 Z= 0.336 Chirality : 0.040 0.635 24562 Planarity : 0.005 0.088 12214 Dihedral : 22.911 179.629 59282 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.08 % Favored : 91.52 % Rotamer: Outliers : 4.94 % Allowed : 19.52 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 6348 helix: -0.57 (0.11), residues: 2018 sheet: -0.90 (0.16), residues: 940 loop : -1.62 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 95 HIS 0.010 0.001 HIS a 40 PHE 0.033 0.002 PHE D 260 TYR 0.058 0.002 TYR w 379 ARG 0.008 0.001 ARG o 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12696 Ramachandran restraints generated. 6348 Oldfield, 0 Emsley, 6348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1066 time to evaluate : 5.937 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: B 5 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8095 (tptt) REVERT: B 227 GLU cc_start: 0.6776 (tp30) cc_final: 0.6502 (tp30) REVERT: B 333 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8146 (mttt) REVERT: D 120 LYS cc_start: 0.8000 (mttt) cc_final: 0.7669 (mmtt) REVERT: F 59 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7158 (mt-10) REVERT: F 145 ARG cc_start: 0.8271 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: G 33 ASN cc_start: 0.7725 (t0) cc_final: 0.7422 (t0) REVERT: G 38 GLN cc_start: 0.7769 (pm20) cc_final: 0.6468 (pm20) REVERT: G 84 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7897 (mtm180) REVERT: G 202 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6961 (mm-30) REVERT: G 226 TYR cc_start: 0.8503 (t80) cc_final: 0.8140 (t80) REVERT: H 171 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6392 (t70) REVERT: J 53 THR cc_start: 0.7142 (m) cc_final: 0.6891 (p) REVERT: L 117 LYS cc_start: 0.7591 (mmtp) cc_final: 0.6888 (ttpp) REVERT: L 176 GLU cc_start: 0.7472 (tp30) cc_final: 0.7266 (mm-30) REVERT: N 119 TYR cc_start: 0.8481 (p90) cc_final: 0.8153 (p90) REVERT: P 120 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7613 (p0) REVERT: P 126 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7329 (mtm-85) REVERT: Q 95 GLU cc_start: 0.6604 (tm-30) cc_final: 0.5984 (tm-30) REVERT: R 72 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: R 111 ASP cc_start: 0.8721 (m-30) cc_final: 0.8485 (m-30) REVERT: R 140 GLU cc_start: 0.8085 (tp30) cc_final: 0.7793 (tm-30) REVERT: S 13 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8035 (tpt90) REVERT: S 61 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7610 (tp) REVERT: S 93 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6294 (mm-30) REVERT: T 58 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7864 (tp-100) REVERT: W 17 ARG cc_start: 0.7467 (mmt180) cc_final: 0.7249 (mmt-90) REVERT: W 30 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7816 (ttm110) REVERT: X 33 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7295 (mtp-110) REVERT: X 74 LYS cc_start: 0.7749 (tptm) cc_final: 0.7025 (mtmt) REVERT: X 104 GLU cc_start: 0.8432 (mp0) cc_final: 0.7941 (mp0) REVERT: X 138 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8536 (ttp80) REVERT: a 21 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7487 (mtt180) REVERT: b 29 TYR cc_start: 0.8388 (m-80) cc_final: 0.8000 (m-10) REVERT: e 60 ASN cc_start: 0.8514 (t0) cc_final: 0.8262 (t0) REVERT: g 55 SER cc_start: 0.8915 (m) cc_final: 0.8458 (p) REVERT: h 109 ILE cc_start: 0.8770 (mt) cc_final: 0.8490 (mt) REVERT: i 67 LYS cc_start: 0.8307 (tttm) cc_final: 0.8042 (mptt) REVERT: k 74 LYS cc_start: 0.7432 (mttm) cc_final: 0.7115 (ptmm) REVERT: l 41 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8245 (mmm-85) REVERT: o 38 GLN cc_start: 0.8804 (tp40) cc_final: 0.8520 (tp-100) REVERT: o 45 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6388 (ttm-80) REVERT: o 71 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7047 (tmm160) REVERT: p 89 MET cc_start: 0.7630 (ttm) cc_final: 0.7256 (ttp) REVERT: w 284 GLN cc_start: 0.5424 (tt0) cc_final: 0.5065 (tt0) REVERT: w 286 MET cc_start: 0.7548 (ttm) cc_final: 0.6817 (tpp) REVERT: y 1 MET cc_start: 0.5954 (tpp) cc_final: 0.5707 (tpp) REVERT: z 393 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6818 (tm-30) REVERT: z 401 MET cc_start: 0.7519 (mtt) cc_final: 0.7169 (mtp) outliers start: 264 outliers final: 242 residues processed: 1220 average time/residue: 1.1152 time to fit residues: 2334.6412 Evaluate side-chains 1295 residues out of total 5382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1043 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 234 GLU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 62 THR Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 124 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 155 MET Chi-restraints excluded: chain Q residue 165 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 72 GLU Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain T residue 58 GLN Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 SER Chi-restraints excluded: chain V residue 122 CYS Chi-restraints excluded: chain V residue 125 LEU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain X residue 88 MET Chi-restraints excluded: chain Y residue 32 SER Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain a residue 46 ASP Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 77 LYS Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 27 TYR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 62 LEU Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 100 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 51 LEU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 96 GLU Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 20 MET Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain k residue 22 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 48 SER Chi-restraints excluded: chain k residue 65 LEU Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 34 THR Chi-restraints excluded: chain o residue 4 VAL Chi-restraints excluded: chain o residue 45 ARG Chi-restraints excluded: chain o residue 66 LYS Chi-restraints excluded: chain o residue 69 VAL Chi-restraints excluded: chain o residue 71 ARG Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 LEU Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain w residue 271 SER Chi-restraints excluded: chain w residue 279 ILE Chi-restraints excluded: chain w residue 283 VAL Chi-restraints excluded: chain w residue 311 ASP Chi-restraints excluded: chain w residue 313 THR Chi-restraints excluded: chain w residue 340 VAL Chi-restraints excluded: chain w residue 342 ARG Chi-restraints excluded: chain w residue 343 THR Chi-restraints excluded: chain w residue 357 SER Chi-restraints excluded: chain w residue 374 ILE Chi-restraints excluded: chain w residue 389 ILE Chi-restraints excluded: chain w residue 397 LEU Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 198 VAL Chi-restraints excluded: chain y residue 224 LEU Chi-restraints excluded: chain z residue 403 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 603 optimal weight: 6.9990 chunk 809 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 700 optimal weight: 7.9990 chunk 112 optimal weight: 50.0000 chunk 211 optimal weight: 10.0000 chunk 761 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 781 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 GLN ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN N 122 ASN ** N 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN R 118 HIS S 142 GLN ** T 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 GLN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.149262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.119843 restraints weight = 193214.193| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.52 r_work: 0.3565 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 132421 Z= 0.392 Angle : 0.720 16.878 195281 Z= 0.369 Chirality : 0.043 0.533 24562 Planarity : 0.006 0.090 12214 Dihedral : 22.973 179.486 59282 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.48 % Favored : 91.13 % Rotamer: Outliers : 5.01 % Allowed : 19.60 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.03 % Twisted Proline : 0.43 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6348 helix: -0.74 (0.11), residues: 2018 sheet: -0.98 (0.16), residues: 955 loop : -1.74 (0.10), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP O 147 HIS 0.013 0.002 HIS a 40 PHE 0.033 0.002 PHE D 260 TYR 0.042 0.002 TYR C 194 ARG 0.009 0.001 ARG y 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36129.58 seconds wall clock time: 627 minutes 18.77 seconds (37638.77 seconds total)