Starting phenix.real_space_refine on Mon Apr 15 06:02:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu9_42576/04_2024/8uu9_42576_updated.pdb" } resolution = 3.1 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= -0.002 sd= 1.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4613 5.49 5 Mg 475 5.21 5 S 122 5.16 5 C 70667 2.51 5 N 26230 2.21 5 O 40066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 223": "OE1" <-> "OE2" Residue "e ASP 67": "OD1" <-> "OD2" Residue "f TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "p ASP 30": "OD1" <-> "OD2" Residue "p GLU 35": "OE1" <-> "OE2" Residue "p ASP 68": "OD1" <-> "OD2" Residue "r ASP 29": "OD1" <-> "OD2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 179": "OD1" <-> "OD2" Residue "v GLU 303": "OE1" <-> "OE2" Residue "v PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 391": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "F ASP 6": "OD1" <-> "OD2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "P GLU 28": "OE1" <-> "OE2" Residue "P GLU 39": "OE1" <-> "OE2" Residue "P ASP 100": "OD1" <-> "OD2" Residue "P TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "U PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 114": "OE1" <-> "OE2" Residue "V GLU 43": "OE1" <-> "OE2" Residue "Y TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 64": "OD1" <-> "OD2" Residue "Y ASP 72": "OD1" <-> "OD2" Residue "2 ASP 39": "OD1" <-> "OD2" Residue "3 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 142177 Number of models: 1 Model: "" Number of chains: 90 Chain: "a" Number of atoms: 32493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32493 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 114, 'rna2p_pyr': 79, 'rna3p_pur': 745, 'rna3p_pyr': 577} Link IDs: {'rna2p': 193, 'rna3p': 1321} Chain breaks: 3 Chain: "b" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1588 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 123 Chain: "c" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1150 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 200} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 489 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 298 Chain: "d" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 191} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "e" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1116 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 148} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "f" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 655 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 91} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 88 Chain: "g" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 866 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 169 Chain: "h" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1022 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 833 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'ARG%COO:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "j" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 608 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 89} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "k" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 824 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1002 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "m" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 616 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 5, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 158 Chain: "n" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 445 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "o" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 696 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "p" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 711 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 629 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "r" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 527 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "s" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 459 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "t" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 79} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "x" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1591 Classifications: {'RNA': 74} Modifications used: {'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "v" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3200 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 405} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 62278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2899, 62278 Classifications: {'RNA': 2899} Modifications used: {'rna2p_pur': 311, 'rna2p_pyr': 150, 'rna3p_pur': 1392, 'rna3p_pyr': 1046} Link IDs: {'rna2p': 461, 'rna3p': 2437} Chain breaks: 3 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2428 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "C" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1545 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1564 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1232 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1318 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 165} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1128 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1112 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "O" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1057 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 867 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'PHE%COO:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "U" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "V" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 760 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "W" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 734 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 93} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Y" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 585 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Z" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 462 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "2" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "3" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 424 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "4" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "5" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 394 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 365 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 529 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "8" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "a" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Unusual residues: {' MG': 202} Classifications: {'undetermined': 202} Link IDs: {None: 201} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 3, 'GCP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Unusual residues: {' MG': 256} Classifications: {'undetermined': 256} Link IDs: {None: 255} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 255 Classifications: {'water': 255} Link IDs: {None: 254} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44464 SG CYS n 24 119.962 178.385 58.698 1.00 49.53 S ATOM 44490 SG CYS n 27 119.328 174.682 60.589 1.00 50.28 S ATOM 44587 SG CYS n 40 122.595 176.594 60.579 1.00 40.43 S ATOM 44612 SG CYS n 43 121.191 175.355 57.362 1.00 41.17 S ATOM A0UHC SG CYS 4 30 88.661 43.159 195.413 1.00 90.03 S ATOM A0UHW SG CYS 4 33 91.829 43.960 197.364 1.00 95.03 S ATOM A0UK7 SG CYS 4 43 91.874 43.876 193.440 1.00 85.08 S ATOM A0UKT SG CYS 4 46 91.886 40.824 195.468 1.00 95.57 S ATOM A0UOI SG CYS 5 9 135.496 190.535 175.727 1.00 81.89 S ATOM A0UP4 SG CYS 5 12 136.751 190.122 179.419 1.00 86.47 S ATOM A0UUH SG CYS 5 36 133.104 189.409 178.552 1.00 75.27 S ATOM A0VON SG CYS 8 11 47.237 128.589 128.512 1.00 83.36 S ATOM A0VPB SG CYS 8 14 48.381 126.921 131.702 1.00 81.11 S ATOM A0VS7 SG CYS 8 27 46.366 124.879 129.240 1.00 76.44 S Time building chain proxies: 55.17, per 1000 atoms: 0.39 Number of scatterers: 142177 At special positions: 0 Unit cell: (226.1, 245.65, 277.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 122 16.00 P 4613 15.00 Mg 475 11.99 O 40066 8.00 N 26230 7.00 C 70667 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: 56.34 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " Number of angles added : 15 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10494 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 167 helices and 73 sheets defined 37.5% alpha, 18.9% beta 1585 base pairs and 2453 stacking pairs defined. Time for finding SS restraints: 72.88 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.122A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.718A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU b 59 " --> pdb=" O ASN b 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA b 61 " --> pdb=" O MET b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.774A pdb=" N LYS b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS b 119 " --> pdb=" O LYS b 115 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU b 121 " --> pdb=" O ILE b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 149 removed outlier: 3.652A pdb=" N GLU b 140 " --> pdb=" O LEU b 136 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN b 141 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU b 142 " --> pdb=" O LYS b 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.817A pdb=" N ARG b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 removed outlier: 3.627A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.630A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 226 removed outlier: 3.556A pdb=" N LYS b 211 " --> pdb=" O ILE b 207 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU b 212 " --> pdb=" O ARG b 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA b 220 " --> pdb=" O LYS b 216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE b 221 " --> pdb=" O MET b 217 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN b 226 " --> pdb=" O ILE b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.209A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 4.889A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP c 40 " --> pdb=" O LEU c 36 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL c 42 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU c 46 " --> pdb=" O VAL c 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 3.888A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 4.382A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 4.019A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN c 122 " --> pdb=" O ASN c 118 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU c 124 " --> pdb=" O ALA c 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.684A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG c 139 " --> pdb=" O GLN c 135 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA c 143 " --> pdb=" O ARG c 139 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.760A pdb=" N VAL d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.838A pdb=" N GLU d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN d 55 " --> pdb=" O GLN d 51 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS d 56 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.715A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY d 76 " --> pdb=" O PHE d 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 3.583A pdb=" N ILE d 88 " --> pdb=" O GLU d 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU d 90 " --> pdb=" O PHE d 86 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.527A pdb=" N GLY d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.832A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS d 116 " --> pdb=" O GLN d 112 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.636A pdb=" N LEU d 155 " --> pdb=" O ILE d 151 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.978A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 4.259A pdb=" N LYS e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN e 71 " --> pdb=" O ASP e 67 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 removed outlier: 3.739A pdb=" N ALA e 114 " --> pdb=" O GLY e 110 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL e 115 " --> pdb=" O PRO e 111 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU e 116 " --> pdb=" O VAL e 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA e 119 " --> pdb=" O VAL e 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 149 removed outlier: 3.674A pdb=" N THR e 141 " --> pdb=" O MET e 137 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN e 147 " --> pdb=" O ASP e 143 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS e 149 " --> pdb=" O ILE e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 159 Processing helix chain 'e' and resid 161 through 166 Processing helix chain 'f' and resid 16 through 35 removed outlier: 3.641A pdb=" N ALA f 22 " --> pdb=" O ASP f 18 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL f 23 " --> pdb=" O GLU f 19 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU f 25 " --> pdb=" O LYS f 21 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY f 29 " --> pdb=" O GLU f 25 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY f 35 " --> pdb=" O LEU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 85 removed outlier: 4.054A pdb=" N ASN f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP f 85 " --> pdb=" O ALA f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.607A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE g 27 " --> pdb=" O VAL g 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS g 29 " --> pdb=" O ARG g 25 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 20 through 31' Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.502A pdb=" N ILE g 42 " --> pdb=" O LYS g 38 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR g 54 " --> pdb=" O ILE g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.885A pdb=" N ALA g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET g 66 " --> pdb=" O PHE g 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.813A pdb=" N LEU g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU g 104 " --> pdb=" O GLY g 100 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL g 105 " --> pdb=" O LEU g 101 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.827A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE g 124 " --> pdb=" O VAL g 120 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN g 130 " --> pdb=" O ASP g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.778A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.617A pdb=" N ILE h 14 " --> pdb=" O PHE h 10 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.508A pdb=" N GLU h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU h 38 " --> pdb=" O LYS h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.715A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN h 122 " --> pdb=" O ALA h 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 40 Proline residue: i 40 - end of helix Processing helix chain 'i' and resid 41 through 52 removed outlier: 3.765A pdb=" N ARG i 45 " --> pdb=" O PHE i 41 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE i 48 " --> pdb=" O LEU i 44 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN i 50 " --> pdb=" O GLU i 46 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.823A pdb=" N ALA i 76 " --> pdb=" O TYR i 72 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY i 77 " --> pdb=" O THR i 73 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA i 78 " --> pdb=" O GLY i 74 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA i 86 " --> pdb=" O GLY i 82 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU i 88 " --> pdb=" O ALA i 84 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN i 89 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 93 through 102 removed outlier: 4.803A pdb=" N ALA i 97 " --> pdb=" O GLU i 93 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER i 100 " --> pdb=" O PRO i 96 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.564A pdb=" N LEU j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.278A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU j 90 " --> pdb=" O SER j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.815A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 4.697A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 78 removed outlier: 3.668A pdb=" N ALA k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER k 69 " --> pdb=" O MET k 65 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER k 73 " --> pdb=" O SER k 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU k 76 " --> pdb=" O LYS k 72 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.535A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA k 99 " --> pdb=" O ALA k 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA k 103 " --> pdb=" O ALA k 99 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.781A pdb=" N LYS l 10 " --> pdb=" O GLN l 6 " (cutoff:3.500A) Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 21 through 27 removed outlier: 4.026A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY l 27 " --> pdb=" O ALA l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 27' Processing helix chain 'l' and resid 126 through 131 removed outlier: 4.779A pdb=" N TYR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 21 removed outlier: 3.962A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.684A pdb=" N GLU m 32 " --> pdb=" O GLN m 28 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.937A pdb=" N GLY m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG m 57 " --> pdb=" O LEU m 53 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU m 58 " --> pdb=" O GLY m 54 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE m 59 " --> pdb=" O LYS m 55 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS m 64 " --> pdb=" O LEU m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 removed outlier: 4.549A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE m 81 " --> pdb=" O ILE m 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.603A pdb=" N MET m 89 " --> pdb=" O SER m 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG m 90 " --> pdb=" O TYR m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 4.515A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY m 111 " --> pdb=" O ARG m 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 106 through 111' Processing helix chain 'n' and resid 2 through 12 removed outlier: 5.678A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 3.984A pdb=" N ALA n 20 " --> pdb=" O TYR n 16 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N TYR n 21 " --> pdb=" O ALA n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.944A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.506A pdb=" N ALA o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.550A pdb=" N ALA o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER o 38 " --> pdb=" O ALA o 34 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS o 42 " --> pdb=" O SER o 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS o 47 " --> pdb=" O VAL o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.677A pdb=" N TYR o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR o 69 " --> pdb=" O ASN o 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU o 70 " --> pdb=" O LEU o 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP o 74 " --> pdb=" O LEU o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.970A pdb=" N GLU o 80 " --> pdb=" O GLN o 76 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE o 82 " --> pdb=" O TYR o 78 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.948A pdb=" N THR p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN p 62 " --> pdb=" O LYS p 58 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY p 63 " --> pdb=" O TRP p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.777A pdb=" N ASN p 72 " --> pdb=" O ASP p 68 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.778A pdb=" N PHE p 83 " --> pdb=" O ILE p 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS p 84 " --> pdb=" O MET p 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 21 Processing helix chain 'r' and resid 29 through 38 removed outlier: 3.530A pdb=" N LYS r 34 " --> pdb=" O VAL r 30 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS r 35 " --> pdb=" O GLU r 31 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER r 38 " --> pdb=" O LYS r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 52 through 70 removed outlier: 3.909A pdb=" N LYS r 58 " --> pdb=" O LYS r 54 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET r 69 " --> pdb=" O ARG r 65 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA r 70 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 22 removed outlier: 7.581A pdb=" N MET s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS s 17 " --> pdb=" O ASP s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 4.070A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 42 removed outlier: 3.716A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU t 15 " --> pdb=" O VAL t 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG t 17 " --> pdb=" O THR t 13 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA t 31 " --> pdb=" O ALA t 27 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE t 32 " --> pdb=" O MET t 28 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 64 removed outlier: 5.052A pdb=" N VAL t 51 " --> pdb=" O LYS t 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU t 52 " --> pdb=" O ASP t 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS t 56 " --> pdb=" O GLU t 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL t 61 " --> pdb=" O LEU t 57 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS t 63 " --> pdb=" O SER t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 80 removed outlier: 4.338A pdb=" N ALA t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) Processing helix chain 'v' and resid 16 through 32 removed outlier: 3.954A pdb=" N GLU v 22 " --> pdb=" O ASP v 18 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU v 24 " --> pdb=" O SER v 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA v 25 " --> pdb=" O MET v 21 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN v 31 " --> pdb=" O LEU v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 68 removed outlier: 3.698A pdb=" N VAL v 57 " --> pdb=" O GLY v 53 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP v 58 " --> pdb=" O LYS v 54 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU v 59 " --> pdb=" O GLY v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 91 removed outlier: 3.700A pdb=" N GLU v 88 " --> pdb=" O ARG v 84 " (cutoff:3.500A) Processing helix chain 'v' and resid 96 through 109 removed outlier: 3.561A pdb=" N LEU v 102 " --> pdb=" O THR v 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN v 107 " --> pdb=" O ALA v 103 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG v 108 " --> pdb=" O ILE v 104 " (cutoff:3.500A) Processing helix chain 'v' and resid 113 through 131 removed outlier: 4.035A pdb=" N GLN v 117 " --> pdb=" O GLU v 113 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU v 126 " --> pdb=" O LYS v 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU v 127 " --> pdb=" O LEU v 123 " (cutoff:3.500A) Proline residue: v 128 - end of helix removed outlier: 4.398A pdb=" N PHE v 131 " --> pdb=" O LEU v 127 " (cutoff:3.500A) Processing helix chain 'v' and resid 154 through 192 removed outlier: 3.870A pdb=" N ILE v 163 " --> pdb=" O ASP v 159 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN v 166 " --> pdb=" O THR v 162 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE v 167 " --> pdb=" O ILE v 163 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL v 178 " --> pdb=" O LEU v 174 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP v 179 " --> pdb=" O ASP v 175 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL v 183 " --> pdb=" O ASP v 179 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG v 184 " --> pdb=" O ASP v 180 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG v 186 " --> pdb=" O GLU v 182 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS v 187 " --> pdb=" O VAL v 183 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG v 188 " --> pdb=" O ARG v 184 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU v 192 " --> pdb=" O ARG v 188 " (cutoff:3.500A) Processing helix chain 'v' and resid 205 through 217 removed outlier: 3.686A pdb=" N ARG v 215 " --> pdb=" O ASN v 211 " (cutoff:3.500A) Processing helix chain 'v' and resid 263 through 274 removed outlier: 4.039A pdb=" N LYS v 268 " --> pdb=" O HIS v 264 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA v 269 " --> pdb=" O GLN v 265 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER v 272 " --> pdb=" O LYS v 268 " (cutoff:3.500A) Processing helix chain 'v' and resid 275 through 280 Processing helix chain 'v' and resid 293 through 309 removed outlier: 3.835A pdb=" N LYS v 299 " --> pdb=" O LYS v 295 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR v 304 " --> pdb=" O THR v 300 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL v 307 " --> pdb=" O GLU v 303 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL v 308 " --> pdb=" O THR v 304 " (cutoff:3.500A) Processing helix chain 'v' and resid 321 through 326 removed outlier: 4.181A pdb=" N LEU v 325 " --> pdb=" O LYS v 321 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU v 326 " --> pdb=" O ALA v 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 321 through 326' Processing helix chain 'v' and resid 344 through 360 removed outlier: 3.516A pdb=" N LEU v 348 " --> pdb=" O GLU v 344 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU v 353 " --> pdb=" O GLU v 349 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS v 357 " --> pdb=" O GLU v 353 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU v 358 " --> pdb=" O VAL v 354 " (cutoff:3.500A) Processing helix chain 'v' and resid 375 through 385 removed outlier: 6.534A pdb=" N ALA v 379 " --> pdb=" O GLY v 375 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR v 380 " --> pdb=" O GLN v 376 " (cutoff:3.500A) Processing helix chain 'v' and resid 404 through 412 removed outlier: 4.031A pdb=" N GLN v 409 " --> pdb=" O PRO v 405 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS v 410 " --> pdb=" O ALA v 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.517A pdb=" N ILE C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.510A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.267A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.891A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'D' and resid 57 through 62 removed outlier: 4.384A pdb=" N SER D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.169A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.950A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 6.641A pdb=" N ARG E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.631A pdb=" N LYS E 117 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 4.347A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.878A pdb=" N SER E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.545A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.656A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.788A pdb=" N GLU F 11 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.622A pdb=" N LEU F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 4.437A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 removed outlier: 4.496A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 111' Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.966A pdb=" N SER F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.940A pdb=" N SER F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.315A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.533A pdb=" N ARG G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.606A pdb=" N GLU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'L' and resid 25 through 39 removed outlier: 3.654A pdb=" N GLU L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 89 through 97 removed outlier: 3.808A pdb=" N MET L 93 " --> pdb=" O THR L 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR L 95 " --> pdb=" O GLY L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 111 removed outlier: 4.020A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Proline residue: L 111 - end of helix Processing helix chain 'L' and resid 113 through 123 removed outlier: 3.614A pdb=" N LYS L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.431A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.626A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix No H-bonds generated for 'chain 'N' and resid 56 through 62' Processing helix chain 'N' and resid 78 through 84 removed outlier: 3.543A pdb=" N LEU N 82 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 100 removed outlier: 3.593A pdb=" N GLY N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 140 Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.504A pdb=" N ILE O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.627A pdb=" N HIS O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 9 through 28 Processing helix chain 'P' and resid 34 through 54 removed outlier: 4.517A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL P 43 " --> pdb=" O GLU P 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 66 removed outlier: 4.059A pdb=" N PHE P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 108 removed outlier: 3.939A pdb=" N VAL P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA P 103 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Proline residue: P 104 - end of helix removed outlier: 3.708A pdb=" N ALA P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU P 108 " --> pdb=" O PRO P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.771A pdb=" N LYS Q 21 " --> pdb=" O ARG Q 17 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE Q 22 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 88 removed outlier: 3.750A pdb=" N ALA Q 72 " --> pdb=" O SER Q 68 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA Q 73 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.736A pdb=" N ASN Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 10 Processing helix chain 'R' and resid 97 through 104 removed outlier: 4.756A pdb=" N ARG R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 97 through 104' Processing helix chain 'S' and resid 8 through 22 removed outlier: 3.728A pdb=" N LYS S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 4.618A pdb=" N HIS S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.639A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 3.877A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP S 73 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 Processing helix chain 'S' and resid 102 through 119 Processing helix chain 'U' and resid 18 through 30 removed outlier: 4.027A pdb=" N ILE U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP U 27 " --> pdb=" O ARG U 23 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG U 30 " --> pdb=" O ILE U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 45 Proline residue: U 45 - end of helix Processing helix chain 'U' and resid 48 through 66 Processing helix chain 'V' and resid 2 through 8 removed outlier: 5.162A pdb=" N LYS V 8 " --> pdb=" O ARG V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 removed outlier: 4.453A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 47 removed outlier: 4.440A pdb=" N GLU V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU V 44 " --> pdb=" O TYR V 40 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE V 46 " --> pdb=" O ILE V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 69 removed outlier: 4.620A pdb=" N VAL W 68 " --> pdb=" O HIS W 64 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET W 69 " --> pdb=" O VAL W 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.758A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 removed outlier: 3.905A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 3 through 8' Processing helix chain '1' and resid 10 through 35 removed outlier: 5.713A pdb=" N ILE 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 62 removed outlier: 3.904A pdb=" N GLU 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU 1 61 " --> pdb=" O VAL 1 57 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU 1 62 " --> pdb=" O ARG 1 58 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 Processing helix chain '3' and resid 69 through 78 removed outlier: 3.810A pdb=" N ARG 3 73 " --> pdb=" O GLY 3 69 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE 3 74 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS 3 77 " --> pdb=" O ARG 3 73 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 5.055A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.204A pdb=" N THR 6 24 " --> pdb=" O THR 6 20 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.669A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 7 14 " --> pdb=" O SER 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.092A pdb=" N LYS 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 removed outlier: 4.429A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 3.621A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.835A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 67 through 70 removed outlier: 3.537A pdb=" N VAL b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 19 through 22 removed outlier: 6.936A pdb=" N ASP c 19 " --> pdb=" O VAL c 54 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE c 56 " --> pdb=" O ASP c 19 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG c 58 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU c 55 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR c 66 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN c 101 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.826A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU c 195 " --> pdb=" O ALA c 188 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ALA c 188 " --> pdb=" O LEU c 195 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG c 203 " --> pdb=" O ASP c 180 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP c 180 " --> pdb=" O ARG c 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 136 through 140 removed outlier: 5.283A pdb=" N GLN d 137 " --> pdb=" O LEU d 176 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU d 176 " --> pdb=" O GLN d 137 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR d 164 " --> pdb=" O ASN d 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 12 through 17 removed outlier: 5.115A pdb=" N GLY e 41 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 85 through 89 removed outlier: 6.117A pdb=" N GLU e 94 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA e 100 " --> pdb=" O ASP e 123 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP e 123 " --> pdb=" O ALA e 100 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 34 through 42 removed outlier: 3.919A pdb=" N HIS e 46 " --> pdb=" O ASP e 42 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 40 through 46 removed outlier: 4.170A pdb=" N GLU f 40 " --> pdb=" O LYS f 65 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS f 42 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR f 61 " --> pdb=" O TRP f 44 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS f 46 " --> pdb=" O GLY f 59 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY f 59 " --> pdb=" O LYS f 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR f 9 " --> pdb=" O HIS f 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET f 91 " --> pdb=" O MET f 8 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.090A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU h 64 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 104 through 108 removed outlier: 6.692A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 8 through 11 Processing sheet with id= 14, first strand: chain 'j' and resid 35 through 38 removed outlier: 4.217A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU j 99 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP j 97 " --> pdb=" O LYS j 11 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 53 removed outlier: 3.783A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N SER j 61 " --> pdb=" O ARG j 53 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 30 through 35 removed outlier: 3.575A pdb=" N THR k 108 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'k' and resid 83 through 87 Processing sheet with id= 18, first strand: chain 'l' and resid 42 through 45 removed outlier: 4.948A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.647A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY l 51 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE l 80 " --> pdb=" O LYS l 64 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.501A pdb=" N THR p 39 " --> pdb=" O LYS p 50 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.873A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG q 62 " --> pdb=" O LEU q 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 's' and resid 31 through 34 removed outlier: 3.505A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'v' and resid 33 through 36 removed outlier: 7.560A pdb=" N ILE v 7 " --> pdb=" O VAL v 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'v' and resid 236 through 244 removed outlier: 7.126A pdb=" N GLU v 236 " --> pdb=" O VAL v 256 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL v 256 " --> pdb=" O GLU v 236 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER v 238 " --> pdb=" O ASP v 254 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS v 248 " --> pdb=" O LEU v 244 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU v 282 " --> pdb=" O VAL v 195 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN v 336 " --> pdb=" O VAL v 315 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'v' and resid 365 through 371 removed outlier: 3.951A pdb=" N GLY v 396 " --> pdb=" O LEU v 393 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU v 389 " --> pdb=" O VAL v 400 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'v' and resid 5 through 9 Processing sheet with id= 28, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.560A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY C 127 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.793A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.256A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.218A pdb=" N LYS D 3 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.735A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP D 180 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.821A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR D 46 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 49 through 53 removed outlier: 6.466A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 37, first strand: chain 'F' and resid 65 through 70 removed outlier: 6.359A pdb=" N VAL F 66 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA F 87 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR F 38 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'F' and resid 72 through 75 removed outlier: 4.620A pdb=" N SER F 73 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG F 80 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA F 75 " --> pdb=" O ARG F 78 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.990A pdb=" N LEU G 33 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 42 through 45 removed outlier: 4.552A pdb=" N THR G 42 " --> pdb=" O SER G 53 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.344A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.797A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN G 106 " --> pdb=" O ARG G 95 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'L' and resid 15 through 20 Processing sheet with id= 44, first strand: chain 'L' and resid 75 through 79 removed outlier: 7.414A pdb=" N GLY L 84 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.346A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER M 6 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU M 81 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG M 64 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'M' and resid 37 through 41 removed outlier: 4.492A pdb=" N ASP M 37 " --> pdb=" O ILE M 62 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'M' and resid 68 through 71 removed outlier: 4.450A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'N' and resid 74 through 77 Processing sheet with id= 49, first strand: chain 'O' and resid 38 through 42 removed outlier: 6.870A pdb=" N GLU O 38 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG O 99 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.940A pdb=" N PHE O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU O 34 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'O' and resid 31 through 37 removed outlier: 7.928A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS O 128 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'P' and resid 29 through 33 removed outlier: 4.629A pdb=" N ARG P 122 " --> pdb=" O GLY P 126 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY P 120 " --> pdb=" O PRO P 128 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL P 130 " --> pdb=" O LYS P 118 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS P 118 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE P 132 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE P 116 " --> pdb=" O ILE P 132 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU P 134 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR P 114 " --> pdb=" O LEU P 134 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'P' and resid 72 through 76 removed outlier: 3.672A pdb=" N GLU P 72 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS P 88 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Q' and resid 29 through 35 removed outlier: 3.869A pdb=" N ALA Q 54 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'R' and resid 38 through 45 removed outlier: 6.696A pdb=" N THR R 25 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'R' and resid 49 through 52 removed outlier: 3.890A pdb=" N LYS R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU R 57 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.592A pdb=" N TYR T 2 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 18 through 23 removed outlier: 4.440A pdb=" N GLN T 18 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS T 94 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR T 59 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP T 31 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 64 through 68 removed outlier: 3.502A pdb=" N GLY T 66 " --> pdb=" O TYR T 92 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLN T 90 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 7 through 13 removed outlier: 6.620A pdb=" N VAL U 111 " --> pdb=" O GLU U 77 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 84 through 93 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'V' and resid 23 through 29 removed outlier: 6.533A pdb=" N LYS V 23 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG V 76 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN V 73 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY V 60 " --> pdb=" O ASN V 73 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS V 52 " --> pdb=" O THR V 81 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS V 61 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TYR V 68 " --> pdb=" O MET V 65 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.390A pdb=" N ASN W 39 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Y' and resid 37 through 40 removed outlier: 4.466A pdb=" N GLN Y 37 " --> pdb=" O VAL Y 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Y 86 " --> pdb=" O GLU Y 78 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL Y 89 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Y' and resid 59 through 62 removed outlier: 4.470A pdb=" N THR Y 66 " --> pdb=" O GLY Y 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.230A pdb=" N SER Z 19 " --> pdb=" O ASN Z 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '2' and resid 32 through 38 removed outlier: 4.128A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 22 through 26 Processing sheet with id= 69, first strand: chain '4' and resid 28 through 31 removed outlier: 4.182A pdb=" N GLU 4 35 " --> pdb=" O CYS 4 30 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '5' and resid 4 through 7 removed outlier: 3.552A pdb=" N TYR 5 17 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '5' and resid 30 through 33 removed outlier: 6.174A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain '8' and resid 1 through 4 removed outlier: 6.275A pdb=" N HIS 8 32 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 36 " (cutoff:3.500A) 1553 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3976 hydrogen bonds 6322 hydrogen bond angles 0 basepair planarities 1585 basepair parallelities 2453 stacking parallelities Total time for adding SS restraints: 291.69 Time building geometry restraints manager: 61.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18867 1.33 - 1.45: 69114 1.45 - 1.58: 56325 1.58 - 1.71: 9210 1.71 - 1.83: 221 Bond restraints: 153737 Sorted by residual: bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N1 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.635 1.339 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C2' GCP v 502 " pdb=" C3' GCP v 502 " ideal model delta sigma weight residual 1.241 1.516 -0.275 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C5 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.155 1.386 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C13 MIA x 37 " pdb=" C14 MIA x 37 " ideal model delta sigma weight residual 1.317 1.524 -0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 153732 not shown) Histogram of bond angle deviations from ideal: 96.12 - 104.72: 20797 104.72 - 113.32: 97152 113.32 - 121.93: 77835 121.93 - 130.53: 33129 130.53 - 139.14: 1772 Bond angle restraints: 230685 Sorted by residual: angle pdb=" N GLU V 44 " pdb=" CA GLU V 44 " pdb=" C GLU V 44 " ideal model delta sigma weight residual 113.41 105.99 7.42 1.22e+00 6.72e-01 3.70e+01 angle pdb=" C TYR j 58 " pdb=" N LYS j 59 " pdb=" CA LYS j 59 " ideal model delta sigma weight residual 120.99 131.61 -10.62 1.86e+00 2.89e-01 3.26e+01 angle pdb=" C GLN L 136 " pdb=" N LYS L 137 " pdb=" CA LYS L 137 " ideal model delta sigma weight residual 121.80 134.67 -12.87 2.44e+00 1.68e-01 2.78e+01 angle pdb=" C1' GCP v 502 " pdb=" N9 GCP v 502 " pdb=" C4 GCP v 502 " ideal model delta sigma weight residual 108.44 123.50 -15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C6 5MU x 54 " pdb=" C5 5MU x 54 " pdb=" C5M 5MU x 54 " ideal model delta sigma weight residual 106.09 120.92 -14.83 3.00e+00 1.11e-01 2.44e+01 ... (remaining 230680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 87208 35.94 - 71.89: 9592 71.89 - 107.83: 1145 107.83 - 143.77: 27 143.77 - 179.72: 40 Dihedral angle restraints: 98012 sinusoidal: 81718 harmonic: 16294 Sorted by residual: dihedral pdb=" O4' U A2339 " pdb=" C1' U A2339 " pdb=" N1 U A2339 " pdb=" C2 U A2339 " ideal model delta sinusoidal sigma weight residual 200.00 22.35 177.65 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C a 476 " pdb=" C1' C a 476 " pdb=" N1 C a 476 " pdb=" C2 C a 476 " ideal model delta sinusoidal sigma weight residual -160.00 16.01 -176.01 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A1904 " pdb=" C1' C A1904 " pdb=" N1 C A1904 " pdb=" C2 C A1904 " ideal model delta sinusoidal sigma weight residual 200.00 27.58 172.42 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 98009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 27425 0.070 - 0.140: 2034 0.140 - 0.210: 200 0.210 - 0.280: 28 0.280 - 0.350: 6 Chirality restraints: 29693 Sorted by residual: chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3' G a 113 " pdb=" C4' G a 113 " pdb=" O3' G a 113 " pdb=" C2' G a 113 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C3' A a 756 " pdb=" C4' A a 756 " pdb=" O3' A a 756 " pdb=" C2' A a 756 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 29690 not shown) Planarity restraints: 12099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG x 46 " -0.846 2.00e-02 2.50e+03 5.64e-01 7.16e+03 pdb=" C4' 7MG x 46 " 0.217 2.00e-02 2.50e+03 pdb=" O4' 7MG x 46 " 0.739 2.00e-02 2.50e+03 pdb=" C3' 7MG x 46 " -0.252 2.00e-02 2.50e+03 pdb=" O3' 7MG x 46 " 0.822 2.00e-02 2.50e+03 pdb=" C2' 7MG x 46 " -0.589 2.00e-02 2.50e+03 pdb=" O2' 7MG x 46 " -0.513 2.00e-02 2.50e+03 pdb=" C1' 7MG x 46 " 0.451 2.00e-02 2.50e+03 pdb=" N9 7MG x 46 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU x 54 " 0.024 2.00e-02 2.50e+03 5.61e-01 7.08e+03 pdb=" C4' 5MU x 54 " 0.435 2.00e-02 2.50e+03 pdb=" O4' 5MU x 54 " 0.624 2.00e-02 2.50e+03 pdb=" C3' 5MU x 54 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 5MU x 54 " -0.551 2.00e-02 2.50e+03 pdb=" C2' 5MU x 54 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 5MU x 54 " 0.888 2.00e-02 2.50e+03 pdb=" C1' 5MU x 54 " 0.231 2.00e-02 2.50e+03 pdb=" N1 5MU x 54 " -0.847 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GCP v 502 " 0.377 2.00e-02 2.50e+03 3.63e-01 2.96e+03 pdb=" C2' GCP v 502 " -0.497 2.00e-02 2.50e+03 pdb=" C3' GCP v 502 " -0.378 2.00e-02 2.50e+03 pdb=" C4' GCP v 502 " 0.312 2.00e-02 2.50e+03 pdb=" C5' GCP v 502 " -0.431 2.00e-02 2.50e+03 pdb=" N9 GCP v 502 " -0.171 2.00e-02 2.50e+03 pdb=" O2' GCP v 502 " -0.033 2.00e-02 2.50e+03 pdb=" O3' GCP v 502 " 0.438 2.00e-02 2.50e+03 pdb=" O4' GCP v 502 " 0.384 2.00e-02 2.50e+03 ... (remaining 12096 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 789 2.46 - 3.07: 82602 3.07 - 3.68: 245676 3.68 - 4.29: 387873 4.29 - 4.90: 540299 Nonbonded interactions: 1257239 Sorted by model distance: nonbonded pdb=" CZ ARG Y 82 " pdb="MG MG Y 101 " model vdw 1.847 2.400 nonbonded pdb=" OP2 A A2879 " pdb="MG MG A3246 " model vdw 1.893 2.170 nonbonded pdb=" N7 G A2535 " pdb="MG MG A3238 " model vdw 1.895 2.250 nonbonded pdb=" N7 A a 928 " pdb="MG MG a3190 " model vdw 1.895 2.250 nonbonded pdb=" N6 A a 973 " pdb="MG MG a3192 " model vdw 1.896 2.250 ... (remaining 1257234 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: 6.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 31.080 Check model and map are aligned: 1.590 Set scattering table: 0.980 Process input model: 602.850 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 649.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.321 153737 Z= 0.331 Angle : 0.621 15.062 230685 Z= 0.325 Chirality : 0.039 0.350 29693 Planarity : 0.010 0.564 12099 Dihedral : 22.646 179.717 87518 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 92.99 % Rotamer: Outliers : 0.20 % Allowed : 0.42 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5610 helix: -0.92 (0.13), residues: 1661 sheet: -0.82 (0.16), residues: 1089 loop : -1.48 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP b 23 HIS 0.005 0.001 HIS c 166 PHE 0.020 0.002 PHE v 372 TYR 0.028 0.002 TYR s 52 ARG 0.012 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1042 time to evaluate : 6.151 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: b 72 THR cc_start: 0.8327 (p) cc_final: 0.8069 (p) REVERT: c 169 GLU cc_start: 0.7037 (pp20) cc_final: 0.6754 (pp20) REVERT: h 126 GLU cc_start: 0.7653 (tt0) cc_final: 0.7370 (tt0) REVERT: n 10 GLN cc_start: 0.4055 (tp40) cc_final: 0.3346 (mt0) REVERT: U 27 ASP cc_start: 0.8176 (m-30) cc_final: 0.7945 (m-30) REVERT: W 40 MET cc_start: 0.8794 (mmm) cc_final: 0.8300 (mmm) REVERT: Z 30 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8688 (mptt) REVERT: Z 39 LEU cc_start: 0.8608 (mm) cc_final: 0.8367 (mt) REVERT: 2 40 ASN cc_start: 0.8336 (m110) cc_final: 0.8036 (m-40) REVERT: 5 8 GLU cc_start: 0.8393 (tt0) cc_final: 0.8086 (tt0) outliers start: 8 outliers final: 2 residues processed: 1046 average time/residue: 1.3256 time to fit residues: 2336.4336 Evaluate side-chains 822 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 820 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain V residue 43 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 852 optimal weight: 10.0000 chunk 764 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 515 optimal weight: 10.0000 chunk 408 optimal weight: 7.9990 chunk 790 optimal weight: 8.9990 chunk 306 optimal weight: 0.6980 chunk 480 optimal weight: 8.9990 chunk 588 optimal weight: 10.0000 chunk 916 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 73 ASN d 82 HIS d 85 ASN d 112 GLN d 116 HIS e 71 ASN h 22 HIS i 81 HIS k 75 GLN l 86 ASN o 18 HIS o 46 HIS q 5 ASN r 56 GLN t 21 ASN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN v 148 ASN v 264 HIS C 53 HIS C 194 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS D 126 HIS D 152 ASN E 29 ASN E 119 ASN G 51 ASN G 97 GLN G 128 ASN L 97 ASN M 4 GLN N 27 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN S 107 ASN T 90 GLN U 107 HIS W 58 ASN W 67 ASN Y 20 ASN Z 34 GLN 3 55 HIS 4 48 GLN 5 16 ASN 5 26 ASN 7 35 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 153737 Z= 0.348 Angle : 0.698 23.755 230685 Z= 0.361 Chirality : 0.042 0.369 29693 Planarity : 0.006 0.116 12099 Dihedral : 22.972 179.560 77879 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.94 % Favored : 93.92 % Rotamer: Outliers : 2.67 % Allowed : 11.64 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5610 helix: -0.73 (0.12), residues: 1778 sheet: -0.68 (0.16), residues: 1089 loop : -1.64 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP s 34 HIS 0.017 0.002 HIS p 84 PHE 0.024 0.002 PHE d 86 TYR 0.025 0.002 TYR v 289 ARG 0.013 0.001 ARG V 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 885 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 15 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8249 (mm) REVERT: d 87 MET cc_start: 0.8305 (ttm) cc_final: 0.8043 (mtp) REVERT: e 62 ARG cc_start: 0.7946 (tmm160) cc_final: 0.7677 (ttp80) REVERT: f 63 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (mt) REVERT: h 52 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7775 (mp) REVERT: k 65 MET cc_start: 0.7569 (mmt) cc_final: 0.7311 (mmm) REVERT: l 122 ASN cc_start: 0.8103 (t0) cc_final: 0.7835 (m-40) REVERT: o 7 ARG cc_start: 0.8795 (tpt170) cc_final: 0.8300 (tpt170) REVERT: o 39 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7334 (tt) REVERT: s 69 HIS cc_start: 0.3351 (OUTLIER) cc_final: 0.1853 (m170) REVERT: s 76 PRO cc_start: 0.6402 (Cg_endo) cc_final: 0.6184 (Cg_exo) REVERT: F 90 THR cc_start: 0.8432 (m) cc_final: 0.8227 (p) REVERT: F 110 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7682 (ptp-170) REVERT: F 137 ILE cc_start: 0.7645 (mp) cc_final: 0.7208 (mp) REVERT: G 62 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7416 (mtm110) REVERT: G 130 GLN cc_start: 0.8136 (mp10) cc_final: 0.7678 (mp10) REVERT: L 35 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8573 (p) REVERT: M 7 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8437 (mtt180) REVERT: M 53 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8860 (mmtt) REVERT: P 100 ASP cc_start: 0.8640 (m-30) cc_final: 0.8375 (m-30) REVERT: S 84 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8224 (mmtm) REVERT: T 31 ASP cc_start: 0.8366 (m-30) cc_final: 0.7976 (m-30) REVERT: U 27 ASP cc_start: 0.8191 (m-30) cc_final: 0.7842 (m-30) REVERT: W 40 MET cc_start: 0.8883 (mmm) cc_final: 0.8371 (mmm) REVERT: Z 39 LEU cc_start: 0.8579 (mm) cc_final: 0.8297 (mt) REVERT: 5 8 GLU cc_start: 0.8437 (tt0) cc_final: 0.8157 (tt0) REVERT: 5 31 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7972 (mt-10) outliers start: 109 outliers final: 72 residues processed: 946 average time/residue: 1.2877 time to fit residues: 2088.9911 Evaluate side-chains 889 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 811 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 48 VAL Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 48 GLN Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 7 residue 19 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 509 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 762 optimal weight: 2.9990 chunk 623 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 917 optimal weight: 6.9990 chunk 991 optimal weight: 1.9990 chunk 817 optimal weight: 0.0060 chunk 910 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 736 optimal weight: 9.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 132 GLN d 137 GLN q 49 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 14 GLN v 67 GLN v 148 ASN v 203 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 194 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN L 97 ASN L 136 GLN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Q 58 ASN W 58 ASN 5 4 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 153737 Z= 0.170 Angle : 0.552 17.110 230685 Z= 0.288 Chirality : 0.034 0.303 29693 Planarity : 0.004 0.119 12099 Dihedral : 22.913 179.401 77874 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 2.67 % Allowed : 15.68 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5610 helix: 0.04 (0.12), residues: 1774 sheet: -0.50 (0.16), residues: 1080 loop : -1.41 (0.11), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 200 HIS 0.003 0.001 HIS q 74 PHE 0.021 0.001 PHE i 41 TYR 0.015 0.001 TYR s 52 ARG 0.008 0.000 ARG b 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 866 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 57 MET cc_start: 0.6818 (ptt) cc_final: 0.6595 (ptt) REVERT: c 155 ARG cc_start: 0.6386 (tmm-80) cc_final: 0.6097 (ttp80) REVERT: d 112 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: d 181 GLU cc_start: 0.7029 (pp20) cc_final: 0.6749 (pp20) REVERT: e 143 ASP cc_start: 0.8803 (t0) cc_final: 0.8585 (t0) REVERT: h 23 ASP cc_start: 0.7854 (t70) cc_final: 0.7109 (t0) REVERT: k 68 GLU cc_start: 0.7246 (mt-10) cc_final: 0.7021 (mt-10) REVERT: n 34 ILE cc_start: 0.6361 (OUTLIER) cc_final: 0.5815 (mp) REVERT: s 76 PRO cc_start: 0.7080 (Cg_endo) cc_final: 0.6861 (Cg_exo) REVERT: t 49 LEU cc_start: 0.7939 (mt) cc_final: 0.7718 (mt) REVERT: v 275 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7233 (tm-30) REVERT: v 369 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7210 (tt) REVERT: F 81 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6407 (mm-30) REVERT: F 90 THR cc_start: 0.8582 (m) cc_final: 0.8107 (p) REVERT: F 110 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7594 (ptp-170) REVERT: F 137 ILE cc_start: 0.7866 (mp) cc_final: 0.7446 (mp) REVERT: F 168 GLU cc_start: 0.7980 (pp20) cc_final: 0.7766 (pp20) REVERT: M 3 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: M 53 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8905 (mmtt) REVERT: T 31 ASP cc_start: 0.8311 (m-30) cc_final: 0.7961 (m-30) REVERT: Y 85 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8792 (mtmt) REVERT: Z 39 LEU cc_start: 0.8577 (mm) cc_final: 0.8269 (mt) REVERT: 5 8 GLU cc_start: 0.8407 (tt0) cc_final: 0.8150 (tt0) outliers start: 109 outliers final: 69 residues processed: 921 average time/residue: 1.3356 time to fit residues: 2129.8086 Evaluate side-chains 880 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 807 time to evaluate : 6.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 126 SER Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 8 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 34 ASP Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 53 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 369 LEU Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 906 optimal weight: 7.9990 chunk 690 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 438 optimal weight: 8.9990 chunk 616 optimal weight: 10.0000 chunk 921 optimal weight: 10.0000 chunk 975 optimal weight: 6.9990 chunk 481 optimal weight: 10.0000 chunk 873 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 55 GLN d 59 HIS ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 122 ASN p 86 GLN t 74 ASN v 148 ASN v 165 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN G 128 ASN L 136 GLN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Q 58 ASN W 58 ASN 5 4 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 153737 Z= 0.482 Angle : 0.794 17.345 230685 Z= 0.401 Chirality : 0.046 0.407 29693 Planarity : 0.006 0.116 12099 Dihedral : 22.977 179.995 77874 Min Nonbonded Distance : 0.863 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.97 % Favored : 92.87 % Rotamer: Outliers : 5.19 % Allowed : 16.93 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 5610 helix: -0.26 (0.12), residues: 1791 sheet: -0.63 (0.16), residues: 1128 loop : -1.68 (0.11), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP g 103 HIS 0.009 0.002 HIS c 166 PHE 0.022 0.002 PHE i 127 TYR 0.029 0.002 TYR P 3 ARG 0.008 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 835 time to evaluate : 6.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 57 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7286 (ptt) REVERT: d 55 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8727 (mm110) REVERT: d 59 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.7501 (m90) REVERT: d 106 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8250 (t) REVERT: f 20 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7060 (ttmt) REVERT: f 63 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8300 (mt) REVERT: g 4 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7501 (mtpp) REVERT: h 23 ASP cc_start: 0.7959 (t70) cc_final: 0.7205 (t0) REVERT: h 35 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: h 52 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7896 (mp) REVERT: h 79 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8133 (ttt180) REVERT: i 75 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: j 52 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6154 (tt) REVERT: n 34 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6061 (mp) REVERT: o 39 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7714 (tt) REVERT: o 72 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8781 (mttt) REVERT: o 74 ASP cc_start: 0.8324 (p0) cc_final: 0.8079 (p0) REVERT: s 73 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5744 (mt-10) REVERT: t 65 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8578 (pp) REVERT: v 268 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8021 (mmmt) REVERT: F 90 THR cc_start: 0.8700 (m) cc_final: 0.8107 (p) REVERT: F 110 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7774 (ptp-170) REVERT: L 35 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8570 (p) REVERT: W 40 MET cc_start: 0.9082 (mmm) cc_final: 0.8350 (mmm) REVERT: Y 85 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8611 (mtpp) REVERT: 2 19 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7718 (mt0) outliers start: 212 outliers final: 141 residues processed: 955 average time/residue: 1.3727 time to fit residues: 2287.5610 Evaluate side-chains 960 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 804 time to evaluate : 6.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 57 MET Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 59 HIS Chi-restraints excluded: chain d residue 69 LYS Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 8 MET Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 53 ILE Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 117 GLU Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 122 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 48 GLN Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 4 residue 32 ASN Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 25 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 812 optimal weight: 10.0000 chunk 553 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 726 optimal weight: 0.9990 chunk 402 optimal weight: 3.9990 chunk 832 optimal weight: 3.9990 chunk 674 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 498 optimal weight: 7.9990 chunk 875 optimal weight: 0.8980 chunk 246 optimal weight: 0.0030 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 92 GLN e 71 ASN k 38 HIS ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS t 42 ASN v 14 GLN v 148 ASN v 165 HIS ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN L 97 ASN L 136 GLN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN W 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 153737 Z= 0.156 Angle : 0.567 16.781 230685 Z= 0.296 Chirality : 0.035 0.298 29693 Planarity : 0.004 0.115 12099 Dihedral : 22.891 179.580 77874 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 3.50 % Allowed : 19.94 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5610 helix: 0.34 (0.13), residues: 1770 sheet: -0.49 (0.16), residues: 1088 loop : -1.40 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 200 HIS 0.039 0.001 HIS d 59 PHE 0.011 0.001 PHE d 68 TYR 0.014 0.001 TYR G 157 ARG 0.006 0.000 ARG b 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 860 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 57 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7109 (ptt) REVERT: b 91 PHE cc_start: 0.7284 (p90) cc_final: 0.6896 (p90) REVERT: d 106 THR cc_start: 0.8432 (p) cc_final: 0.8179 (t) REVERT: h 35 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: h 79 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8195 (ttt180) REVERT: i 75 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: j 52 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5703 (tt) REVERT: s 69 HIS cc_start: 0.4612 (OUTLIER) cc_final: 0.4265 (m170) REVERT: t 49 LEU cc_start: 0.8165 (mt) cc_final: 0.7826 (mp) REVERT: t 52 GLU cc_start: 0.7739 (tp30) cc_final: 0.7533 (tp30) REVERT: F 81 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6253 (mm-30) REVERT: F 90 THR cc_start: 0.8517 (m) cc_final: 0.7989 (p) REVERT: F 110 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7632 (ptp-170) REVERT: F 168 GLU cc_start: 0.7965 (pp20) cc_final: 0.7740 (pp20) REVERT: M 3 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: M 53 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8874 (mmtt) REVERT: T 31 ASP cc_start: 0.8269 (m-30) cc_final: 0.7738 (m-30) REVERT: W 40 MET cc_start: 0.9037 (mmm) cc_final: 0.8329 (mmm) REVERT: W 56 ILE cc_start: 0.9337 (mm) cc_final: 0.9114 (mm) REVERT: Y 85 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8397 (mtpp) REVERT: Z 13 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7921 (mmm160) REVERT: 1 8 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8191 (p0) outliers start: 143 outliers final: 92 residues processed: 941 average time/residue: 1.3143 time to fit residues: 2121.6095 Evaluate side-chains 922 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 821 time to evaluate : 6.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 57 MET Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain r residue 75 VAL Chi-restraints excluded: chain s residue 69 HIS Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 196 VAL Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 334 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 58 ASN Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 328 optimal weight: 8.9990 chunk 878 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 572 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 976 optimal weight: 0.7980 chunk 810 optimal weight: 0.0970 chunk 452 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 512 optimal weight: 10.0000 overall best weight: 4.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN k 38 HIS q 6 GLN v 14 GLN v 119 GLN v 148 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN L 41 ASN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 153737 Z= 0.311 Angle : 0.627 17.309 230685 Z= 0.325 Chirality : 0.039 0.365 29693 Planarity : 0.005 0.115 12099 Dihedral : 22.862 178.365 77874 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.31 % Favored : 93.55 % Rotamer: Outliers : 4.51 % Allowed : 19.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 5610 helix: 0.30 (0.13), residues: 1781 sheet: -0.53 (0.16), residues: 1115 loop : -1.49 (0.11), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP s 34 HIS 0.008 0.001 HIS d 59 PHE 0.020 0.002 PHE v 372 TYR 0.020 0.002 TYR P 3 ARG 0.006 0.000 ARG s 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 829 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 57 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7272 (ptt) REVERT: b 91 PHE cc_start: 0.7121 (p90) cc_final: 0.6847 (p90) REVERT: c 155 ARG cc_start: 0.6288 (ttp-170) cc_final: 0.6082 (ttp80) REVERT: d 106 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8202 (t) REVERT: f 63 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8322 (mt) REVERT: h 35 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: h 52 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (mp) REVERT: h 79 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8186 (ttt180) REVERT: i 75 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: j 52 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.5881 (tt) REVERT: k 128 ARG cc_start: 0.8083 (mpt90) cc_final: 0.7836 (mpt-90) REVERT: l 7 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9166 (mp) REVERT: n 34 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6073 (mt) REVERT: s 34 TRP cc_start: 0.4870 (OUTLIER) cc_final: 0.2103 (t60) REVERT: t 49 LEU cc_start: 0.8211 (mt) cc_final: 0.7907 (mp) REVERT: t 65 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8513 (pp) REVERT: v 21 MET cc_start: 0.8898 (mmm) cc_final: 0.8680 (tpt) REVERT: F 110 ARG cc_start: 0.7982 (ptm160) cc_final: 0.7661 (ptp-170) REVERT: F 168 GLU cc_start: 0.7898 (pp20) cc_final: 0.7659 (pp20) REVERT: M 53 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8876 (mmtt) REVERT: T 31 ASP cc_start: 0.8319 (m-30) cc_final: 0.8018 (m-30) REVERT: W 40 MET cc_start: 0.9090 (mmm) cc_final: 0.8448 (mmm) REVERT: Y 85 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8521 (mtpp) REVERT: Z 13 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7990 (mmm160) REVERT: 1 8 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8252 (p0) REVERT: 2 19 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8354 (mt0) REVERT: 4 35 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7317 (pm20) outliers start: 184 outliers final: 133 residues processed: 936 average time/residue: 1.2884 time to fit residues: 2084.3828 Evaluate side-chains 966 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 817 time to evaluate : 6.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 57 MET Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 53 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain s residue 34 TRP Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 57 VAL Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 334 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 59 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 4 residue 35 GLU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 941 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 556 optimal weight: 10.0000 chunk 712 optimal weight: 20.0000 chunk 552 optimal weight: 10.0000 chunk 821 optimal weight: 3.9990 chunk 545 optimal weight: 8.9990 chunk 972 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 592 optimal weight: 20.0000 chunk 448 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 55 GLN e 71 ASN k 38 HIS ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS v 119 GLN v 148 ASN v 165 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 97 ASN L 136 GLN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN W 58 ASN 7 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 153737 Z= 0.451 Angle : 0.739 17.093 230685 Z= 0.380 Chirality : 0.045 0.424 29693 Planarity : 0.006 0.115 12099 Dihedral : 22.948 179.849 77874 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.76 % Rotamer: Outliers : 5.71 % Allowed : 18.99 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5610 helix: 0.04 (0.12), residues: 1780 sheet: -0.73 (0.16), residues: 1113 loop : -1.69 (0.11), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP s 34 HIS 0.007 0.002 HIS d 59 PHE 0.031 0.002 PHE v 372 TYR 0.040 0.002 TYR C 96 ARG 0.012 0.001 ARG p 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 828 time to evaluate : 6.287 Fit side-chains revert: symmetry clash REVERT: d 106 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8286 (t) REVERT: f 63 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8565 (mt) REVERT: g 95 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7079 (ttt180) REVERT: h 35 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: h 52 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7945 (mp) REVERT: h 79 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8209 (ttt180) REVERT: k 65 MET cc_start: 0.7405 (mmm) cc_final: 0.7011 (mmt) REVERT: k 128 ARG cc_start: 0.8186 (mpt90) cc_final: 0.7980 (mpt-90) REVERT: l 7 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (mp) REVERT: l 10 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8539 (ptmt) REVERT: n 34 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6324 (mt) REVERT: p 82 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7727 (ttpt) REVERT: s 34 TRP cc_start: 0.5940 (OUTLIER) cc_final: 0.3697 (t60) REVERT: t 49 LEU cc_start: 0.8292 (mt) cc_final: 0.8050 (mp) REVERT: t 65 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8579 (pp) REVERT: F 101 ASP cc_start: 0.6215 (t0) cc_final: 0.5315 (t0) REVERT: F 110 ARG cc_start: 0.8054 (ptm160) cc_final: 0.7801 (ptp-170) REVERT: F 168 GLU cc_start: 0.7886 (pp20) cc_final: 0.7614 (pp20) REVERT: Q 49 ASN cc_start: 0.9009 (m110) cc_final: 0.8790 (m-40) REVERT: S 55 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8378 (mtm180) REVERT: T 31 ASP cc_start: 0.8353 (m-30) cc_final: 0.7974 (m-30) REVERT: W 40 MET cc_start: 0.8939 (mmm) cc_final: 0.8197 (mmm) REVERT: Y 85 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8501 (mtpp) REVERT: Z 13 ARG cc_start: 0.8288 (mmm160) cc_final: 0.8075 (mmm160) REVERT: 1 8 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8218 (p0) REVERT: 2 19 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: 4 35 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: 4 45 GLU cc_start: 0.6324 (tm-30) cc_final: 0.5846 (tm-30) outliers start: 233 outliers final: 168 residues processed: 972 average time/residue: 1.2683 time to fit residues: 2124.6524 Evaluate side-chains 1002 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 818 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 ARG Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain r residue 22 ILE Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain s residue 34 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 89 ASN Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 115 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 59 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 57 LYS Chi-restraints excluded: chain 4 residue 32 ASN Chi-restraints excluded: chain 4 residue 35 GLU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 36 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 601 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 580 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 618 optimal weight: 7.9990 chunk 662 optimal weight: 6.9990 chunk 480 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 764 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 55 GLN e 71 ASN k 38 HIS ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN v 148 ASN v 165 HIS ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 153737 Z= 0.229 Angle : 0.603 17.672 230685 Z= 0.315 Chirality : 0.037 0.343 29693 Planarity : 0.005 0.115 12099 Dihedral : 22.867 178.426 77874 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 4.73 % Allowed : 20.06 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5610 helix: 0.32 (0.13), residues: 1780 sheet: -0.60 (0.16), residues: 1097 loop : -1.52 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 200 HIS 0.006 0.001 HIS o 46 PHE 0.030 0.001 PHE 3 23 TYR 0.017 0.001 TYR G 157 ARG 0.009 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 836 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 189 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8531 (mp) REVERT: g 95 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7092 (ttt180) REVERT: h 35 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: h 52 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8004 (mp) REVERT: h 79 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8179 (ttt180) REVERT: k 65 MET cc_start: 0.7357 (mmm) cc_final: 0.6985 (mmt) REVERT: m 93 ARG cc_start: 0.6110 (mtm180) cc_final: 0.5907 (mtm180) REVERT: n 34 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.6145 (mt) REVERT: s 34 TRP cc_start: 0.5810 (OUTLIER) cc_final: 0.3855 (t60) REVERT: s 38 SER cc_start: 0.7137 (OUTLIER) cc_final: 0.6670 (m) REVERT: t 49 LEU cc_start: 0.8320 (mt) cc_final: 0.8050 (mp) REVERT: t 52 GLU cc_start: 0.7773 (tp30) cc_final: 0.7416 (tp30) REVERT: t 65 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8429 (pp) REVERT: D 3 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8193 (mtpp) REVERT: D 90 GLU cc_start: 0.8187 (mp0) cc_final: 0.7964 (mp0) REVERT: E 74 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7095 (ptp-170) REVERT: F 110 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7678 (ptp-170) REVERT: F 133 ARG cc_start: 0.5679 (mmp-170) cc_final: 0.5313 (mmp-170) REVERT: F 168 GLU cc_start: 0.7951 (pp20) cc_final: 0.7696 (pp20) REVERT: T 31 ASP cc_start: 0.8327 (m-30) cc_final: 0.7981 (m-30) REVERT: W 40 MET cc_start: 0.9002 (mmm) cc_final: 0.8288 (mmm) REVERT: Y 85 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: Z 13 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7976 (mmm160) REVERT: 1 8 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8262 (p0) REVERT: 2 19 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: 2 24 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: 4 35 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7142 (pm20) outliers start: 193 outliers final: 147 residues processed: 953 average time/residue: 1.2506 time to fit residues: 2045.7062 Evaluate side-chains 983 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 820 time to evaluate : 6.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 126 SER Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 ARG Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 4 ARG Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 34 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 24 GLN Chi-restraints excluded: chain 2 residue 57 LYS Chi-restraints excluded: chain 4 residue 35 GLU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 61 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 884 optimal weight: 8.9990 chunk 931 optimal weight: 1.9990 chunk 850 optimal weight: 6.9990 chunk 906 optimal weight: 5.9990 chunk 545 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 711 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 818 optimal weight: 9.9990 chunk 857 optimal weight: 6.9990 chunk 903 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 55 GLN d 148 ASN e 71 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN v 14 GLN v 148 ASN v 165 HIS ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 97 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN W 53 GLN W 58 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 153737 Z= 0.284 Angle : 0.616 17.972 230685 Z= 0.320 Chirality : 0.038 0.359 29693 Planarity : 0.005 0.115 12099 Dihedral : 22.843 178.221 77874 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 4.88 % Allowed : 19.97 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 5610 helix: 0.37 (0.13), residues: 1780 sheet: -0.53 (0.16), residues: 1108 loop : -1.51 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP s 34 HIS 0.006 0.001 HIS o 46 PHE 0.018 0.002 PHE 3 23 TYR 0.021 0.002 TYR h 51 ARG 0.010 0.001 ARG e 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 831 time to evaluate : 6.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 189 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8537 (mp) REVERT: g 95 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7267 (tpt-90) REVERT: h 35 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: h 38 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8028 (mm-30) REVERT: h 52 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8016 (mp) REVERT: h 79 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8168 (ttt180) REVERT: k 65 MET cc_start: 0.7361 (mmm) cc_final: 0.7011 (mmt) REVERT: m 93 ARG cc_start: 0.6164 (mtm180) cc_final: 0.5912 (mtm180) REVERT: n 34 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6160 (mt) REVERT: s 34 TRP cc_start: 0.5946 (OUTLIER) cc_final: 0.3796 (t60) REVERT: s 38 SER cc_start: 0.7141 (OUTLIER) cc_final: 0.6622 (m) REVERT: t 49 LEU cc_start: 0.8339 (mt) cc_final: 0.8003 (mp) REVERT: t 52 GLU cc_start: 0.7798 (tp30) cc_final: 0.7412 (tp30) REVERT: t 65 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 3 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8236 (mtpp) REVERT: D 90 GLU cc_start: 0.8177 (mp0) cc_final: 0.7930 (mp0) REVERT: E 74 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7098 (ptp-170) REVERT: F 110 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7700 (ptp-170) REVERT: F 133 ARG cc_start: 0.5684 (mmp-170) cc_final: 0.5338 (mmp-170) REVERT: F 168 GLU cc_start: 0.7971 (pp20) cc_final: 0.7712 (pp20) REVERT: M 5 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: P 131 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8740 (mt) REVERT: S 55 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8279 (mtm180) REVERT: T 31 ASP cc_start: 0.8313 (m-30) cc_final: 0.7962 (m-30) REVERT: W 40 MET cc_start: 0.8988 (mmm) cc_final: 0.8270 (mmm) REVERT: W 53 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8134 (mp-120) REVERT: Y 85 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8459 (mtpp) REVERT: Z 13 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7994 (mmm160) REVERT: 1 8 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8246 (p0) REVERT: 2 19 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8353 (mt0) REVERT: 2 24 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: 4 35 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7282 (pm20) outliers start: 199 outliers final: 159 residues processed: 946 average time/residue: 1.2906 time to fit residues: 2104.2582 Evaluate side-chains 1005 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 826 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 126 SER Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 ARG Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 129 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 34 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 5 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 53 GLN Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 24 GLN Chi-restraints excluded: chain 2 residue 57 LYS Chi-restraints excluded: chain 4 residue 35 GLU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 7 residue 61 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 595 optimal weight: 10.0000 chunk 958 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 666 optimal weight: 10.0000 chunk 1005 optimal weight: 1.9990 chunk 925 optimal weight: 0.9990 chunk 800 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 618 optimal weight: 8.9990 chunk 490 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 55 GLN d 148 ASN e 71 ASN i 75 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN v 148 ASN v 165 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 153737 Z= 0.410 Angle : 0.699 20.968 230685 Z= 0.361 Chirality : 0.043 0.407 29693 Planarity : 0.005 0.115 12099 Dihedral : 22.881 179.428 77874 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.12 % Rotamer: Outliers : 4.80 % Allowed : 20.21 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.11), residues: 5610 helix: 0.16 (0.12), residues: 1786 sheet: -0.60 (0.16), residues: 1106 loop : -1.65 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP s 34 HIS 0.007 0.001 HIS o 46 PHE 0.023 0.002 PHE 3 23 TYR 0.023 0.002 TYR P 3 ARG 0.011 0.001 ARG e 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11220 Ramachandran restraints generated. 5610 Oldfield, 0 Emsley, 5610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 825 time to evaluate : 6.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: g 95 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7252 (ttt180) REVERT: h 35 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: h 38 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7981 (mm-30) REVERT: h 52 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8007 (mp) REVERT: h 79 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8213 (ttt180) REVERT: k 65 MET cc_start: 0.7369 (mmm) cc_final: 0.7021 (mmt) REVERT: m 79 ARG cc_start: 0.7350 (tmt170) cc_final: 0.7083 (ttt-90) REVERT: m 93 ARG cc_start: 0.6164 (mtm180) cc_final: 0.5856 (mtm180) REVERT: n 34 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6293 (mt) REVERT: r 39 GLU cc_start: 0.8093 (pm20) cc_final: 0.7792 (pm20) REVERT: s 34 TRP cc_start: 0.6437 (OUTLIER) cc_final: 0.5110 (t60) REVERT: t 49 LEU cc_start: 0.8348 (mt) cc_final: 0.8128 (mp) REVERT: t 65 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8526 (pp) REVERT: v 21 MET cc_start: 0.8885 (mmm) cc_final: 0.8615 (tpt) REVERT: D 3 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8263 (mtpp) REVERT: E 74 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7205 (ptp-170) REVERT: F 81 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6812 (mm-30) REVERT: F 110 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7768 (ptp-170) REVERT: F 168 GLU cc_start: 0.7952 (pp20) cc_final: 0.7675 (pp20) REVERT: M 4 GLN cc_start: 0.8733 (tt0) cc_final: 0.8446 (tt0) REVERT: M 5 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: P 131 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8744 (mt) REVERT: S 55 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8346 (mtm180) REVERT: W 40 MET cc_start: 0.8993 (mmm) cc_final: 0.8276 (mmm) REVERT: Y 85 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8831 (mtpp) REVERT: Z 13 ARG cc_start: 0.8248 (mmm160) cc_final: 0.8032 (mmm160) REVERT: 1 8 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8201 (p0) REVERT: 2 19 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: 2 24 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: 4 35 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: 4 45 GLU cc_start: 0.6224 (tm-30) cc_final: 0.5787 (tm-30) outliers start: 196 outliers final: 165 residues processed: 940 average time/residue: 1.3130 time to fit residues: 2116.3846 Evaluate side-chains 999 residues out of total 4816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 817 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 195 GLU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 10 MET Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 126 SER Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain e residue 161 THR Chi-restraints excluded: chain f residue 44 TRP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain g residue 17 ILE Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 25 ARG Chi-restraints excluded: chain g residue 95 ARG Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 34 LYS Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain h residue 52 ILE Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 77 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 56 HIS Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain l residue 128 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 13 LYS Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 44 LEU Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 34 TRP Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain v residue 112 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 208 THR Chi-restraints excluded: chain v residue 255 THR Chi-restraints excluded: chain v residue 279 ASP Chi-restraints excluded: chain v residue 296 THR Chi-restraints excluded: chain v residue 334 THR Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 5 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 91 LYS Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 50 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 68 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 55 ARG Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 83 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 85 LYS Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 24 GLN Chi-restraints excluded: chain 2 residue 57 LYS Chi-restraints excluded: chain 4 residue 35 GLU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 635 optimal weight: 60.0000 chunk 852 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 738 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 801 optimal weight: 20.0000 chunk 335 optimal weight: 0.8980 chunk 823 optimal weight: 0.5980 chunk 101 optimal weight: 40.0000 chunk 147 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 55 ASN d 55 GLN e 71 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 ASN t 21 ASN v 119 GLN v 148 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 97 ASN M 110 ASN ** Q 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 ASN W 58 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.094895 restraints weight = 242027.460| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.05 r_work: 0.3013 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 153737 Z= 0.123 Angle : 0.552 19.955 230685 Z= 0.288 Chirality : 0.033 0.306 29693 Planarity : 0.004 0.114 12099 Dihedral : 22.839 179.558 77874 Min Nonbonded Distance : 1.194 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.31 % Rotamer: Outliers : 3.26 % Allowed : 21.93 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5610 helix: 0.58 (0.13), residues: 1786 sheet: -0.42 (0.16), residues: 1090 loop : -1.36 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 200 HIS 0.005 0.001 HIS o 46 PHE 0.035 0.001 PHE v 372 TYR 0.020 0.001 TYR F 97 ARG 0.009 0.000 ARG V 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34512.65 seconds wall clock time: 602 minutes 36.50 seconds (36156.50 seconds total)