Starting phenix.real_space_refine on Wed Mar 27 14:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agz_15428/03_2024/8agz_15428_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.131 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 7 6.06 5 P 3642 5.49 5 Mg 13 5.21 5 S 177 5.16 5 C 81316 2.51 5 N 27605 2.21 5 O 38579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "T GLU 87": "OE1" <-> "OE2" Residue "U GLU 8": "OE1" <-> "OE2" Residue "U GLU 15": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "j GLU 74": "OE1" <-> "OE2" Residue "j GLU 118": "OE1" <-> "OE2" Residue "k GLU 71": "OE1" <-> "OE2" Residue "k GLU 190": "OE1" <-> "OE2" Residue "k GLU 291": "OE1" <-> "OE2" Residue "k GLU 353": "OE1" <-> "OE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 337": "OE1" <-> "OE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 148": "OE1" <-> "OE2" Residue "q GLU 143": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r GLU 58": "OE1" <-> "OE2" Residue "s GLU 15": "OE1" <-> "OE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "u GLU 37": "OE1" <-> "OE2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a GLU 162": "OE1" <-> "OE2" Residue "a PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 203": "OE1" <-> "OE2" Residue "e GLU 900": "OE1" <-> "OE2" Residue "e GLU 937": "OE1" <-> "OE2" Residue "e GLU 972": "OE1" <-> "OE2" Residue "e GLU 989": "OE1" <-> "OE2" Residue "e GLU 991": "OE1" <-> "OE2" Residue "e GLU 996": "OE1" <-> "OE2" Residue "e GLU 1507": "OE1" <-> "OE2" Residue "v GLU 71": "OE1" <-> "OE2" Residue "0 ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151339 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "E" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1272 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "J" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1169 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 78} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 207 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "f" Number of atoms: 68782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 219, 'rna3p_pur': 1449, 'rna3p_pyr': 1218} Link IDs: {'rna2p': 549, 'rna3p': 2666} Chain breaks: 3 Chain: "h" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "i" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "j" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "k" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "p" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "s" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1346 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "u" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6579 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 161 Chain: "e" Number of atoms: 11506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11506 Classifications: {'peptide': 1527} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 984 Unresolved non-hydrogen angles: 1255 Unresolved non-hydrogen dihedrals: 817 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 566 Chain: "g" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1651 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "v" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1085 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'5CT:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "w" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1709 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "x" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p': 1, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 1, 'rna3p_pur': 29, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "z" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 728 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 182 Chain: "0" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3, 'SPD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" 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: "k" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20901 SG CYS T 44 119.888 171.536 212.490 1.00 54.16 S ATOM 20919 SG CYS T 47 121.961 168.865 211.408 1.00 59.61 S ATOM 21191 SG CYS T 84 123.160 171.329 214.242 1.00 57.91 S ATOM 23302 SG CYS W 19 84.981 189.588 169.989 1.00 40.18 S ATOM 23327 SG CYS W 22 83.254 189.690 166.696 1.00 41.00 S ATOM 23427 SG CYS W 34 86.985 189.656 166.765 1.00 38.42 S ATOM 23445 SG CYS W 37 85.043 192.763 167.916 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.433 140.582 76.541 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.780 138.920 78.530 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.672 138.399 74.849 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.637 141.631 76.093 1.00 52.77 S ATOM 25359 SG CYS b 12 133.260 248.007 110.419 1.00 63.95 S ATOM 25394 SG CYS b 17 134.581 251.533 109.536 1.00 72.10 S ATOM 25858 SG CYS b 74 136.755 248.989 111.674 1.00 60.93 S ATOM 25880 SG CYS b 77 133.668 250.858 112.836 1.00 66.15 S ATOM 26403 SG CYS c 39 138.551 168.870 205.768 1.00 58.71 S ATOM 26426 SG CYS c 42 137.892 165.892 207.850 1.00 62.48 S ATOM 26535 SG CYS c 57 135.698 166.436 204.846 1.00 55.64 S ATOM 26553 SG CYS c 60 135.285 168.900 207.603 1.00 57.82 S ATOM A0W6E SG CYS e1527 30.787 117.962 188.205 1.00285.10 S ATOM A0W6Y SG CYS e1530 30.560 115.317 185.931 1.00279.23 S ATOM A0WBQ SG CYS e1551 29.219 118.370 184.684 1.00286.27 S ATOM A0WCB SG CYS e1554 27.239 117.412 187.841 1.00284.05 S ATOM A0W2C SG CYS e1508 36.338 116.328 177.306 1.00285.58 S ATOM A0W2V SG CYS e1511 36.914 115.346 173.871 1.00284.14 S ATOM A0W8O SG CYS e1538 36.949 119.571 174.857 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N AVAL B 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 3 " occ=0.50 residue: pdb=" N AGLU B 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU B 4 " occ=0.50 residue: pdb=" N APRO B 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO B 5 " occ=0.50 residue: pdb=" N AVAL B 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 6 " occ=0.50 residue: pdb=" N AVAL B 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 7 " occ=0.50 residue: pdb=" N AVAL B 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 8 " occ=0.50 residue: pdb=" N AILE B 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE B 9 " occ=0.50 residue: pdb=" N AASP B 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP B 10 " occ=0.50 residue: pdb=" N AGLY B 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 11 " occ=0.50 residue: pdb=" N ALYS B 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS B 12 " occ=0.50 residue: pdb=" N AGLY B 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 13 " occ=0.50 residue: pdb=" N AHIS B 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS B 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 58.48, per 1000 atoms: 0.39 Number of scatterers: 151339 At special positions: 0 Unit cell: (232.98, 284.871, 262.632, 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 7 29.99 S 177 16.00 P 3642 15.00 Mg 13 11.99 O 38579 8.00 N 27605 7.00 C 81316 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: 61.87 Conformation dependent library (CDL) restraints added in 10.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1511 " Number of angles added : 33 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17764 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: 364 helices and 88 sheets defined 48.8% alpha, 13.0% beta 1186 base pairs and 2012 stacking pairs defined. Time for finding SS restraints: 84.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.806A pdb=" N TYR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.753A pdb=" N TRP A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.844A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 139 through 145 removed outlier: 4.410A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 5.054A pdb=" N TRP A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 153' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.689A pdb=" N ALYS B 25 " --> pdb=" O ASER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.077A pdb=" N ALYS B 60 " --> pdb=" O AASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.023A pdb=" N AGLY B 69 " --> pdb=" O AASN B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.835A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.926A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALYS B 103 " --> pdb=" O ALEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.914A pdb=" N ALYS B 114 " --> pdb=" O APRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 151 through 186 removed outlier: 3.813A pdb=" N ALYS B 170 " --> pdb=" O AGLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.729A pdb=" N SER C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.639A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 84 through 106 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.765A pdb=" N GLY C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.812A pdb=" N GLN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.144A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 154' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.908A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.177A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.709A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.827A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.686A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 117 through 122 removed outlier: 5.661A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.882A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.513A pdb=" N TYR G 30 " --> pdb=" O HIS G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.286A pdb=" N ILE G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 99 through 121 removed outlier: 3.891A pdb=" N GLN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.166A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 26 " --> pdb=" O PRO H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'I' and resid 66 through 71 removed outlier: 5.400A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.884A pdb=" N LEU I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Proline residue: I 127 - end of helix Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.562A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.644A pdb=" N ILE K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.733A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.835A pdb=" N ASN K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.028A pdb=" N VAL L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.568A pdb=" N LEU L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 112 through 123 Processing helix chain 'M' and resid 58 through 67 removed outlier: 5.381A pdb=" N VAL M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS M 67 " --> pdb=" O ALA M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 removed outlier: 3.569A pdb=" N LEU M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 81' Processing helix chain 'M' and resid 92 through 97 removed outlier: 5.472A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 125 removed outlier: 3.596A pdb=" N VAL M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'N' and resid 2 through 7 removed outlier: 4.160A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS N 7 " --> pdb=" O SER N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 7' Processing helix chain 'N' and resid 41 through 49 Processing helix chain 'N' and resid 64 through 69 removed outlier: 4.420A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 74 through 83 removed outlier: 4.577A pdb=" N TRP N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.643A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.532A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 26 through 37 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 73 through 82 removed outlier: 3.829A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.971A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 21 removed outlier: 3.857A pdb=" N ARG Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 Processing helix chain 'Q' and resid 52 through 61 Processing helix chain 'R' and resid 21 through 26 removed outlier: 5.154A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.853A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 87 " --> pdb=" O GLU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.187A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.452A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR S 44 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 66 removed outlier: 3.621A pdb=" N TYR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 58 through 66' Processing helix chain 'T' and resid 81 through 113 removed outlier: 3.752A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 12 removed outlier: 4.178A pdb=" N THR U 11 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.565A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.590A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.175A pdb=" N ALA U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 Processing helix chain 'U' and resid 93 through 99 Processing helix chain 'U' and resid 101 through 111 Processing helix chain 'V' and resid 25 through 30 removed outlier: 4.459A pdb=" N LYS V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS V 30 " --> pdb=" O ILE V 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 25 through 30' Processing helix chain 'V' and resid 34 through 49 Processing helix chain 'V' and resid 51 through 64 Processing helix chain 'V' and resid 65 through 77 Processing helix chain 'V' and resid 79 through 100 Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.650A pdb=" N GLY W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS W 10 " --> pdb=" O PRO W 6 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG W 11 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 58 Processing helix chain 'W' and resid 65 through 77 removed outlier: 5.840A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.318A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.498A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 30' Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.873A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.577A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.150A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.694A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 11 removed outlier: 4.394A pdb=" N GLY j 11 " --> pdb=" O ASN j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 5.744A pdb=" N ARG j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.098A pdb=" N VAL j 107 " --> pdb=" O PRO j 103 " (cutoff:3.500A) Proline residue: j 108 - end of helix No H-bonds generated for 'chain 'j' and resid 103 through 108' Processing helix chain 'j' and resid 181 through 193 removed outlier: 4.173A pdb=" N LEU j 191 " --> pdb=" O HIS j 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 205 removed outlier: 3.825A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN j 205 " --> pdb=" O GLY j 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 200 through 205' Processing helix chain 'j' and resid 173 through 178 removed outlier: 3.641A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.414A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR k 119 " --> pdb=" O LYS k 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS k 120 " --> pdb=" O ARG k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 139 removed outlier: 3.973A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN k 139 " --> pdb=" O ALA k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.413A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU k 147 " --> pdb=" O GLY k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 170 removed outlier: 4.238A pdb=" N THR k 169 " --> pdb=" O GLN k 165 " (cutoff:3.500A) Proline residue: k 170 - end of helix No H-bonds generated for 'chain 'k' and resid 165 through 170' Processing helix chain 'k' and resid 187 through 199 Processing helix chain 'k' and resid 204 through 209 removed outlier: 4.180A pdb=" N VAL k 208 " --> pdb=" O ALA k 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 228 through 233 Processing helix chain 'k' and resid 347 through 352 removed outlier: 6.411A pdb=" N LEU k 351 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU k 352 " --> pdb=" O ARG k 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 347 through 352' Processing helix chain 'k' and resid 372 through 381 Processing helix chain 'l' and resid 31 through 46 removed outlier: 3.787A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS l 44 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.923A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 139 Processing helix chain 'l' and resid 154 through 159 removed outlier: 4.896A pdb=" N SER l 158 " --> pdb=" O THR l 154 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE l 159 " --> pdb=" O ASP l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 154 through 159' Processing helix chain 'l' and resid 161 through 173 Processing helix chain 'l' and resid 174 through 185 removed outlier: 4.234A pdb=" N LYS l 185 " --> pdb=" O VAL l 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 196 removed outlier: 3.778A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN l 196 " --> pdb=" O GLY l 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 191 through 196' Processing helix chain 'l' and resid 214 through 221 removed outlier: 4.755A pdb=" N ASN l 221 " --> pdb=" O LYS l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 234 through 240 Proline residue: l 240 - end of helix Processing helix chain 'l' and resid 251 through 262 removed outlier: 4.669A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN l 260 " --> pdb=" O THR l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 292 Processing helix chain 'l' and resid 293 through 299 removed outlier: 3.686A pdb=" N ALA l 298 " --> pdb=" O GLU l 294 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 328 Processing helix chain 'l' and resid 329 through 338 removed outlier: 4.450A pdb=" N VAL l 333 " --> pdb=" O PRO l 329 " (cutoff:3.500A) Processing helix chain 'l' and resid 352 through 361 Processing helix chain 'm' and resid 9 through 16 Processing helix chain 'm' and resid 20 through 26 Processing helix chain 'm' and resid 29 through 37 removed outlier: 3.681A pdb=" N ARG m 35 " --> pdb=" O TYR m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 87 removed outlier: 4.613A pdb=" N LEU m 83 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Proline residue: m 84 - end of helix Processing helix chain 'm' and resid 94 through 114 Processing helix chain 'm' and resid 115 through 120 removed outlier: 4.700A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'm' and resid 157 through 170 removed outlier: 3.763A pdb=" N GLY m 161 " --> pdb=" O ALA m 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY m 170 " --> pdb=" O ALA m 166 " (cutoff:3.500A) Processing helix chain 'm' and resid 191 through 201 removed outlier: 3.619A pdb=" N LEU m 195 " --> pdb=" O ASP m 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 215 removed outlier: 3.708A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP m 214 " --> pdb=" O GLU m 210 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 223 removed outlier: 4.783A pdb=" N PHE m 223 " --> pdb=" O PHE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 224 through 230 Processing helix chain 'm' and resid 234 through 250 removed outlier: 4.367A pdb=" N ASP m 238 " --> pdb=" O ASP m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 273 removed outlier: 3.767A pdb=" N GLU m 268 " --> pdb=" O GLN m 264 " (cutoff:3.500A) Processing helix chain 'm' and resid 278 through 294 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.993A pdb=" N VAL n 84 " --> pdb=" O ASN n 80 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 85 " --> pdb=" O ALA n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'n' and resid 102 through 107 removed outlier: 3.963A pdb=" N PHE n 106 " --> pdb=" O ASN n 102 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA n 107 " --> pdb=" O VAL n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 107' Processing helix chain 'n' and resid 131 through 150 removed outlier: 3.875A pdb=" N LYS n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA n 147 " --> pdb=" O LYS n 143 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 154 through 162 removed outlier: 5.285A pdb=" N SER n 162 " --> pdb=" O TYR n 158 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 73 Processing helix chain 'o' and resid 96 through 107 Processing helix chain 'o' and resid 120 through 131 removed outlier: 4.042A pdb=" N LEU o 126 " --> pdb=" O ALA o 122 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 151 Processing helix chain 'o' and resid 165 through 173 removed outlier: 4.156A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.170A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.110A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.633A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.222A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE p 67 " --> pdb=" O LYS p 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 80 removed outlier: 4.847A pdb=" N ALA p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE p 78 " --> pdb=" O THR p 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.002A pdb=" N LYS p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR p 97 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG p 98 " --> pdb=" O PHE p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 135 through 146 Processing helix chain 'p' and resid 159 through 174 removed outlier: 4.604A pdb=" N VAL p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU p 166 " --> pdb=" O LEU p 162 " (cutoff:3.500A) Proline residue: p 167 - end of helix Processing helix chain 'p' and resid 182 through 191 Processing helix chain 'p' and resid 204 through 222 removed outlier: 3.675A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA p 210 " --> pdb=" O GLU p 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR p 217 " --> pdb=" O LYS p 213 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.681A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.216A pdb=" N SER p 255 " --> pdb=" O LYS p 251 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 84 removed outlier: 3.640A pdb=" N ARG q 69 " --> pdb=" O VAL q 65 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 166 removed outlier: 4.143A pdb=" N CYS q 165 " --> pdb=" O LEU q 161 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.108A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.430A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.413A pdb=" N PHE r 46 " --> pdb=" O THR r 42 " (cutoff:3.500A) Proline residue: r 47 - end of helix No H-bonds generated for 'chain 'r' and resid 42 through 47' Processing helix chain 'r' and resid 61 through 80 Processing helix chain 'r' and resid 107 through 112 removed outlier: 4.663A pdb=" N LEU r 111 " --> pdb=" O GLY r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 160 removed outlier: 3.558A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.577A pdb=" N PHE r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 219 removed outlier: 4.577A pdb=" N ALA r 219 " --> pdb=" O GLU r 215 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 42 Processing helix chain 's' and resid 73 through 88 Processing helix chain 's' and resid 108 through 113 removed outlier: 4.450A pdb=" N LEU s 112 " --> pdb=" O GLU s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 136 through 141 removed outlier: 3.837A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 167 removed outlier: 4.922A pdb=" N TYR s 167 " --> pdb=" O PHE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 22 removed outlier: 4.153A pdb=" N ARG t 21 " --> pdb=" O HIS t 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL t 22 " --> pdb=" O TRP t 18 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 22' Processing helix chain 't' and resid 27 through 47 Processing helix chain 't' and resid 76 through 84 Processing helix chain 't' and resid 86 through 94 Processing helix chain 't' and resid 105 through 123 Processing helix chain 't' and resid 140 through 146 Proline residue: t 146 - end of helix Processing helix chain 't' and resid 165 through 180 removed outlier: 6.292A pdb=" N THR t 169 " --> pdb=" O SER t 165 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU t 170 " --> pdb=" O ALA t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 193 Processing helix chain 'u' and resid 59 through 64 removed outlier: 4.074A pdb=" N VAL u 63 " --> pdb=" O ASN u 59 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 59 through 64' Processing helix chain 'u' and resid 77 through 89 Processing helix chain 'u' and resid 90 through 98 removed outlier: 3.836A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.239A pdb=" N ALA u 136 " --> pdb=" O LYS u 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 21 removed outlier: 3.807A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 84 Processing helix chain 'a' and resid 153 through 160 removed outlier: 4.345A pdb=" N PHE a 157 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 5.476A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 3.944A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 228 Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.251A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 4.109A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER a 323 " --> pdb=" O GLY a 319 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 396 removed outlier: 6.632A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 413 removed outlier: 3.570A pdb=" N GLN a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 4.138A pdb=" N LEU a 437 " --> pdb=" O ILE a 433 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 562 removed outlier: 3.591A pdb=" N GLN a 530 " --> pdb=" O LYS a 526 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS a 531 " --> pdb=" O THR a 527 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP a 551 " --> pdb=" O GLU a 547 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS a 556 " --> pdb=" O GLN a 552 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS a 562 " --> pdb=" O LEU a 558 " (cutoff:3.500A) Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 removed outlier: 4.240A pdb=" N GLU a 647 " --> pdb=" O MET a 643 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.585A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER a 666 " --> pdb=" O ALA a 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 661 through 666' Processing helix chain 'a' and resid 839 through 850 removed outlier: 4.554A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS a 846 " --> pdb=" O GLY a 842 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 3.921A pdb=" N ARG a 886 " --> pdb=" O GLU a 882 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS a 906 " --> pdb=" O LEU a 902 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE a 907 " --> pdb=" O GLN a 903 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR a 908 " --> pdb=" O ALA a 904 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS a 909 " --> pdb=" O LEU a 905 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 924 removed outlier: 4.222A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS a 921 " --> pdb=" O TYR a 917 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.689A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 4.405A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.519A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.884A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU a1008 " --> pdb=" O ASP a1004 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N CYS a1010 " --> pdb=" O VAL a1006 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 35 through 42 removed outlier: 3.535A pdb=" N LEU e 42 " --> pdb=" O LEU e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.465A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 4.066A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 5.008A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 99 removed outlier: 4.061A pdb=" N LYS e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 Processing helix chain 'e' and resid 125 through 142 removed outlier: 4.220A pdb=" N LYS e 130 " --> pdb=" O SER e 126 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Proline residue: e 134 - end of helix removed outlier: 3.584A pdb=" N GLU e 142 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 160 Proline residue: e 150 - end of helix Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 186 Processing helix chain 'e' and resid 189 through 195 removed outlier: 4.401A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 227 removed outlier: 3.695A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 234 Processing helix chain 'e' and resid 235 through 243 Processing helix chain 'e' and resid 244 through 251 removed outlier: 4.078A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.275A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 Processing helix chain 'e' and resid 282 through 299 removed outlier: 5.358A pdb=" N THR e 299 " --> pdb=" O LEU e 295 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 311 Proline residue: e 308 - end of helix Proline residue: e 311 - end of helix Processing helix chain 'e' and resid 312 through 325 removed outlier: 3.557A pdb=" N TYR e 323 " --> pdb=" O THR e 319 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 4.239A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.820A pdb=" N SER e 349 " --> pdb=" O VAL e 345 " (cutoff:3.500A) Proline residue: e 350 - end of helix Processing helix chain 'e' and resid 353 through 369 removed outlier: 3.995A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 376 through 392 Processing helix chain 'e' and resid 395 through 417 removed outlier: 4.287A pdb=" N ALA e 399 " --> pdb=" O ALA e 395 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU e 400 " --> pdb=" O ARG e 396 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 438 through 443 Processing helix chain 'e' and resid 444 through 454 removed outlier: 4.863A pdb=" N GLY e 451 " --> pdb=" O GLN e 447 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL e 452 " --> pdb=" O THR e 448 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE e 453 " --> pdb=" O LEU e 449 " (cutoff:3.500A) Proline residue: e 454 - end of helix Processing helix chain 'e' and resid 455 through 469 removed outlier: 5.443A pdb=" N ASP e 469 " --> pdb=" O TYR e 465 " (cutoff:3.500A) Processing helix chain 'e' and resid 470 through 477 removed outlier: 4.509A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 491 Proline residue: e 491 - end of helix Processing helix chain 'e' and resid 493 through 509 Processing helix chain 'e' and resid 511 through 519 removed outlier: 3.987A pdb=" N ASN e 517 " --> pdb=" O SER e 513 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS e 518 " --> pdb=" O ASN e 514 " (cutoff:3.500A) Processing helix chain 'e' and resid 520 through 532 Processing helix chain 'e' and resid 535 through 548 Processing helix chain 'e' and resid 556 through 571 removed outlier: 4.582A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 4.668A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.631A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 4.892A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.098A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 635 removed outlier: 4.855A pdb=" N LYS e 635 " --> pdb=" O MET e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 646 removed outlier: 4.539A pdb=" N ASN e 646 " --> pdb=" O ILE e 642 " (cutoff:3.500A) Processing helix chain 'e' and resid 651 through 666 Processing helix chain 'e' and resid 667 through 679 removed outlier: 4.483A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 691 removed outlier: 3.858A pdb=" N ASP e 691 " --> pdb=" O LEU e 687 " (cutoff:3.500A) Processing helix chain 'e' and resid 692 through 700 removed outlier: 5.045A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU e 699 " --> pdb=" O CYS e 695 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 717 Processing helix chain 'e' and resid 719 through 737 Processing helix chain 'e' and resid 740 through 757 removed outlier: 4.036A pdb=" N GLU e 744 " --> pdb=" O PRO e 740 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS e 745 " --> pdb=" O GLY e 741 " (cutoff:3.500A) Processing helix chain 'e' and resid 758 through 766 Proline residue: e 766 - end of helix Processing helix chain 'e' and resid 768 through 777 removed outlier: 4.153A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 781 through 789 removed outlier: 5.324A pdb=" N SER e 789 " --> pdb=" O SER e 785 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 3.628A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) Processing helix chain 'e' and resid 805 through 827 removed outlier: 3.818A pdb=" N MET e 809 " --> pdb=" O ASN e 805 " (cutoff:3.500A) Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 832 through 852 Processing helix chain 'e' and resid 856 through 862 removed outlier: 3.741A pdb=" N TYR e 860 " --> pdb=" O ASN e 856 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE e 862 " --> pdb=" O LEU e 858 " (cutoff:3.500A) Processing helix chain 'e' and resid 875 through 886 Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 902 removed outlier: 3.809A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 removed outlier: 3.501A pdb=" N ARG e 911 " --> pdb=" O PHE e 907 " (cutoff:3.500A) Processing helix chain 'e' and resid 925 through 944 Processing helix chain 'e' and resid 950 through 968 removed outlier: 4.545A pdb=" N ARG e 966 " --> pdb=" O LEU e 962 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER e 967 " --> pdb=" O MET e 963 " (cutoff:3.500A) Processing helix chain 'e' and resid 970 through 986 removed outlier: 3.547A pdb=" N THR e 974 " --> pdb=" O LYS e 970 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 995 Processing helix chain 'e' and resid 996 through 1008 Processing helix chain 'e' and resid 1020 through 1038 removed outlier: 4.588A pdb=" N ASP e1038 " --> pdb=" O TRP e1034 " (cutoff:3.500A) Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 4.313A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1069 Processing helix chain 'e' and resid 1070 through 1090 removed outlier: 3.543A pdb=" N ILE e1089 " --> pdb=" O SER e1085 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASP e1090 " --> pdb=" O MET e1086 " (cutoff:3.500A) Processing helix chain 'e' and resid 1094 through 1111 Processing helix chain 'e' and resid 1123 through 1137 removed outlier: 3.812A pdb=" N PHE e1136 " --> pdb=" O ILE e1132 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 4.913A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1181 removed outlier: 4.146A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG e1173 " --> pdb=" O SER e1169 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 4.657A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 removed outlier: 3.708A pdb=" N LEU e1193 " --> pdb=" O ASN e1189 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU e1197 " --> pdb=" O LEU e1193 " (cutoff:3.500A) Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 5.213A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) Processing helix chain 'e' and resid 1241 through 1252 removed outlier: 3.648A pdb=" N LEU e1245 " --> pdb=" O PRO e1241 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL e1252 " --> pdb=" O VAL e1248 " (cutoff:3.500A) Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.613A pdb=" N PHE e1265 " --> pdb=" O ASN e1261 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR e1278 " --> pdb=" O LEU e1274 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE e1279 " --> pdb=" O ILE e1275 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 5.137A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 3.972A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP e1323 " --> pdb=" O TRP e1319 " (cutoff:3.500A) Processing helix chain 'e' and resid 1324 through 1329 Processing helix chain 'e' and resid 1341 through 1363 Processing helix chain 'e' and resid 1364 through 1374 removed outlier: 5.161A pdb=" N SER e1368 " --> pdb=" O GLY e1364 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.328A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1448 through 1453 removed outlier: 4.377A pdb=" N ASN e1453 " --> pdb=" O TYR e1449 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1481 Processing helix chain 'e' and resid 1486 through 1502 Processing helix chain 'e' and resid 1535 through 1547 removed outlier: 3.932A pdb=" N GLY e1547 " --> pdb=" O PHE e1543 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.234A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.830A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.797A pdb=" N MET g 62 " --> pdb=" O ILE g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 88 Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 122 through 133 Processing helix chain 'g' and resid 147 through 152 Processing helix chain 'g' and resid 166 through 178 Processing helix chain 'g' and resid 192 through 197 Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'v' and resid 22 through 27 removed outlier: 5.217A pdb=" N ARG v 27 " --> pdb=" O CYS v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 131 Processing helix chain 'w' and resid 5 through 21 Processing helix chain 'w' and resid 70 through 81 removed outlier: 3.729A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.660A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.877A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.557A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN w 119 " --> pdb=" O VAL w 115 " (cutoff:3.500A) Proline residue: w 121 - end of helix Processing helix chain 'w' and resid 126 through 132 Processing helix chain 'w' and resid 143 through 154 Processing helix chain 'w' and resid 175 through 195 removed outlier: 5.072A pdb=" N LYS w 195 " --> pdb=" O VAL w 191 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 Proline residue: z 34 - end of helix Processing helix chain 'z' and resid 39 through 52 Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.034A pdb=" N GLU z 87 " --> pdb=" O THR z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 118 Processing helix chain 'z' and resid 125 through 138 removed outlier: 4.663A pdb=" N SER z 138 " --> pdb=" O GLY z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 156 removed outlier: 5.015A pdb=" N ASN z 156 " --> pdb=" O ILE z 152 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 163 Proline residue: z 163 - end of helix Processing helix chain '0' and resid 3 through 23 removed outlier: 4.980A pdb=" N LYS 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 46 Processing helix chain '0' and resid 55 through 71 removed outlier: 4.923A pdb=" N SER 0 68 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP 0 69 " --> pdb=" O GLY 0 65 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU 0 70 " --> pdb=" O PHE 0 66 " (cutoff:3.500A) Proline residue: 0 71 - end of helix Processing helix chain '0' and resid 72 through 81 removed outlier: 4.429A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.205A pdb=" N LYS 0 81 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 72 through 81' Processing helix chain '0' and resid 93 through 103 Processing sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.466A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 133 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.634A pdb=" N ASN A 117 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 129 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'C' and resid 16 through 20 Processing sheet with id= 5, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.435A pdb=" N LYS C 80 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 124 through 131 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.878A pdb=" N THR D 100 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.707A pdb=" N ILE F 10 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 87 through 96 removed outlier: 5.102A pdb=" N ASN F 74 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.566A pdb=" N GLU F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.577A pdb=" N ASP G 38 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.171A pdb=" N ASN H 101 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 79 through 82 removed outlier: 3.920A pdb=" N ALA I 82 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP I 56 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 84 through 87 removed outlier: 4.505A pdb=" N VAL I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 75 through 78 Processing sheet with id= 16, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.441A pdb=" N GLU J 4 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 12 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP J 6 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 18 through 22 Processing sheet with id= 18, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.734A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 56 through 59 removed outlier: 4.092A pdb=" N GLN L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 21, first strand: chain 'L' and resid 86 through 89 removed outlier: 4.344A pdb=" N ALA L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 8 through 13 removed outlier: 4.144A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.644A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.372A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU P 41 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS P 66 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.934A pdb=" N ASP Q 48 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.753A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG S 48 " --> pdb=" O PHE S 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 8 through 14 removed outlier: 4.047A pdb=" N ALA S 96 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 19 through 24 removed outlier: 4.586A pdb=" N LYS T 19 " --> pdb=" O VAL T 35 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 2 through 5 removed outlier: 4.535A pdb=" N VAL X 55 " --> pdb=" O ILE X 5 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR X 22 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Z' and resid 100 through 103 removed outlier: 4.138A pdb=" N ALA Z 101 " --> pdb=" O CYS Z 96 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS Z 93 " --> pdb=" O LYS Z 124 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLN Z 120 " --> pdb=" O ARG Z 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 7 through 10 removed outlier: 4.477A pdb=" N VAL b 68 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR b 79 " --> pdb=" O CYS b 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 47 through 50 removed outlier: 6.881A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN j 86 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'j' and resid 111 through 114 removed outlier: 4.419A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.405A pdb=" N ALA j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.889A pdb=" N ALA k 42 " --> pdb=" O ASN k 184 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS k 201 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'k' and resid 53 through 59 removed outlier: 6.661A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE k 335 " --> pdb=" O VAL k 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL k 220 " --> pdb=" O ILE k 335 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS k 273 " --> pdb=" O THR k 221 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'k' and resid 98 through 101 Processing sheet with id= 42, first strand: chain 'k' and resid 284 through 288 removed outlier: 3.741A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN k 319 " --> pdb=" O GLY k 288 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 76 through 80 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'k' and resid 88 through 93 removed outlier: 3.744A pdb=" N GLY k 88 " --> pdb=" O LEU k 161 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'k' and resid 213 through 216 removed outlier: 4.189A pdb=" N GLU k 213 " --> pdb=" O ILE k 282 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 75 through 78 removed outlier: 4.383A pdb=" N GLN l 87 " --> pdb=" O VAL l 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 205 through 208 Processing sheet with id= 48, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.834A pdb=" N ILE m 64 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.956A pdb=" N THR n 38 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS n 50 " --> pdb=" O LEU n 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 133 through 138 removed outlier: 7.863A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.623A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.944A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 17 through 20 removed outlier: 5.994A pdb=" N ARG q 23 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 132 through 137 removed outlier: 4.964A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP q 142 " --> pdb=" O TYR q 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 86 through 90 Processing sheet with id= 57, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.337A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU r 52 " --> pdb=" O ILE r 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN r 133 " --> pdb=" O SER r 54 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 56 through 59 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 189 through 193 removed outlier: 7.659A pdb=" N GLU r 189 " --> pdb=" O LEU r 200 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 196 " --> pdb=" O ASP r 193 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 49 through 55 removed outlier: 5.068A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN r 162 " --> pdb=" O ASN r 55 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 's' and resid 45 through 49 removed outlier: 5.683A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.191A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.627A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU s 91 " --> pdb=" O ASP s 170 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'u' and resid 19 through 24 removed outlier: 4.472A pdb=" N ARG u 19 " --> pdb=" O ILE u 35 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS u 31 " --> pdb=" O ILE u 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 36 through 39 removed outlier: 6.764A pdb=" N LYS u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 24 through 27 removed outlier: 4.391A pdb=" N TYR a 24 " --> pdb=" O LEU a 89 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS a 87 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 28 through 32 removed outlier: 3.592A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 91 through 94 removed outlier: 6.887A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN a 121 " --> pdb=" O GLU a 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 306 through 310 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'a' and resid 446 through 454 removed outlier: 8.826A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 577 through 581 removed outlier: 4.044A pdb=" N LEU a 587 " --> pdb=" O LYS a 623 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY a 591 " --> pdb=" O HIS a 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS a 619 " --> pdb=" O GLY a 591 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 656 through 660 Processing sheet with id= 74, first strand: chain 'a' and resid 939 through 942 removed outlier: 4.719A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY a 959 " --> pdb=" O LYS a1013 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS a1013 " --> pdb=" O GLY a 959 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 5.490A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 77, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 78, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 79, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 80, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.676A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.740A pdb=" N GLY v 30 " --> pdb=" O ILE v 41 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL v 60 " --> pdb=" O VAL v 42 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'v' and resid 101 through 104 removed outlier: 3.654A pdb=" N ASP v 108 " --> pdb=" O ASN v 104 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.294A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.222A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 86, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.356A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.527A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain '0' and resid 49 through 53 removed outlier: 3.837A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) 3388 hydrogen bonds defined for protein. 10071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2921 hydrogen bonds 4660 hydrogen bond angles 0 basepair planarities 1186 basepair parallelities 2012 stacking parallelities Total time for adding SS restraints: 236.18 Time building geometry restraints manager: 66.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 20031 1.32 - 1.45: 63029 1.45 - 1.57: 71237 1.57 - 1.70: 7275 1.70 - 1.82: 279 Bond restraints: 161851 Sorted by residual: bond pdb=" N UNK 1 58 " pdb=" CA UNK 1 58 " ideal model delta sigma weight residual 1.458 1.667 -0.209 1.90e-02 2.77e+03 1.21e+02 bond pdb=" C2 I y 34 " pdb=" N3 I y 34 " ideal model delta sigma weight residual 1.462 1.306 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C2 I x 34 " pdb=" N3 I x 34 " ideal model delta sigma weight residual 1.462 1.307 0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C4 I x 34 " pdb=" N3 I x 34 " ideal model delta sigma weight residual 1.492 1.356 0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C4 I y 34 " pdb=" N3 I y 34 " ideal model delta sigma weight residual 1.492 1.358 0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 161846 not shown) Histogram of bond angle deviations from ideal: 95.64 - 103.83: 11523 103.83 - 112.02: 91105 112.02 - 120.21: 72565 120.21 - 128.40: 56150 128.40 - 136.58: 5076 Bond angle restraints: 236419 Sorted by residual: angle pdb=" N ILE e 884 " pdb=" CA ILE e 884 " pdb=" C ILE e 884 " ideal model delta sigma weight residual 110.62 101.28 9.34 1.02e+00 9.61e-01 8.38e+01 angle pdb=" N GLY e 19 " pdb=" CA GLY e 19 " pdb=" C GLY e 19 " ideal model delta sigma weight residual 111.36 122.07 -10.71 1.17e+00 7.31e-01 8.38e+01 angle pdb=" N LYS e1182 " pdb=" CA LYS e1182 " pdb=" C LYS e1182 " ideal model delta sigma weight residual 111.28 121.06 -9.78 1.09e+00 8.42e-01 8.05e+01 angle pdb=" N GLY e1364 " pdb=" CA GLY e1364 " pdb=" C GLY e1364 " ideal model delta sigma weight residual 112.49 122.64 -10.15 1.21e+00 6.83e-01 7.03e+01 angle pdb=" N LYS e 868 " pdb=" CA LYS e 868 " pdb=" C LYS e 868 " ideal model delta sigma weight residual 111.28 120.35 -9.07 1.09e+00 8.42e-01 6.92e+01 ... (remaining 236414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 92990 35.99 - 71.99: 8404 71.99 - 107.98: 867 107.98 - 143.98: 20 143.98 - 179.97: 57 Dihedral angle restraints: 102338 sinusoidal: 74883 harmonic: 27455 Sorted by residual: dihedral pdb=" CA GLY e 392 " pdb=" C GLY e 392 " pdb=" N PHE e 393 " pdb=" CA PHE e 393 " ideal model delta harmonic sigma weight residual -180.00 -92.74 -87.26 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" CA THR p 30 " pdb=" C THR p 30 " pdb=" N PRO p 31 " pdb=" CA PRO p 31 " ideal model delta harmonic sigma weight residual -180.00 -124.91 -55.09 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLY O 20 " pdb=" C GLY O 20 " pdb=" N ILE O 21 " pdb=" CA ILE O 21 " ideal model delta harmonic sigma weight residual -180.00 -132.46 -47.54 0 5.00e+00 4.00e-02 9.04e+01 ... (remaining 102335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28966 0.149 - 0.299: 508 0.299 - 0.448: 33 0.448 - 0.598: 4 0.598 - 0.747: 1 Chirality restraints: 29512 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA ASP p 158 " pdb=" N ASP p 158 " pdb=" C ASP p 158 " pdb=" CB ASP p 158 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C3' G f 282 " pdb=" C4' G f 282 " pdb=" O3' G f 282 " pdb=" C2' G f 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 29509 not shown) Planarity restraints: 16481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I y 34 " 0.196 2.00e-02 2.50e+03 5.59e-01 7.04e+03 pdb=" C2' I y 34 " -0.211 2.00e-02 2.50e+03 pdb=" C3' I y 34 " -0.550 2.00e-02 2.50e+03 pdb=" C4' I y 34 " 0.462 2.00e-02 2.50e+03 pdb=" C5' I y 34 " 0.003 2.00e-02 2.50e+03 pdb=" N9 I y 34 " -0.887 2.00e-02 2.50e+03 pdb=" O2' I y 34 " 0.819 2.00e-02 2.50e+03 pdb=" O3' I y 34 " -0.525 2.00e-02 2.50e+03 pdb=" O4' I y 34 " 0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I x 34 " 0.319 2.00e-02 2.50e+03 3.19e-01 2.30e+03 pdb=" C2' I x 34 " -0.396 2.00e-02 2.50e+03 pdb=" C3' I x 34 " -0.460 2.00e-02 2.50e+03 pdb=" C4' I x 34 " 0.338 2.00e-02 2.50e+03 pdb=" C5' I x 34 " -0.206 2.00e-02 2.50e+03 pdb=" N9 I x 34 " -0.312 2.00e-02 2.50e+03 pdb=" O2' I x 34 " 0.275 2.00e-02 2.50e+03 pdb=" O3' I x 34 " 0.119 2.00e-02 2.50e+03 pdb=" O4' I x 34 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 95 " -0.034 2.00e-02 2.50e+03 3.46e-02 2.99e+01 pdb=" CG TRP m 95 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP m 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 95 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 95 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 ... (remaining 16478 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 23 1.92 - 2.66: 6296 2.66 - 3.41: 189535 3.41 - 4.15: 478084 4.15 - 4.90: 689386 Nonbonded interactions: 1363324 Sorted by model distance: nonbonded pdb=" O ASN e 882 " pdb=" O GLN e 885 " model vdw 1.172 3.040 nonbonded pdb=" CE MET e 277 " pdb=" CB MET e 284 " model vdw 1.275 3.860 nonbonded pdb=" O3' A x 76 " pdb=" O UNK 1 58 " model vdw 1.378 3.040 nonbonded pdb=" O GLU e 324 " pdb=" OG1 THR e 327 " model vdw 1.499 2.440 nonbonded pdb=" OP1 U f1258 " pdb=" NH1 ARG 0 46 " model vdw 1.522 2.520 ... (remaining 1363319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and (resid 1 through 17 or resid 21 through 76)) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.99 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: 5.300 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: 0.180 Extract box with map and model: 23.260 Check model and map are aligned: 1.610 Set scattering table: 1.120 Process input model: 581.730 Find NCS groups from input model: 3.450 Set up NCS constraints: 0.420 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:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 627.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.209 161851 Z= 0.381 Angle : 0.912 21.620 236419 Z= 0.506 Chirality : 0.053 0.747 29512 Planarity : 0.009 0.559 16481 Dihedral : 21.693 179.974 84574 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 1.49 % Allowed : 2.13 % Favored : 96.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.11 % 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: -0.39 (0.08), residues: 9312 helix: 0.71 (0.08), residues: 3910 sheet: -0.03 (0.14), residues: 1220 loop : -1.23 (0.08), residues: 4182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP m 95 HIS 0.017 0.002 HIS r 123 PHE 0.046 0.002 PHE o 229 TYR 0.067 0.003 TYR N 60 ARG 0.026 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 985 time to evaluate : 8.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 148 ASP cc_start: 0.8585 (t70) cc_final: 0.8269 (t0) REVERT: G 156 TYR cc_start: 0.8793 (t80) cc_final: 0.8584 (t80) REVERT: I 133 SER cc_start: 0.9023 (p) cc_final: 0.8794 (p) REVERT: M 85 TYR cc_start: 0.8448 (m-80) cc_final: 0.8184 (m-80) REVERT: P 20 SER cc_start: 0.8449 (t) cc_final: 0.8063 (t) REVERT: P 99 ASP cc_start: 0.8277 (p0) cc_final: 0.8048 (p0) REVERT: T 100 ILE cc_start: 0.9268 (mt) cc_final: 0.9049 (mt) REVERT: U 30 GLU cc_start: 0.7026 (tp30) cc_final: 0.6752 (tp30) REVERT: X 27 ILE cc_start: 0.9294 (mm) cc_final: 0.9044 (mm) REVERT: Y 25 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7221 (tm-30) REVERT: m 206 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8172 (tm-30) REVERT: n 133 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7211 (tm-30) REVERT: n 137 ASP cc_start: 0.7931 (m-30) cc_final: 0.7726 (m-30) REVERT: r 115 MET cc_start: 0.9239 (mmm) cc_final: 0.9025 (mmm) REVERT: s 15 GLU cc_start: 0.8214 (tt0) cc_final: 0.7474 (tt0) REVERT: s 22 SER cc_start: 0.9292 (m) cc_final: 0.8991 (t) REVERT: s 78 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8303 (tm-30) REVERT: s 79 ILE cc_start: 0.9728 (mt) cc_final: 0.9390 (mp) REVERT: s 95 ASN cc_start: 0.9296 (m-40) cc_final: 0.9053 (m110) REVERT: s 132 ASN cc_start: 0.8245 (p0) cc_final: 0.7463 (p0) REVERT: e 63 GLU cc_start: 0.8999 (tt0) cc_final: 0.8793 (tm-30) REVERT: e 77 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9041 (p0) REVERT: e 178 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9220 (pp) REVERT: e 277 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7236 (ppp) REVERT: e 372 ASP cc_start: 0.9632 (OUTLIER) cc_final: 0.9083 (p0) REVERT: e 387 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8691 (tmt170) REVERT: e 826 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6166 (tt) REVERT: e 862 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.4456 (t80) REVERT: e 989 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: e 1055 PHE cc_start: 0.8996 (t80) cc_final: 0.8510 (t80) REVERT: e 1086 MET cc_start: 0.8205 (ptt) cc_final: 0.7664 (pp-130) REVERT: e 1303 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8836 (tpp) REVERT: e 1477 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.9041 (tp-100) REVERT: g 6 GLN cc_start: 0.8817 (mt0) cc_final: 0.8462 (mt0) REVERT: g 67 ARG cc_start: 0.8899 (ptm-80) cc_final: 0.8684 (ptm-80) REVERT: g 112 ASP cc_start: 0.9071 (m-30) cc_final: 0.8808 (m-30) REVERT: v 26 LEU cc_start: 0.7721 (mt) cc_final: 0.7390 (mt) REVERT: v 124 LEU cc_start: 0.9531 (tp) cc_final: 0.9264 (mm) REVERT: w 46 ASP cc_start: 0.7352 (m-30) cc_final: 0.7005 (m-30) REVERT: w 124 LEU cc_start: 0.9225 (mt) cc_final: 0.8974 (tm) REVERT: 0 7 LYS cc_start: 0.9482 (tppt) cc_final: 0.8923 (tppp) REVERT: 0 11 TYR cc_start: 0.8937 (t80) cc_final: 0.8670 (t80) REVERT: 0 18 TYR cc_start: 0.9323 (m-80) cc_final: 0.9025 (m-80) REVERT: 0 22 TYR cc_start: 0.9198 (m-80) cc_final: 0.8906 (m-80) REVERT: 0 53 MET cc_start: 0.8185 (mmm) cc_final: 0.7921 (mmm) REVERT: 0 69 ASP cc_start: 0.8625 (p0) cc_final: 0.7154 (p0) REVERT: 0 189 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: 0 191 TYR cc_start: 0.8718 (t80) cc_final: 0.8078 (t80) outliers start: 113 outliers final: 29 residues processed: 1090 average time/residue: 2.1797 time to fit residues: 3446.4756 Evaluate side-chains 757 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 717 time to evaluate : 8.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain s residue 29 ARG Chi-restraints excluded: chain a residue 893 LYS Chi-restraints excluded: chain e residue 77 ASN Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain e residue 228 ASP Chi-restraints excluded: chain e residue 254 ASN Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 327 THR Chi-restraints excluded: chain e residue 372 ASP Chi-restraints excluded: chain e residue 387 ARG Chi-restraints excluded: chain e residue 412 PHE Chi-restraints excluded: chain e residue 731 LEU Chi-restraints excluded: chain e residue 737 TYR Chi-restraints excluded: chain e residue 743 LYS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 757 CYS Chi-restraints excluded: chain e residue 760 THR Chi-restraints excluded: chain e residue 826 LEU Chi-restraints excluded: chain e residue 844 LEU Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 950 THR Chi-restraints excluded: chain e residue 987 ILE Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 993 VAL Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1094 TYR Chi-restraints excluded: chain e residue 1102 CYS Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1303 MET Chi-restraints excluded: chain e residue 1379 LEU Chi-restraints excluded: chain e residue 1391 ILE Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1470 LYS Chi-restraints excluded: chain e residue 1477 GLN Chi-restraints excluded: chain w residue 143 ASP Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 0 residue 189 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1083 optimal weight: 8.9990 chunk 972 optimal weight: 10.0000 chunk 539 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 655 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 1005 optimal weight: 2.9990 chunk 389 optimal weight: 10.0000 chunk 611 optimal weight: 10.0000 chunk 748 optimal weight: 0.0030 chunk 1165 optimal weight: 20.0000 overall best weight: 6.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 50 ASN A C 137 ASN D 136 ASN G 103 GLN I 132 ASN N 120 ASN U 16 GLN V 12 ASN V 91 ASN X 40 GLN X 57 ASN X 76 ASN b 22 GLN l 361 HIS m 39 GLN n 4 GLN r 51 HIS ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 175 ASN s 90 GLN e 13 ASN e 189 ASN e 795 HIS e 805 ASN e 810 GLN ** e 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1288 GLN ** e1358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1457 ASN 0 36 GLN ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 161851 Z= 0.407 Angle : 0.665 15.728 236419 Z= 0.352 Chirality : 0.042 0.319 29512 Planarity : 0.006 0.111 16481 Dihedral : 22.655 179.709 66899 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 2.23 % Allowed : 8.75 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % 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: 0.00 (0.08), residues: 9312 helix: 1.07 (0.08), residues: 3935 sheet: -0.10 (0.14), residues: 1205 loop : -0.98 (0.09), residues: 4172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP e1034 HIS 0.010 0.001 HIS N 40 PHE 0.048 0.002 PHE e1028 TYR 0.028 0.002 TYR N 60 ARG 0.008 0.001 ARG g 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 741 time to evaluate : 8.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3 ILE cc_start: 0.8998 (mm) cc_final: 0.8733 (mt) REVERT: E 148 ASP cc_start: 0.8508 (t70) cc_final: 0.8299 (t0) REVERT: L 26 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7394 (tp-100) REVERT: P 99 ASP cc_start: 0.8464 (p0) cc_final: 0.8236 (p0) REVERT: U 30 GLU cc_start: 0.6974 (tp30) cc_final: 0.6665 (tp30) REVERT: X 10 GLN cc_start: 0.8679 (tt0) cc_final: 0.8450 (tt0) REVERT: b 71 ARG cc_start: 0.8323 (ttt90) cc_final: 0.8029 (ttt180) REVERT: d 4 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: d 9 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.8015 (mtp85) REVERT: j 24 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: k 308 MET cc_start: 0.8779 (mmm) cc_final: 0.8542 (mtt) REVERT: m 206 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8146 (tm-30) REVERT: n 133 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7254 (tm-30) REVERT: n 137 ASP cc_start: 0.8027 (m-30) cc_final: 0.7700 (m-30) REVERT: s 15 GLU cc_start: 0.8206 (tt0) cc_final: 0.7689 (tt0) REVERT: s 22 SER cc_start: 0.9353 (m) cc_final: 0.8878 (p) REVERT: s 79 ILE cc_start: 0.9747 (mt) cc_final: 0.9411 (mp) REVERT: s 90 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7927 (mm-40) REVERT: s 95 ASN cc_start: 0.9311 (m-40) cc_final: 0.9104 (m110) REVERT: s 108 GLU cc_start: 0.8503 (pm20) cc_final: 0.8297 (pp20) REVERT: a 658 TRP cc_start: 0.8267 (p-90) cc_final: 0.7794 (p-90) REVERT: e 63 GLU cc_start: 0.8911 (tt0) cc_final: 0.8623 (tm-30) REVERT: e 284 MET cc_start: 0.8881 (ttp) cc_final: 0.8445 (ptp) REVERT: e 387 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8784 (tmt170) REVERT: e 809 MET cc_start: 0.9605 (mtp) cc_final: 0.9355 (ptp) REVERT: e 826 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5741 (tt) REVERT: e 840 VAL cc_start: 0.1152 (OUTLIER) cc_final: 0.0923 (t) REVERT: e 998 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5596 (mtpp) REVERT: e 1002 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5472 (mt) REVERT: e 1055 PHE cc_start: 0.9188 (t80) cc_final: 0.8718 (t80) REVERT: e 1102 CYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7315 (p) REVERT: e 1132 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8194 (tp) REVERT: e 1162 MET cc_start: 0.8902 (tmt) cc_final: 0.8026 (ppp) REVERT: e 1206 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: e 1281 ASP cc_start: 0.9079 (m-30) cc_final: 0.8530 (t0) REVERT: e 1470 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9097 (mmtm) REVERT: g 1 MET cc_start: 0.5448 (mtt) cc_final: 0.4792 (mtt) REVERT: g 6 GLN cc_start: 0.8769 (mt0) cc_final: 0.8421 (mt0) REVERT: g 12 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: v 120 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (pt) REVERT: w 124 LEU cc_start: 0.9258 (mt) cc_final: 0.9022 (tm) REVERT: w 174 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7951 (mpm) REVERT: 0 7 LYS cc_start: 0.9255 (tppt) cc_final: 0.8794 (tppp) REVERT: 0 14 LYS cc_start: 0.9353 (ttpp) cc_final: 0.8816 (ttmt) REVERT: 0 16 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8618 (tpp80) REVERT: 0 18 TYR cc_start: 0.9353 (m-80) cc_final: 0.9015 (m-10) REVERT: 0 48 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8735 (ptm160) REVERT: 0 64 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8606 (mtm110) REVERT: 0 69 ASP cc_start: 0.8157 (p0) cc_final: 0.7604 (p0) REVERT: 0 78 PRO cc_start: 0.9392 (Cg_exo) cc_final: 0.9174 (Cg_endo) REVERT: 0 88 PHE cc_start: 0.7787 (m-80) cc_final: 0.7582 (m-80) REVERT: 0 191 TYR cc_start: 0.8610 (t80) cc_final: 0.7985 (t80) outliers start: 169 outliers final: 67 residues processed: 838 average time/residue: 2.1830 time to fit residues: 2666.3081 Evaluate side-chains 767 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 683 time to evaluate : 8.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain d residue 9 ARG Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 34 SER Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 90 GLN Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 699 MET Chi-restraints excluded: chain e residue 205 GLU Chi-restraints excluded: chain e residue 324 GLU Chi-restraints excluded: chain e residue 387 ARG Chi-restraints excluded: chain e residue 412 PHE Chi-restraints excluded: chain e residue 737 TYR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 760 THR Chi-restraints excluded: chain e residue 826 LEU Chi-restraints excluded: chain e residue 840 VAL Chi-restraints excluded: chain e residue 845 VAL Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 998 LYS Chi-restraints excluded: chain e residue 1002 LEU Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1102 CYS Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1132 ILE Chi-restraints excluded: chain e residue 1206 GLN Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1470 LYS Chi-restraints excluded: chain e residue 1490 SER Chi-restraints excluded: chain e residue 1507 GLU Chi-restraints excluded: chain g residue 12 GLU Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 48 ARG Chi-restraints excluded: chain 0 residue 51 VAL Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 96 ILE Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 647 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 969 optimal weight: 40.0000 chunk 793 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 1167 optimal weight: 9.9990 chunk 1260 optimal weight: 20.0000 chunk 1039 optimal weight: 8.9990 chunk 1157 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN I 98 ASN S 42 GLN V 12 ASN V 91 ASN X 10 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN b 102 GLN j 97 ASN ** o 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN p 79 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 233 ASN e 254 ASN ** e 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1141 GLN e1190 GLN e1288 GLN ** g 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 170 GLN v 22 GLN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 161851 Z= 0.421 Angle : 0.653 15.635 236419 Z= 0.346 Chirality : 0.042 0.328 29512 Planarity : 0.005 0.115 16481 Dihedral : 22.589 179.785 66840 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 2.50 % Allowed : 11.41 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.08), residues: 9312 helix: 1.33 (0.08), residues: 3933 sheet: -0.04 (0.15), residues: 1175 loop : -0.86 (0.09), residues: 4204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 944 HIS 0.011 0.001 HIS g 162 PHE 0.028 0.002 PHE o 229 TYR 0.028 0.002 TYR l 194 ARG 0.010 0.001 ARG k 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 712 time to evaluate : 8.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7713 (tp30) cc_final: 0.7385 (tp30) REVERT: B 150 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: C 126 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7540 (mtp85) REVERT: C 182 ILE cc_start: 0.8825 (tp) cc_final: 0.8554 (tp) REVERT: H 92 TRP cc_start: 0.7972 (m-90) cc_final: 0.7528 (m-90) REVERT: L 26 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7452 (tp-100) REVERT: P 99 ASP cc_start: 0.8483 (p0) cc_final: 0.8213 (p0) REVERT: T 98 GLN cc_start: 0.8840 (tp40) cc_final: 0.8606 (tp40) REVERT: U 30 GLU cc_start: 0.7100 (tp30) cc_final: 0.6846 (tp30) REVERT: X 10 GLN cc_start: 0.8689 (tt0) cc_final: 0.8450 (tt0) REVERT: b 71 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (ttt90) REVERT: d 4 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: d 19 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.6144 (mmtm) REVERT: j 143 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7624 (tm-30) REVERT: k 308 MET cc_start: 0.8745 (mmm) cc_final: 0.8534 (mtt) REVERT: m 206 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8067 (tm-30) REVERT: n 133 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7204 (tm-30) REVERT: n 137 ASP cc_start: 0.8003 (m-30) cc_final: 0.7760 (m-30) REVERT: p 219 ASP cc_start: 0.8420 (m-30) cc_final: 0.8163 (m-30) REVERT: s 22 SER cc_start: 0.9397 (m) cc_final: 0.9018 (t) REVERT: s 38 GLU cc_start: 0.8577 (tp30) cc_final: 0.8363 (tp30) REVERT: s 77 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7121 (tm-30) REVERT: s 79 ILE cc_start: 0.9710 (mt) cc_final: 0.9495 (mp) REVERT: s 81 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8054 (mm-30) REVERT: s 90 GLN cc_start: 0.8606 (tp40) cc_final: 0.8278 (mm-40) REVERT: a 658 TRP cc_start: 0.8499 (p-90) cc_final: 0.7581 (p-90) REVERT: e 277 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7924 (ppp) REVERT: e 1055 PHE cc_start: 0.9199 (t80) cc_final: 0.8686 (t80) REVERT: e 1086 MET cc_start: 0.8116 (ptt) cc_final: 0.7552 (pp-130) REVERT: e 1188 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8984 (tp) REVERT: e 1206 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: e 1281 ASP cc_start: 0.9018 (m-30) cc_final: 0.8562 (t0) REVERT: e 1470 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9010 (mmtt) REVERT: e 1474 MET cc_start: 0.9641 (OUTLIER) cc_final: 0.9198 (mtp) REVERT: e 1512 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8153 (m-10) REVERT: g 6 GLN cc_start: 0.8592 (mt0) cc_final: 0.8235 (mt0) REVERT: g 12 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: g 139 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7055 (mtt180) REVERT: v 120 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8272 (pt) REVERT: w 124 LEU cc_start: 0.9352 (mt) cc_final: 0.9029 (tm) REVERT: w 174 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8163 (mpm) REVERT: 0 7 LYS cc_start: 0.9120 (tppt) cc_final: 0.8875 (mmmm) REVERT: 0 8 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9192 (mttt) REVERT: 0 10 GLU cc_start: 0.9122 (pp20) cc_final: 0.8889 (pp20) REVERT: 0 38 MET cc_start: 0.8996 (tmm) cc_final: 0.8512 (tmm) REVERT: 0 48 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8813 (ptm160) REVERT: 0 191 TYR cc_start: 0.8686 (t80) cc_final: 0.8008 (t80) outliers start: 189 outliers final: 82 residues processed: 821 average time/residue: 2.1699 time to fit residues: 2607.6267 Evaluate side-chains 771 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 672 time to evaluate : 8.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 76 GLU Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 92 LYS Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 71 ARG Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain d residue 19 LYS Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 699 MET Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 412 PHE Chi-restraints excluded: chain e residue 737 TYR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 760 THR Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1094 TYR Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1188 ILE Chi-restraints excluded: chain e residue 1206 GLN Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1470 LYS Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1512 TYR Chi-restraints excluded: chain g residue 12 GLU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 8 LYS Chi-restraints excluded: chain 0 residue 48 ARG Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1153 optimal weight: 30.0000 chunk 877 optimal weight: 0.9980 chunk 605 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 557 optimal weight: 50.0000 chunk 783 optimal weight: 20.0000 chunk 1171 optimal weight: 50.0000 chunk 1240 optimal weight: 0.7980 chunk 612 optimal weight: 8.9990 chunk 1110 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN X 76 ASN ** o 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN p 79 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1499 HIS ** g 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 182 GLN w 188 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 161851 Z= 0.316 Angle : 0.604 15.162 236419 Z= 0.321 Chirality : 0.039 0.297 29512 Planarity : 0.005 0.111 16481 Dihedral : 22.576 179.762 66832 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 2.42 % Allowed : 12.94 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 9312 helix: 1.48 (0.08), residues: 3928 sheet: 0.02 (0.14), residues: 1214 loop : -0.80 (0.09), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 944 HIS 0.008 0.001 HIS g 162 PHE 0.024 0.001 PHE o 229 TYR 0.023 0.001 TYR l 194 ARG 0.020 0.000 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 699 time to evaluate : 8.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7726 (tp30) cc_final: 0.7454 (tp30) REVERT: B 84 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 150 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: C 126 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: C 182 ILE cc_start: 0.8913 (tp) cc_final: 0.8632 (tp) REVERT: H 23 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9213 (t) REVERT: J 12 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8692 (mtpp) REVERT: L 26 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7388 (tp-100) REVERT: M 106 GLN cc_start: 0.8815 (mp10) cc_final: 0.8519 (mp10) REVERT: P 99 ASP cc_start: 0.8469 (p0) cc_final: 0.8202 (p0) REVERT: T 98 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8581 (tp40) REVERT: U 30 GLU cc_start: 0.7099 (tp30) cc_final: 0.6891 (tp30) REVERT: V 92 ASN cc_start: 0.8866 (m-40) cc_final: 0.8624 (m-40) REVERT: X 10 GLN cc_start: 0.8680 (tt0) cc_final: 0.8471 (tt0) REVERT: X 77 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8131 (mmm-85) REVERT: d 4 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: d 9 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7194 (mpp80) REVERT: d 16 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7738 (mp) REVERT: j 143 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7713 (tm-30) REVERT: n 142 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: s 22 SER cc_start: 0.9394 (m) cc_final: 0.9026 (t) REVERT: s 44 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9107 (p) REVERT: s 77 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7434 (tm-30) REVERT: s 81 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8143 (mm-30) REVERT: a 658 TRP cc_start: 0.8438 (p-90) cc_final: 0.7640 (p-90) REVERT: a 699 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4921 (mmm) REVERT: e 809 MET cc_start: 0.9558 (ptp) cc_final: 0.9191 (pmm) REVERT: e 857 ASP cc_start: 0.9579 (OUTLIER) cc_final: 0.9368 (t0) REVERT: e 1031 ILE cc_start: 0.9507 (mt) cc_final: 0.9286 (pp) REVERT: e 1055 PHE cc_start: 0.9209 (t80) cc_final: 0.8798 (t80) REVERT: e 1086 MET cc_start: 0.8166 (ptt) cc_final: 0.7670 (pp-130) REVERT: e 1162 MET cc_start: 0.8751 (tmt) cc_final: 0.7636 (ppp) REVERT: e 1206 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: e 1281 ASP cc_start: 0.9083 (m-30) cc_final: 0.8629 (t0) REVERT: e 1303 MET cc_start: 0.8694 (tpp) cc_final: 0.8462 (tpp) REVERT: e 1384 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: e 1470 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9038 (mmtm) REVERT: e 1474 MET cc_start: 0.9632 (mtp) cc_final: 0.9268 (mtp) REVERT: g 1 MET cc_start: 0.5801 (ttt) cc_final: 0.5464 (ttt) REVERT: g 6 GLN cc_start: 0.8538 (mt0) cc_final: 0.8137 (mt0) REVERT: g 12 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: g 139 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7936 (mtt180) REVERT: v 120 LEU cc_start: 0.8525 (mm) cc_final: 0.8272 (pt) REVERT: w 124 LEU cc_start: 0.9378 (mt) cc_final: 0.9073 (tm) REVERT: w 174 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8175 (mpm) REVERT: 0 6 GLU cc_start: 0.9032 (mp0) cc_final: 0.8822 (mp0) REVERT: 0 7 LYS cc_start: 0.9105 (tppt) cc_final: 0.8787 (mmmm) REVERT: 0 8 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9177 (mmtt) REVERT: 0 10 GLU cc_start: 0.9159 (pp20) cc_final: 0.8886 (pp20) REVERT: 0 14 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8807 (tmtt) REVERT: 0 18 TYR cc_start: 0.9161 (m-80) cc_final: 0.8793 (m-80) REVERT: 0 26 PHE cc_start: 0.9217 (m-10) cc_final: 0.8531 (m-80) REVERT: 0 37 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: 0 38 MET cc_start: 0.8842 (tmm) cc_final: 0.8498 (tmm) REVERT: 0 48 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8982 (ptm160) REVERT: 0 191 TYR cc_start: 0.8554 (t80) cc_final: 0.7856 (t80) outliers start: 183 outliers final: 88 residues processed: 810 average time/residue: 2.2058 time to fit residues: 2628.2744 Evaluate side-chains 778 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 670 time to evaluate : 8.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 77 ARG Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 699 MET Chi-restraints excluded: chain e residue 412 PHE Chi-restraints excluded: chain e residue 737 TYR Chi-restraints excluded: chain e residue 760 THR Chi-restraints excluded: chain e residue 845 VAL Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 865 THR Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 1033 LYS Chi-restraints excluded: chain e residue 1094 TYR Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1206 GLN Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1384 GLU Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1470 LYS Chi-restraints excluded: chain e residue 1490 SER Chi-restraints excluded: chain g residue 12 GLU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 8 LYS Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 37 GLN Chi-restraints excluded: chain 0 residue 48 ARG Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4631 > 50: distance: 56 - 72: 23.776 distance: 70 - 72: 23.395 distance: 72 - 73: 7.576 distance: 73 - 74: 16.645 distance: 73 - 76: 33.393 distance: 74 - 75: 11.549 distance: 74 - 80: 23.879 distance: 76 - 77: 17.595 distance: 77 - 78: 16.166 distance: 77 - 79: 9.069 distance: 80 - 81: 14.850 distance: 81 - 82: 18.626 distance: 81 - 84: 18.302 distance: 82 - 83: 26.784 distance: 82 - 89: 12.604 distance: 84 - 85: 34.496 distance: 85 - 86: 25.163 distance: 86 - 87: 23.956 distance: 87 - 88: 25.122 distance: 89 - 90: 4.396 distance: 90 - 91: 4.488 distance: 90 - 93: 6.685 distance: 91 - 92: 9.795 distance: 91 - 98: 4.142 distance: 92 - 123: 19.868 distance: 93 - 94: 14.857 distance: 94 - 95: 10.371 distance: 95 - 96: 10.830 distance: 95 - 97: 10.854 distance: 98 - 99: 13.439 distance: 99 - 100: 9.628 distance: 99 - 102: 16.545 distance: 100 - 101: 15.312 distance: 100 - 107: 15.876 distance: 102 - 103: 3.636 distance: 103 - 104: 8.150 distance: 104 - 105: 7.484 distance: 104 - 106: 9.165 distance: 107 - 108: 6.628 distance: 108 - 109: 13.737 distance: 108 - 111: 8.762 distance: 109 - 110: 12.547 distance: 111 - 112: 12.953 distance: 112 - 113: 29.919 distance: 112 - 114: 12.261 distance: 115 - 116: 19.773 distance: 116 - 117: 11.235 distance: 116 - 119: 23.500 distance: 117 - 118: 24.368 distance: 117 - 123: 19.586 distance: 118 - 146: 30.282 distance: 119 - 120: 11.759 distance: 120 - 121: 16.393 distance: 120 - 122: 12.934 distance: 123 - 124: 35.773 distance: 124 - 125: 13.890 distance: 124 - 127: 14.608 distance: 125 - 126: 31.295 distance: 125 - 130: 12.533 distance: 127 - 128: 33.518 distance: 127 - 129: 30.892 distance: 130 - 131: 11.120 distance: 131 - 132: 25.246 distance: 131 - 134: 11.358 distance: 132 - 133: 25.000 distance: 132 - 138: 13.084 distance: 134 - 135: 19.953 distance: 135 - 136: 21.301 distance: 135 - 137: 16.295 distance: 138 - 139: 17.660 distance: 139 - 140: 11.903 distance: 139 - 142: 18.148 distance: 140 - 141: 16.615 distance: 140 - 146: 19.185 distance: 142 - 143: 17.794 distance: 143 - 144: 26.306 distance: 143 - 145: 19.427 distance: 146 - 147: 12.118 distance: 147 - 148: 24.383 distance: 147 - 150: 36.354 distance: 148 - 149: 4.766 distance: 148 - 154: 30.410 distance: 150 - 151: 36.480 distance: 151 - 152: 20.615 distance: 151 - 153: 19.799