Starting phenix.real_space_refine on Wed Mar 27 13:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agt_15423/03_2024/8agt_15423_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= 0.020 sd= 0.128 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 3643 5.49 5 Mg 13 5.21 5 S 177 5.16 5 C 81316 2.51 5 N 27601 2.21 5 O 38584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151341 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: 68802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 220, 'rna3p_pur': 1449, 'rna3p_pyr': 1217} Link IDs: {'rna2p': 550, 'rna3p': 2665} Chain breaks: 3 Conformer: "B" 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 bond proxies already assigned to first conformer: 76966 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: 2 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: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6569 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 261 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': 6} Unresolved non-hydrogen planarities: 166 Chain: "e" Number of atoms: 11508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11508 Classifications: {'peptide': 1527} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 271} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 982 Unresolved non-hydrogen angles: 1253 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 24, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 569 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: "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: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1584 Classifications: {'RNA': 74, 'peptide': 1} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 57, None: 1} Not linked: pdbres=" A x 76 " pdbres="ALA x 77 " Chain breaks: 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': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain breaks: 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: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 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: "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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 44 120.499 171.734 212.538 1.00 54.16 S ATOM 20919 SG CYS T 47 122.583 169.075 211.448 1.00 59.61 S ATOM 21191 SG CYS T 84 123.787 171.556 214.264 1.00 57.91 S ATOM 23302 SG CYS W 19 85.116 189.395 170.267 1.00 40.18 S ATOM 23327 SG CYS W 22 83.363 189.474 166.988 1.00 41.00 S ATOM 23427 SG CYS W 34 87.094 189.467 167.026 1.00 38.42 S ATOM 23445 SG CYS W 37 85.281 192.575 168.208 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.167 140.452 76.579 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.543 138.777 78.596 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.409 138.243 74.917 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.360 141.471 76.159 1.00 52.77 S ATOM 25359 SG CYS b 12 132.479 247.979 110.126 1.00 63.95 S ATOM 25394 SG CYS b 17 133.767 251.511 109.221 1.00 72.10 S ATOM 25858 SG CYS b 74 135.977 248.990 111.349 1.00 60.93 S ATOM 25880 SG CYS b 77 132.885 250.840 112.531 1.00 66.15 S ATOM 26403 SG CYS c 39 139.127 169.183 205.672 1.00 58.71 S ATOM 26426 SG CYS c 42 138.506 166.207 207.769 1.00 62.48 S ATOM 26535 SG CYS c 57 136.284 166.726 204.781 1.00 55.64 S ATOM 26553 SG CYS c 60 135.875 169.195 207.534 1.00 57.82 S ATOM A0W6Q SG CYS e1527 39.624 126.224 188.600 1.00285.10 S ATOM A0W7A SG CYS e1530 37.267 123.775 187.334 1.00279.23 S ATOM A0WC2 SG CYS e1551 37.905 127.018 185.620 1.00286.27 S ATOM A0WCN SG CYS e1554 36.210 127.875 188.576 1.00284.05 S ATOM A0W2O SG CYS e1508 41.088 120.599 177.946 1.00285.58 S ATOM A0W37 SG CYS e1511 41.138 119.684 174.899 1.00284.14 S ATOM A0W90 SG CYS e1538 42.981 122.882 175.036 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 198 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 186 not shown) Time building chain proxies: 82.42, per 1000 atoms: 0.54 Number of scatterers: 151341 At special positions: 0 Unit cell: (232.98, 283.812, 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 3643 15.00 Mg 13 11.99 O 38584 8.00 N 27601 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: 60.20 Conformation dependent library (CDL) restraints added in 11.5 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 44 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " 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 34 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " 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 e1527 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1511 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " 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: 17762 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: 368 helices and 87 sheets defined 48.8% alpha, 12.9% beta 1185 base pairs and 2008 stacking pairs defined. Time for finding SS restraints: 91.64 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: 4.987A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.752A 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: 5.215A 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: 4.409A 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: 6.736A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.166A 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: 4.078A 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: 3.834A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.927A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.599A 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: 3.640A 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: 4.066A 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: 3.813A 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: 4.447A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.165A 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: 5.179A 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: 3.710A 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: 6.828A 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: 5.662A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.881A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.960A 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: 4.512A 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: 4.140A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.167A 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: 3.883A 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: 3.563A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.801A 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: 5.057A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.734A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.521A 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: 3.537A 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: 4.375A 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: 3.567A 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: 5.380A 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: 3.567A 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: 4.577A 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: 5.940A 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: 4.419A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.796A 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: 4.408A 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: 4.642A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.531A 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: 3.830A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.972A 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: 3.852A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.675A 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: 4.186A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.453A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.526A 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: 4.493A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.403A 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: 5.747A 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: 4.617A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.953A 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: 4.591A 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: 5.841A 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: 4.852A 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: 4.272A 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: 4.149A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.802A 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: 4.097A 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: 3.711A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.339A 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: 4.429A 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: 4.412A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.061A 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: 4.181A 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: 6.412A 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: 3.788A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.301A 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: 4.792A 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: 4.211A 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: 4.235A 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: 4.668A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.212A 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: 3.682A 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: 4.699A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.669A 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: 3.532A 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: 3.709A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.799A 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: 6.010A 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: 3.874A 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: 5.284A 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: 4.157A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.172A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.109A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.632A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.223A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.828A 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: 7.641A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.241A 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: 4.178A 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: 3.674A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.418A 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: 3.806A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.682A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.641A 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: 4.552A 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: 4.412A 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: 4.091A 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: 4.267A 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: 4.307A 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: 4.451A 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: 4.154A 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: 5.311A 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: 3.837A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.601A 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: 4.937A 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 19 removed outlier: 3.917A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 85 Processing helix chain 'a' and resid 153 through 160 removed outlier: 3.562A pdb=" N PHE a 157 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 5.473A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 3.920A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 229 Proline residue: a 229 - end of helix Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 removed outlier: 3.579A pdb=" N THR a 258 " --> pdb=" O LEU a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.342A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 3.603A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 395 removed outlier: 6.566A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE a 344 " --> pdb=" O PHE a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 413 Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 3.528A pdb=" N LEU a 437 " --> pdb=" O ILE a 433 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 527 Processing helix chain 'a' and resid 529 through 543 removed outlier: 4.174A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) Processing helix chain 'a' and resid 545 through 558 Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.631A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 4.940A 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 851 removed outlier: 3.510A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 3.792A pdb=" N LYS a 909 " --> pdb=" O LEU a 905 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 925 removed outlier: 3.699A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS a 925 " --> pdb=" O LYS a 921 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.550A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 4.097A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.489A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.589A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU a1008 " --> pdb=" O ASP a1004 " (cutoff:3.500A) removed outlier: 5.370A 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 Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.355A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 3.922A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 5.131A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 99 removed outlier: 4.005A 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: 4.221A pdb=" N LYS e 130 " --> pdb=" O SER e 126 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Proline residue: e 134 - end of helix removed outlier: 4.117A 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: 4.396A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 227 removed outlier: 3.814A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 4.141A 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 244 removed outlier: 5.667A pdb=" N GLU e 244 " --> pdb=" O ILE e 240 " (cutoff:3.500A) Processing helix chain 'e' and resid 245 through 251 removed outlier: 3.941A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 258 through 275 Processing helix chain 'e' and resid 276 through 281 removed outlier: 3.943A pdb=" N LYS e 281 " --> pdb=" O MET e 277 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 299 removed outlier: 5.418A 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: 5.266A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 3.542A pdb=" N SER e 330 " --> pdb=" O GLY e 326 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.991A 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: 3.647A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix removed outlier: 3.518A pdb=" N GLY e 392 " --> pdb=" O LEU e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 397 through 417 removed outlier: 4.212A pdb=" N SER e 416 " --> pdb=" O PHE e 412 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER e 417 " --> pdb=" O ALA e 413 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 438 through 443 removed outlier: 4.777A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 450 removed outlier: 3.810A pdb=" N SER e 450 " --> pdb=" O ASN e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 468 Processing helix chain 'e' and resid 469 through 477 removed outlier: 4.886A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 490 Processing helix chain 'e' and resid 493 through 512 Proline residue: e 512 - end of helix Processing helix chain 'e' and resid 514 through 520 removed outlier: 3.746A pdb=" N ASP e 520 " --> pdb=" O PHE e 516 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 533 removed outlier: 5.002A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 535 through 549 removed outlier: 3.640A pdb=" N GLY e 539 " --> pdb=" O ILE e 535 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS e 540 " --> pdb=" O PHE e 536 " (cutoff:3.500A) Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 556 through 571 removed outlier: 4.666A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 5.052A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.841A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 4.864A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.038A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 635 removed outlier: 5.503A pdb=" N LYS e 635 " --> pdb=" O MET e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 646 removed outlier: 4.223A 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: 4.509A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 690 Processing helix chain 'e' and resid 691 through 700 removed outlier: 5.082A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU e 699 " --> pdb=" O CYS e 695 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 719 Processing helix chain 'e' and resid 720 through 737 Processing helix chain 'e' and resid 742 through 755 removed outlier: 3.831A pdb=" N TYR e 746 " --> pdb=" O ALA e 742 " (cutoff:3.500A) Processing helix chain 'e' and resid 757 through 766 removed outlier: 3.684A pdb=" N SER e 761 " --> pdb=" O CYS e 757 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN e 762 " --> pdb=" O ASN e 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE e 763 " --> pdb=" O ASP e 759 " (cutoff:3.500A) Proline residue: e 766 - end of helix Processing helix chain 'e' and resid 768 through 778 removed outlier: 4.083A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Proline residue: e 778 - end of helix Processing helix chain 'e' and resid 781 through 789 removed outlier: 3.625A pdb=" N SER e 785 " --> pdb=" O ASP e 781 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU e 786 " --> pdb=" O TYR e 782 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL e 787 " --> pdb=" O ARG e 783 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER e 789 " --> pdb=" O SER e 785 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 4.557A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU e 797 " --> pdb=" O ASN e 793 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 792 through 798' Processing helix chain 'e' and resid 805 through 827 Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 Processing helix chain 'e' and resid 856 through 862 removed outlier: 5.683A 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 903 removed outlier: 3.612A pdb=" N ALA e 899 " --> pdb=" O THR e 895 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER e 903 " --> pdb=" O ALA e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 Processing helix chain 'e' and resid 926 through 947 removed outlier: 3.578A pdb=" N SER e 935 " --> pdb=" O GLY e 931 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLN e 947 " --> pdb=" O THR e 943 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 965 Processing helix chain 'e' and resid 970 through 986 removed outlier: 5.618A 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 1009 removed outlier: 5.250A pdb=" N ILE e1009 " --> pdb=" O ASN e1005 " (cutoff:3.500A) Processing helix chain 'e' and resid 1020 through 1038 removed outlier: 4.628A pdb=" N ASP e1038 " --> pdb=" O TRP e1034 " (cutoff:3.500A) Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 3.854A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 5.086A 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: 4.947A 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 1138 removed outlier: 5.133A pdb=" N ASN e1138 " --> pdb=" O LEU e1134 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 4.900A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1181 removed outlier: 3.558A pdb=" N GLN e1170 " --> pdb=" O LYS e1166 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG e1173 " --> pdb=" O SER e1169 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 4.466A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1210 Processing helix chain 'e' and resid 1212 through 1217 Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 5.320A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) Processing helix chain 'e' and resid 1241 through 1252 removed outlier: 4.607A pdb=" N VAL e1252 " --> pdb=" O VAL e1248 " (cutoff:3.500A) Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.750A 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: 5.026A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 4.523A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 4.993A 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 1331 through 1336 removed outlier: 4.016A pdb=" N ASN e1335 " --> pdb=" O ASN e1331 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN e1336 " --> pdb=" O ILE e1332 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1331 through 1336' Processing helix chain 'e' and resid 1341 through 1364 removed outlier: 4.301A pdb=" N GLY e1364 " --> pdb=" O PHE e1360 " (cutoff:3.500A) Processing helix chain 'e' and resid 1365 through 1375 removed outlier: 5.725A pdb=" N LYS e1375 " --> pdb=" O TRP e1371 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.357A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) Processing helix chain 'e' and resid 1448 through 1453 removed outlier: 4.303A 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 1503 Processing helix chain 'e' and resid 1535 through 1547 removed outlier: 4.404A pdb=" N GLY e1547 " --> pdb=" O PHE e1543 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.233A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.829A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.798A 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 '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: 3.659A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.878A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.556A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.002A 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: 5.071A 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: 5.035A 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: 4.664A 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: 4.981A 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: 6.127A 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: 4.428A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.974A 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 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 sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.467A 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: 6.783A 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: 5.436A 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: 6.706A 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: 5.101A 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: 4.567A 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: 6.173A 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: 3.921A 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: 4.217A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.361A 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: 3.733A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.231A 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: 4.145A 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: 6.373A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.008A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.520A 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: 6.754A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.743A 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: 4.491A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.518A 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: 4.046A 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: 4.587A 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: 4.597A 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: 8.218A 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: 4.478A 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: 6.880A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.053A 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: 4.449A 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: 4.418A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.430A 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: 4.406A 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: 6.784A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.966A 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: 6.662A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.445A 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: 4.552A 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: 5.355A 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: 3.745A 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: 4.188A 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: 4.384A 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: 4.175A 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: 7.864A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.080A 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: 8.624A 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: 4.945A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.650A 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: 5.995A 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: 4.963A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.519A 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: 6.338A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.662A 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: 4.557A 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: 5.069A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.997A 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: 5.682A 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: 4.471A 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 27 through 32 removed outlier: 3.718A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE a 32 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 91 through 95 removed outlier: 3.616A pdb=" N ALA a 91 " --> pdb=" O GLN a 104 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE a 100 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU a 115 " --> pdb=" O ASN a 121 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN a 121 " --> pdb=" O GLU a 115 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL a 122 " --> pdb=" O GLN a 135 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 307 through 310 removed outlier: 3.593A pdb=" N THR a 308 " --> pdb=" O LEU a 286 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 446 through 454 removed outlier: 9.130A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'a' and resid 577 through 581 removed outlier: 3.709A pdb=" N LEU a 587 " --> pdb=" O LYS a 623 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY a 591 " --> pdb=" O HIS a 619 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS a 619 " --> pdb=" O GLY a 591 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 656 through 660 Processing sheet with id= 73, first strand: chain 'a' and resid 939 through 942 removed outlier: 4.779A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 3.567A pdb=" N THR e1418 " --> pdb=" O SER e1431 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 76, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 77, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 78, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 79, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.221A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 81, 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: 3.775A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 82, 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= 83, first strand: chain '0' and resid 49 through 53 removed outlier: 3.838A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.677A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.741A 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= 86, first strand: chain 'v' and resid 101 through 104 removed outlier: 3.655A pdb=" N ASP v 108 " --> pdb=" O ASN v 104 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.295A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) 3384 hydrogen bonds defined for protein. 10059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2919 hydrogen bonds 4654 hydrogen bond angles 0 basepair planarities 1185 basepair parallelities 2008 stacking parallelities Total time for adding SS restraints: 251.04 Time building geometry restraints manager: 65.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17877 1.32 - 1.44: 63859 1.44 - 1.57: 72566 1.57 - 1.69: 7275 1.69 - 1.82: 279 Bond restraints: 161856 Sorted by residual: bond pdb=" CA TYR S 103 " pdb=" C TYR S 103 " ideal model delta sigma weight residual 1.524 1.462 0.063 1.28e-02 6.10e+03 2.41e+01 bond pdb=" CA PHE S 101 " pdb=" C PHE S 101 " ideal model delta sigma weight residual 1.527 1.474 0.053 1.41e-02 5.03e+03 1.43e+01 bond pdb=" CA ASN S 106 " pdb=" C ASN S 106 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.24e-02 6.50e+03 1.16e+01 bond pdb=" C LEU m 83 " pdb=" N PRO m 84 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" C LYS j 221 " pdb=" O LYS j 221 " ideal model delta sigma weight residual 1.233 1.192 0.042 1.28e-02 6.10e+03 1.07e+01 ... (remaining 161851 not shown) Histogram of bond angle deviations from ideal: 96.04 - 104.15: 14184 104.15 - 112.25: 90876 112.25 - 120.36: 73103 120.36 - 128.47: 53471 128.47 - 136.57: 4803 Bond angle restraints: 236437 Sorted by residual: angle pdb=" N PHE a 116 " pdb=" CA PHE a 116 " pdb=" C PHE a 116 " ideal model delta sigma weight residual 112.59 100.88 11.71 1.22e+00 6.72e-01 9.22e+01 angle pdb=" N ASN e 793 " pdb=" CA ASN e 793 " pdb=" C ASN e 793 " ideal model delta sigma weight residual 113.23 101.73 11.50 1.24e+00 6.50e-01 8.60e+01 angle pdb=" C GLY H 51 " pdb=" N ASN H 52 " pdb=" CA ASN H 52 " ideal model delta sigma weight residual 121.54 136.55 -15.01 1.91e+00 2.74e-01 6.18e+01 angle pdb=" N GLY v 53 " pdb=" CA GLY v 53 " pdb=" C GLY v 53 " ideal model delta sigma weight residual 112.51 124.23 -11.72 1.53e+00 4.27e-01 5.87e+01 angle pdb=" N ASP e 637 " pdb=" CA ASP e 637 " pdb=" C ASP e 637 " ideal model delta sigma weight residual 111.28 102.99 8.29 1.09e+00 8.42e-01 5.79e+01 ... (remaining 236432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 93029 36.00 - 71.99: 8371 71.99 - 107.99: 865 107.99 - 143.99: 18 143.99 - 179.98: 56 Dihedral angle restraints: 102339 sinusoidal: 74887 harmonic: 27452 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 -76.18 -103.82 0 5.00e+00 4.00e-02 4.31e+02 dihedral pdb=" CA ARG e 396 " pdb=" C ARG e 396 " pdb=" N ASN e 397 " pdb=" CA ASN e 397 " ideal model delta harmonic sigma weight residual -180.00 -94.17 -85.83 0 5.00e+00 4.00e-02 2.95e+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 -124.93 -55.07 0 5.00e+00 4.00e-02 1.21e+02 ... (remaining 102336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28861 0.149 - 0.298: 625 0.298 - 0.447: 39 0.447 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 29528 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 1.39e+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 2.02 0.49 2.00e-01 2.50e+01 5.94e+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 5.46e+00 ... (remaining 29525 not shown) Planarity restraints: 16477 Sorted by residual: 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 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.001 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 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 5 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.29e+01 pdb=" C ARG d 5 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG d 5 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA d 6 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 60 " 0.015 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR N 60 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR N 60 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 60 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR N 60 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR N 60 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR N 60 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 60 " -0.006 2.00e-02 2.50e+03 ... (remaining 16474 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 12 1.79 - 2.57: 982 2.57 - 3.34: 171132 3.34 - 4.12: 478866 4.12 - 4.90: 713467 Nonbonded interactions: 1364459 Sorted by model distance: nonbonded pdb=" OH TYR e 782 " pdb=" NE2 GLN e1141 " model vdw 1.011 2.520 nonbonded pdb=" CE1 PHE a 580 " pdb=" CG2 VAL a 588 " model vdw 1.368 3.760 nonbonded pdb=" CB GLU e 989 " pdb=" CD2 LEU e1039 " model vdw 1.455 3.860 nonbonded pdb=" CE1 PHE a 580 " pdb=" CB VAL a 588 " model vdw 1.482 3.770 nonbonded pdb=" O ASN a 685 " pdb=" OD1 ASP a 688 " model vdw 1.501 3.040 ... (remaining 1364454 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: 7.090 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: 23.500 Check model and map are aligned: 1.660 Set scattering table: 1.120 Process input model: 626.580 Find NCS groups from input model: 3.830 Set up NCS constraints: 0.620 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: 0.040 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 676.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 0.095 161856 Z= 0.366 Angle : 0.900 15.014 236437 Z= 0.506 Chirality : 0.054 0.746 29528 Planarity : 0.007 0.101 16477 Dihedral : 21.623 179.984 84577 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 1.63 % Allowed : 2.45 % Favored : 95.93 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.12 % 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: 0.14 (0.08), residues: 9312 helix: 1.34 (0.08), residues: 3890 sheet: 0.10 (0.15), residues: 1198 loop : -1.10 (0.08), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP m 95 HIS 0.018 0.002 HIS r 123 PHE 0.045 0.002 PHE o 229 TYR 0.067 0.002 TYR N 60 ARG 0.025 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 1263 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1140 time to evaluate : 8.481 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: D 136 ASN cc_start: 0.8081 (t0) cc_final: 0.7807 (t0) REVERT: E 148 ASP cc_start: 0.8790 (t70) cc_final: 0.8466 (t0) REVERT: G 112 ASN cc_start: 0.8835 (t0) cc_final: 0.8579 (t0) REVERT: L 83 ASP cc_start: 0.7133 (p0) cc_final: 0.6876 (p0) REVERT: P 57 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7573 (mt-10) REVERT: X 10 GLN cc_start: 0.8300 (tt0) cc_final: 0.8073 (tt0) REVERT: Y 25 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7432 (mm110) REVERT: k 308 MET cc_start: 0.8619 (mmm) cc_final: 0.7958 (mtt) REVERT: n 99 GLU cc_start: 0.8073 (pm20) cc_final: 0.7516 (pm20) REVERT: n 137 ASP cc_start: 0.8571 (m-30) cc_final: 0.8083 (m-30) REVERT: q 150 SER cc_start: 0.8741 (t) cc_final: 0.7821 (t) REVERT: s 21 ILE cc_start: 0.9304 (mt) cc_final: 0.9099 (mm) REVERT: s 34 SER cc_start: 0.9169 (p) cc_final: 0.8907 (p) REVERT: s 79 ILE cc_start: 0.9716 (mt) cc_final: 0.9475 (mp) REVERT: s 89 TYR cc_start: 0.8928 (m-80) cc_final: 0.7692 (m-10) REVERT: s 95 ASN cc_start: 0.8963 (m-40) cc_final: 0.8665 (m-40) REVERT: s 107 ASP cc_start: 0.8951 (m-30) cc_final: 0.7957 (m-30) REVERT: s 108 GLU cc_start: 0.7688 (pm20) cc_final: 0.7471 (pp20) REVERT: s 131 MET cc_start: 0.8368 (mmm) cc_final: 0.8114 (mmm) REVERT: u 11 ASN cc_start: 0.8247 (p0) cc_final: 0.8002 (p0) REVERT: a 112 LEU cc_start: 0.9765 (tp) cc_final: 0.9553 (mm) REVERT: a 157 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: a 579 TRP cc_start: 0.9324 (p-90) cc_final: 0.8712 (p-90) REVERT: a 589 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: a 612 MET cc_start: 0.8090 (tmm) cc_final: 0.7749 (tmm) REVERT: a 621 TRP cc_start: 0.7931 (m100) cc_final: 0.7431 (m100) REVERT: a 947 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9184 (mm) REVERT: a 1010 CYS cc_start: 0.7193 (p) cc_final: 0.6904 (p) REVERT: e 125 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9150 (mm) REVERT: e 284 MET cc_start: 0.8756 (ttp) cc_final: 0.8429 (ptp) REVERT: e 733 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8385 (m90) REVERT: e 1144 ASN cc_start: 0.8238 (m-40) cc_final: 0.7722 (t0) REVERT: e 1240 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8742 (mt) REVERT: e 1250 ASP cc_start: 0.7743 (m-30) cc_final: 0.7145 (p0) REVERT: e 1309 ASP cc_start: 0.8917 (m-30) cc_final: 0.8597 (p0) REVERT: e 1403 ILE cc_start: 0.3169 (mt) cc_final: 0.2782 (mm) REVERT: g 6 GLN cc_start: 0.8808 (mt0) cc_final: 0.8286 (mt0) REVERT: g 18 LYS cc_start: 0.9062 (tppt) cc_final: 0.8585 (tppp) REVERT: g 35 TYR cc_start: 0.8518 (m-10) cc_final: 0.8287 (m-80) REVERT: g 62 MET cc_start: 0.9471 (mmt) cc_final: 0.9241 (tpp) REVERT: g 75 GLN cc_start: 0.8757 (mt0) cc_final: 0.8518 (mp10) REVERT: g 139 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.5931 (mtt180) REVERT: g 164 GLN cc_start: 0.9095 (mp-120) cc_final: 0.8807 (mm-40) REVERT: w 102 LYS cc_start: 0.8898 (mttt) cc_final: 0.8410 (tmmt) REVERT: w 174 MET cc_start: 0.6704 (mtm) cc_final: 0.6429 (pp-130) REVERT: w 210 MET cc_start: 0.5073 (mmp) cc_final: 0.4849 (mmt) REVERT: 0 22 TYR cc_start: 0.8796 (m-80) cc_final: 0.8362 (m-80) REVERT: 0 30 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9052 (p) REVERT: 0 38 MET cc_start: 0.9456 (mmm) cc_final: 0.9042 (tmm) REVERT: 0 40 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9109 (pp20) REVERT: 0 52 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7969 (tp) REVERT: 0 60 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8572 (mtt90) REVERT: 0 69 ASP cc_start: 0.7999 (p0) cc_final: 0.7333 (p0) outliers start: 123 outliers final: 17 residues processed: 1246 average time/residue: 2.1140 time to fit residues: 3850.8113 Evaluate side-chains 812 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 787 time to evaluate : 8.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain n residue 104 GLU Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain a residue 157 PHE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 606 GLU Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 884 MET Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 324 GLU Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1195 THR Chi-restraints excluded: chain e residue 1240 LEU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1083 optimal weight: 9.9990 chunk 972 optimal weight: 50.0000 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: 30.0000 chunk 389 optimal weight: 10.0000 chunk 611 optimal weight: 8.9990 chunk 748 optimal weight: 4.9990 chunk 1165 optimal weight: 30.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A B 50 ASN A E 68 GLN G 103 GLN J 42 GLN L 26 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN N 120 ASN P 75 ASN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN W 13 ASN W 76 ASN X 28 ASN X 76 ASN Y 25 GLN Y 32 ASN b 22 GLN b 27 GLN j 97 ASN k 3 HIS l 361 HIS m 39 GLN n 167 ASN p 61 GLN q 51 GLN r 51 HIS ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 113 GLN ** t 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 27 GLN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 GLN a 413 GLN a 445 GLN ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 696 GLN a 854 GLN a 957 GLN e 160 ASN e 189 ASN e 251 ASN e 805 ASN e1141 GLN ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1288 GLN e1293 GLN e1455 GLN ** g 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN 0 39 HIS ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 22 GLN v 52 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.122 161856 Z= 0.559 Angle : 0.742 13.485 236437 Z= 0.388 Chirality : 0.047 0.380 29528 Planarity : 0.006 0.106 16477 Dihedral : 22.625 179.988 66871 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 2.74 % Allowed : 10.51 % Favored : 86.75 % 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: 0.23 (0.08), residues: 9312 helix: 1.32 (0.08), residues: 3950 sheet: -0.03 (0.15), residues: 1179 loop : -0.92 (0.09), residues: 4183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP u 12 HIS 0.013 0.002 HIS R 88 PHE 0.035 0.002 PHE a 580 TYR 0.033 0.003 TYR l 194 ARG 0.012 0.001 ARG l 98 *********************** 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 982 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 775 time to evaluate : 8.596 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: B 4 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 136 ASN cc_start: 0.8398 (t0) cc_final: 0.7962 (t0) REVERT: E 28 GLU cc_start: 0.8164 (mp0) cc_final: 0.7923 (mm-30) REVERT: E 68 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7860 (tp-100) REVERT: E 148 ASP cc_start: 0.8677 (t70) cc_final: 0.8140 (t0) REVERT: G 107 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7982 (pt0) REVERT: I 124 ASP cc_start: 0.8044 (t0) cc_final: 0.7729 (t0) REVERT: M 93 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (ptmm) REVERT: M 103 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: V 88 GLU cc_start: 0.8074 (tp30) cc_final: 0.7849 (tp30) REVERT: X 10 GLN cc_start: 0.8553 (tt0) cc_final: 0.8238 (tt0) REVERT: X 76 ASN cc_start: 0.8654 (t0) cc_final: 0.8435 (t0) REVERT: Z 113 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7873 (tmm-80) REVERT: Z 120 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: n 133 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6991 (tm-30) REVERT: n 137 ASP cc_start: 0.8480 (m-30) cc_final: 0.7985 (m-30) REVERT: q 153 ASP cc_start: 0.7979 (m-30) cc_final: 0.7665 (m-30) REVERT: r 112 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7457 (mm-40) REVERT: s 28 ASP cc_start: 0.8385 (p0) cc_final: 0.7958 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8223 (tp30) cc_final: 0.8005 (tp30) REVERT: s 95 ASN cc_start: 0.9075 (m-40) cc_final: 0.8688 (m110) REVERT: s 108 GLU cc_start: 0.8253 (pm20) cc_final: 0.7541 (pp20) REVERT: s 167 TYR cc_start: 0.8166 (m-80) cc_final: 0.7907 (m-80) REVERT: a 579 TRP cc_start: 0.9268 (p-90) cc_final: 0.8913 (p-90) REVERT: a 649 TRP cc_start: 0.7512 (OUTLIER) cc_final: 0.7287 (t-100) REVERT: a 699 MET cc_start: 0.8855 (tpp) cc_final: 0.8403 (tpp) REVERT: a 996 MET cc_start: 0.9375 (mmp) cc_final: 0.8794 (mtp) REVERT: a 1010 CYS cc_start: 0.6882 (p) cc_final: 0.6561 (p) REVERT: e 125 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9125 (mm) REVERT: e 254 ASN cc_start: 0.9345 (m-40) cc_final: 0.9017 (p0) REVERT: e 733 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8517 (m90) REVERT: e 1309 ASP cc_start: 0.8806 (m-30) cc_final: 0.8512 (p0) REVERT: g 6 GLN cc_start: 0.8796 (mt0) cc_final: 0.8225 (mt0) REVERT: g 18 LYS cc_start: 0.9082 (tppt) cc_final: 0.8493 (tppp) REVERT: g 75 GLN cc_start: 0.8841 (mt0) cc_final: 0.8540 (mp10) REVERT: g 139 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6130 (mtt180) REVERT: g 168 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8930 (mm-40) REVERT: w 102 LYS cc_start: 0.8985 (mttt) cc_final: 0.8536 (mttm) REVERT: w 210 MET cc_start: 0.5380 (mmp) cc_final: 0.4886 (mmp) REVERT: 0 16 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8857 (tpp80) REVERT: 0 26 PHE cc_start: 0.8696 (m-10) cc_final: 0.8494 (m-10) REVERT: 0 37 GLN cc_start: 0.8825 (tt0) cc_final: 0.8137 (tt0) REVERT: 0 38 MET cc_start: 0.9531 (mmm) cc_final: 0.8938 (tmm) REVERT: 0 44 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8354 (mm-30) REVERT: 0 55 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8502 (ttmm) REVERT: 0 58 MET cc_start: 0.9188 (ttp) cc_final: 0.8554 (mpp) REVERT: 0 60 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8584 (mtm-85) REVERT: 0 69 ASP cc_start: 0.7635 (p0) cc_final: 0.7089 (p0) REVERT: 0 75 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8929 (pttt) REVERT: v 120 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8629 (pt) outliers start: 207 outliers final: 81 residues processed: 902 average time/residue: 2.1218 time to fit residues: 2799.9284 Evaluate side-chains 786 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 695 time to evaluate : 8.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 62 SER Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 64 SER Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 113 ARG Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 182 ASP Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain q residue 9 GLN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 106 ILE Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 606 GLU Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 967 SER Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1195 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain v residue 124 LEU 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: 3.9990 chunk 969 optimal weight: 40.0000 chunk 793 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 1167 optimal weight: 20.0000 chunk 1260 optimal weight: 30.0000 chunk 1039 optimal weight: 5.9990 chunk 1157 optimal weight: 40.0000 chunk 397 optimal weight: 10.0000 chunk 936 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A E 68 GLN E 92 GLN L 26 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN T 98 GLN Z 90 ASN b 22 GLN b 27 GLN p 79 GLN q 125 ASN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 27 GLN ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 599 GLN ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 174 GLN ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 GLN w 188 ASN ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS v 58 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 161856 Z= 0.350 Angle : 0.619 10.688 236437 Z= 0.327 Chirality : 0.040 0.311 29528 Planarity : 0.005 0.097 16477 Dihedral : 22.612 179.874 66836 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 2.72 % Allowed : 12.87 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.41 (0.08), residues: 9312 helix: 1.49 (0.08), residues: 3956 sheet: 0.01 (0.15), residues: 1169 loop : -0.82 (0.09), residues: 4187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 649 HIS 0.007 0.001 HIS g 162 PHE 0.026 0.002 PHE o 229 TYR 0.019 0.002 TYR l 194 ARG 0.020 0.001 ARG e1143 *********************** 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 955 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 749 time to evaluate : 8.678 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: B 4 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: D 136 ASN cc_start: 0.8371 (t0) cc_final: 0.7944 (t0) REVERT: H 91 ASP cc_start: 0.8095 (t0) cc_final: 0.7483 (t0) REVERT: H 92 TRP cc_start: 0.7442 (t-100) cc_final: 0.6808 (m-90) REVERT: M 103 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: P 99 ASP cc_start: 0.8357 (p0) cc_final: 0.8112 (p0) REVERT: R 19 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8503 (ttp-170) REVERT: V 88 GLU cc_start: 0.8037 (tp30) cc_final: 0.7785 (tm-30) REVERT: X 76 ASN cc_start: 0.8646 (t0) cc_final: 0.8442 (t0) REVERT: Z 120 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7929 (mm-40) REVERT: j 142 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8008 (p0) REVERT: n 133 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7124 (tm-30) REVERT: n 137 ASP cc_start: 0.8476 (m-30) cc_final: 0.8063 (m-30) REVERT: q 107 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.7001 (p0) REVERT: r 112 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7583 (mm-40) REVERT: r 208 ASN cc_start: 0.8648 (m-40) cc_final: 0.8422 (m-40) REVERT: r 211 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7086 (ttp-110) REVERT: s 28 ASP cc_start: 0.8348 (p0) cc_final: 0.7998 (t0) REVERT: s 81 GLU cc_start: 0.8115 (tp30) cc_final: 0.7864 (OUTLIER) REVERT: s 95 ASN cc_start: 0.9042 (m-40) cc_final: 0.8630 (m110) REVERT: s 108 GLU cc_start: 0.8365 (pm20) cc_final: 0.8061 (pp20) REVERT: s 131 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7886 (mmm) REVERT: s 132 ASN cc_start: 0.8370 (p0) cc_final: 0.8095 (p0) REVERT: a 32 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8257 (pp) REVERT: a 334 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8780 (p0) REVERT: a 612 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7730 (tpp) REVERT: a 947 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9298 (mm) REVERT: a 1010 CYS cc_start: 0.7017 (p) cc_final: 0.6687 (p) REVERT: e 125 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9082 (mm) REVERT: e 254 ASN cc_start: 0.9354 (m-40) cc_final: 0.9041 (p0) REVERT: e 733 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8430 (m90) REVERT: e 755 ASN cc_start: 0.9035 (m-40) cc_final: 0.8435 (p0) REVERT: e 1086 MET cc_start: 0.6822 (pp-130) cc_final: 0.5908 (mpp) REVERT: e 1162 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.4247 (ptm) REVERT: e 1309 ASP cc_start: 0.8856 (m-30) cc_final: 0.8553 (p0) REVERT: g 6 GLN cc_start: 0.8719 (mt0) cc_final: 0.8178 (mt0) REVERT: g 18 LYS cc_start: 0.9074 (tppt) cc_final: 0.8437 (tppp) REVERT: g 67 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8038 (ptm160) REVERT: g 75 GLN cc_start: 0.8812 (mt0) cc_final: 0.8545 (mp10) REVERT: g 95 GLN cc_start: 0.8941 (tp40) cc_final: 0.8237 (tm-30) REVERT: w 63 MET cc_start: 0.7938 (pmm) cc_final: 0.7711 (pmm) REVERT: w 102 LYS cc_start: 0.8957 (mttt) cc_final: 0.8450 (mttm) REVERT: w 124 LEU cc_start: 0.9432 (mt) cc_final: 0.8850 (tm) REVERT: w 210 MET cc_start: 0.4808 (mmp) cc_final: 0.3727 (mmt) REVERT: 0 6 GLU cc_start: 0.9042 (mp0) cc_final: 0.8819 (mp0) REVERT: 0 26 PHE cc_start: 0.8682 (m-10) cc_final: 0.8472 (m-10) REVERT: 0 38 MET cc_start: 0.9552 (mmm) cc_final: 0.8905 (tmm) REVERT: 0 53 MET cc_start: 0.8021 (mmm) cc_final: 0.7253 (tmt) REVERT: 0 55 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8504 (ttmm) REVERT: 0 57 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8108 (t) REVERT: 0 58 MET cc_start: 0.9313 (ttp) cc_final: 0.8719 (mpp) REVERT: 0 60 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8599 (mtm-85) outliers start: 206 outliers final: 104 residues processed: 877 average time/residue: 2.1389 time to fit residues: 2754.8995 Evaluate side-chains 811 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 692 time to evaluate : 8.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 40 HIS Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 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 26 VAL Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 104 GLU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 148 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 606 GLU Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 967 SER Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1143 ARG Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1158 VAL Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1195 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain g residue 67 ARG Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 124 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1153 optimal weight: 10.0000 chunk 877 optimal weight: 8.9990 chunk 605 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 557 optimal weight: 40.0000 chunk 783 optimal weight: 0.9990 chunk 1171 optimal weight: 9.9990 chunk 1240 optimal weight: 30.0000 chunk 612 optimal weight: 10.0000 chunk 1110 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A C 28 ASN D 9 GLN E 68 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN L 42 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN p 77 GLN p 79 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 854 GLN a 899 GLN e 226 ASN ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 832 ASN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN v 52 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 161856 Z= 0.388 Angle : 0.629 18.515 236437 Z= 0.331 Chirality : 0.041 0.331 29528 Planarity : 0.005 0.097 16477 Dihedral : 22.547 179.947 66834 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 3.49 % Allowed : 13.23 % Favored : 83.28 % 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: 0.45 (0.09), residues: 9312 helix: 1.51 (0.08), residues: 3962 sheet: 0.07 (0.15), residues: 1158 loop : -0.79 (0.09), residues: 4192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 649 HIS 0.006 0.001 HIS l 311 PHE 0.027 0.002 PHE o 229 TYR 0.023 0.002 TYR P 23 ARG 0.018 0.001 ARG e1143 *********************** 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 999 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 735 time to evaluate : 8.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 122 GLN cc_start: 0.8601 (pt0) cc_final: 0.8341 (pt0) REVERT: F 96 ASP cc_start: 0.7861 (t0) cc_final: 0.7645 (t0) REVERT: H 91 ASP cc_start: 0.8105 (t70) cc_final: 0.7378 (OUTLIER) REVERT: H 92 TRP cc_start: 0.7400 (t-100) cc_final: 0.6763 (m-90) REVERT: I 7 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6403 (tp40) REVERT: M 103 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: R 19 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8461 (ttp-170) REVERT: V 88 GLU cc_start: 0.8042 (tp30) cc_final: 0.7755 (tm-30) REVERT: X 76 ASN cc_start: 0.8687 (t0) cc_final: 0.8483 (t0) REVERT: Z 120 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7885 (mm-40) REVERT: b 80 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7068 (mtm-85) REVERT: j 142 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8078 (p0) REVERT: n 133 GLU cc_start: 0.7296 (tm-30) cc_final: 0.7022 (tm-30) REVERT: n 137 ASP cc_start: 0.8510 (m-30) cc_final: 0.8100 (m-30) REVERT: q 7 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: s 28 ASP cc_start: 0.8491 (p0) cc_final: 0.8260 (t0) REVERT: s 81 GLU cc_start: 0.8137 (tp30) cc_final: 0.7876 (tp30) REVERT: s 95 ASN cc_start: 0.9096 (m-40) cc_final: 0.8554 (m110) REVERT: s 131 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: a 32 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8258 (pp) REVERT: a 334 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8737 (p0) REVERT: a 414 MET cc_start: 0.8714 (ptp) cc_final: 0.8436 (ptm) REVERT: a 543 MET cc_start: 0.9017 (mmm) cc_final: 0.8666 (mmt) REVERT: a 612 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.7794 (tpp) REVERT: a 947 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9335 (mm) REVERT: a 996 MET cc_start: 0.9357 (mmp) cc_final: 0.8744 (mtp) REVERT: e 125 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9158 (mm) REVERT: e 254 ASN cc_start: 0.9363 (m-40) cc_final: 0.9043 (p0) REVERT: e 733 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8418 (m-70) REVERT: e 755 ASN cc_start: 0.8943 (m-40) cc_final: 0.8303 (p0) REVERT: e 809 MET cc_start: 0.7898 (ttt) cc_final: 0.7471 (tmt) REVERT: e 862 PHE cc_start: 0.0145 (OUTLIER) cc_final: -0.0562 (m-10) REVERT: e 893 MET cc_start: -0.0692 (tmt) cc_final: -0.1387 (tmt) REVERT: e 1086 MET cc_start: 0.6898 (pp-130) cc_final: 0.6340 (mpp) REVERT: e 1162 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.4079 (ppp) REVERT: e 1246 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8970 (tp40) REVERT: e 1309 ASP cc_start: 0.8816 (m-30) cc_final: 0.8531 (p0) REVERT: g 1 MET cc_start: 0.6188 (ttt) cc_final: 0.5208 (mtt) REVERT: g 6 GLN cc_start: 0.8767 (mt0) cc_final: 0.8220 (mt0) REVERT: g 18 LYS cc_start: 0.9098 (tppt) cc_final: 0.8422 (tppp) REVERT: g 67 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7932 (ptm160) REVERT: g 75 GLN cc_start: 0.8821 (mt0) cc_final: 0.8559 (mp10) REVERT: g 95 GLN cc_start: 0.8996 (tp40) cc_final: 0.8589 (tp-100) REVERT: w 102 LYS cc_start: 0.8962 (mttt) cc_final: 0.8441 (mttm) REVERT: w 124 LEU cc_start: 0.9405 (mt) cc_final: 0.8863 (tm) REVERT: 0 16 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8962 (tpp80) REVERT: 0 25 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9131 (tm) REVERT: 0 36 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: 0 38 MET cc_start: 0.9582 (mmm) cc_final: 0.8949 (tmm) REVERT: 0 53 MET cc_start: 0.8023 (mmm) cc_final: 0.7412 (tmt) REVERT: 0 58 MET cc_start: 0.9338 (ttp) cc_final: 0.8747 (mpp) REVERT: 0 60 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8362 (mtm-85) REVERT: 0 75 LYS cc_start: 0.9433 (pttt) cc_final: 0.9154 (pttt) REVERT: 0 189 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7509 (tm-30) REVERT: v 90 TYR cc_start: 0.8194 (m-80) cc_final: 0.7925 (m-80) REVERT: v 120 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8655 (pt) outliers start: 264 outliers final: 138 residues processed: 914 average time/residue: 2.1804 time to fit residues: 2967.6405 Evaluate side-chains 862 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 703 time to evaluate : 8.449 ------------------------------------------------------------------------------- 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 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL 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 M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 5 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 214 MET Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 104 GLU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 26 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 170 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 606 GLU Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 967 SER Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1143 ARG Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1195 THR Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain g residue 67 ARG Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 36 GLN Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain v residue 124 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1032 optimal weight: 20.0000 chunk 703 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 923 optimal weight: 3.9990 chunk 511 optimal weight: 7.9990 chunk 1058 optimal weight: 2.9990 chunk 857 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 633 optimal weight: 10.0000 chunk 1113 optimal weight: 20.0000 chunk 312 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A E 47 ASN G 127 GLN K 85 GLN M 106 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN T 98 GLN b 27 GLN p 59 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN v 52 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 161856 Z= 0.232 Angle : 0.568 11.999 236437 Z= 0.299 Chirality : 0.037 0.298 29528 Planarity : 0.004 0.092 16477 Dihedral : 22.539 179.836 66834 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 15.02 % Favored : 82.33 % 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: 0.58 (0.09), residues: 9312 helix: 1.64 (0.08), residues: 3970 sheet: 0.14 (0.15), residues: 1164 loop : -0.76 (0.09), residues: 4178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 579 HIS 0.006 0.001 HIS r 123 PHE 0.026 0.001 PHE 0 66 TYR 0.034 0.001 TYR H 36 ARG 0.014 0.000 ARG e1143 *********************** REFINEMENT MACRO_CYCLE 5 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 963 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 763 time to evaluate : 8.712 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: B 4 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: B 122 GLN cc_start: 0.8543 (pt0) cc_final: 0.8304 (pt0) REVERT: D 136 ASN cc_start: 0.8339 (t0) cc_final: 0.7882 (t0) REVERT: K 130 TYR cc_start: 0.8740 (m-80) cc_final: 0.8480 (m-80) REVERT: L 74 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: M 103 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: R 19 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8417 (ttp-170) REVERT: V 88 GLU cc_start: 0.8000 (tp30) cc_final: 0.7707 (tm-30) REVERT: X 10 GLN cc_start: 0.8583 (tt0) cc_final: 0.8121 (tp40) REVERT: X 76 ASN cc_start: 0.8670 (t0) cc_final: 0.8459 (t0) REVERT: Z 120 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7891 (mm-40) REVERT: j 74 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: n 133 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6943 (tm-30) REVERT: n 137 ASP cc_start: 0.8525 (m-30) cc_final: 0.8069 (m-30) REVERT: r 211 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.7148 (ttp-110) REVERT: s 28 ASP cc_start: 0.8472 (p0) cc_final: 0.8233 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8212 (tp30) cc_final: 0.7924 (tp30) REVERT: s 95 ASN cc_start: 0.9048 (m-40) cc_final: 0.8500 (m110) REVERT: s 108 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: s 131 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: u 11 ASN cc_start: 0.8238 (p0) cc_final: 0.7972 (p0) REVERT: a 32 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8254 (pp) REVERT: a 334 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8661 (p0) REVERT: a 414 MET cc_start: 0.8709 (ptp) cc_final: 0.8437 (ptm) REVERT: a 612 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7795 (tpp) REVERT: a 947 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9319 (mm) REVERT: a 996 MET cc_start: 0.9327 (mmp) cc_final: 0.8706 (mtp) REVERT: e 125 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9159 (mm) REVERT: e 254 ASN cc_start: 0.9365 (m-40) cc_final: 0.9082 (p0) REVERT: e 733 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8415 (m-70) REVERT: e 755 ASN cc_start: 0.8976 (m-40) cc_final: 0.8395 (p0) REVERT: e 809 MET cc_start: 0.7765 (ttt) cc_final: 0.7352 (tmm) REVERT: e 862 PHE cc_start: 0.0049 (OUTLIER) cc_final: -0.0412 (m-10) REVERT: e 893 MET cc_start: -0.0738 (tmt) cc_final: -0.1349 (tmt) REVERT: e 963 MET cc_start: 0.1104 (ptt) cc_final: 0.0770 (ptt) REVERT: e 1068 MET cc_start: 0.3055 (ptm) cc_final: 0.2835 (ptt) REVERT: e 1086 MET cc_start: 0.6822 (pp-130) cc_final: 0.6404 (mpp) REVERT: e 1162 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.4054 (ppp) REVERT: e 1246 GLN cc_start: 0.9280 (tp-100) cc_final: 0.8988 (tp-100) REVERT: e 1309 ASP cc_start: 0.8798 (m-30) cc_final: 0.8538 (p0) REVERT: g 6 GLN cc_start: 0.8716 (mt0) cc_final: 0.8186 (mt0) REVERT: g 18 LYS cc_start: 0.9080 (tppt) cc_final: 0.8381 (tppp) REVERT: g 75 GLN cc_start: 0.8804 (mt0) cc_final: 0.8561 (mp10) REVERT: g 95 GLN cc_start: 0.9003 (tp40) cc_final: 0.8202 (tm-30) REVERT: w 63 MET cc_start: 0.7522 (pmm) cc_final: 0.7236 (pmm) REVERT: w 102 LYS cc_start: 0.8943 (mttt) cc_final: 0.8424 (mttm) REVERT: w 124 LEU cc_start: 0.9408 (mt) cc_final: 0.8915 (tm) REVERT: w 174 MET cc_start: 0.7766 (pmm) cc_final: 0.7456 (pmm) REVERT: w 210 MET cc_start: 0.4260 (mmp) cc_final: 0.3659 (mmt) REVERT: 0 10 GLU cc_start: 0.9240 (pp20) cc_final: 0.9022 (OUTLIER) REVERT: 0 16 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8864 (tpp80) REVERT: 0 38 MET cc_start: 0.9579 (mmm) cc_final: 0.8944 (tmm) REVERT: 0 53 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7424 (tmt) REVERT: 0 60 ARG cc_start: 0.8819 (mtt180) cc_final: 0.8254 (mtm-85) REVERT: 0 69 ASP cc_start: 0.7827 (p0) cc_final: 0.7357 (p0) REVERT: 0 75 LYS cc_start: 0.9399 (pttt) cc_final: 0.9124 (pttt) REVERT: v 90 TYR cc_start: 0.8182 (m-80) cc_final: 0.7918 (m-80) REVERT: v 120 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8698 (pt) outliers start: 200 outliers final: 109 residues processed: 896 average time/residue: 2.1418 time to fit residues: 2831.3793 Evaluate side-chains 842 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 717 time to evaluate : 8.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 104 GLU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 274 ARG Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1143 ARG Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1195 THR Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain v residue 124 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 417 optimal weight: 10.0000 chunk 1116 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 728 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 1241 optimal weight: 30.0000 chunk 1030 optimal weight: 2.9990 chunk 574 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 651 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A E 47 ASN E 68 GLN F 142 GLN G 127 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** M 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN Y 25 GLN b 27 GLN p 59 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 143 ASN ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN e 995 GLN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN v 52 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 161856 Z= 0.369 Angle : 0.613 14.442 236437 Z= 0.322 Chirality : 0.040 0.315 29528 Planarity : 0.005 0.094 16477 Dihedral : 22.482 179.824 66831 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 3.41 % Allowed : 15.10 % Favored : 81.48 % 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: 0.55 (0.09), residues: 9312 helix: 1.63 (0.08), residues: 3962 sheet: 0.03 (0.15), residues: 1166 loop : -0.75 (0.09), residues: 4184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP a 579 HIS 0.006 0.001 HIS r 123 PHE 0.047 0.002 PHE 0 66 TYR 0.021 0.002 TYR H 36 ARG 0.019 0.001 ARG g 123 *********************** REFINEMENT MACRO_CYCLE 6 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 991 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 733 time to evaluate : 8.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: D 180 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7368 (mtm-85) REVERT: H 91 ASP cc_start: 0.8946 (p0) cc_final: 0.8518 (p0) REVERT: I 7 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6437 (tp40) REVERT: M 103 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: R 19 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8486 (ttp-170) REVERT: V 88 GLU cc_start: 0.8033 (tp30) cc_final: 0.7728 (tm-30) REVERT: X 10 GLN cc_start: 0.8599 (tt0) cc_final: 0.8141 (tp40) REVERT: X 76 ASN cc_start: 0.8683 (t0) cc_final: 0.8478 (t0) REVERT: Y 25 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7810 (mm110) REVERT: Z 120 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7892 (mm-40) REVERT: j 74 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: n 133 GLU cc_start: 0.7271 (tm-30) cc_final: 0.7054 (tm-30) REVERT: n 137 ASP cc_start: 0.8538 (m-30) cc_final: 0.8155 (m-30) REVERT: q 7 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: q 76 ASP cc_start: 0.8382 (m-30) cc_final: 0.8116 (m-30) REVERT: s 28 ASP cc_start: 0.8521 (p0) cc_final: 0.8273 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8247 (tp30) cc_final: 0.7961 (tp30) REVERT: s 90 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: s 95 ASN cc_start: 0.9031 (m-40) cc_final: 0.8520 (m110) REVERT: s 108 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: s 131 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: u 11 ASN cc_start: 0.8272 (p0) cc_final: 0.8010 (p0) REVERT: u 135 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8556 (mm) REVERT: a 32 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8243 (pp) REVERT: a 334 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8653 (p0) REVERT: a 414 MET cc_start: 0.8763 (ptp) cc_final: 0.8509 (ptm) REVERT: a 612 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8095 (tmm) REVERT: a 699 MET cc_start: 0.8431 (tpp) cc_final: 0.8205 (tpp) REVERT: a 947 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9360 (mm) REVERT: a 996 MET cc_start: 0.9326 (mmp) cc_final: 0.8697 (mtp) REVERT: e 125 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9169 (mm) REVERT: e 733 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8376 (m-70) REVERT: e 755 ASN cc_start: 0.9051 (m-40) cc_final: 0.8505 (p0) REVERT: e 809 MET cc_start: 0.7887 (ttt) cc_final: 0.7473 (ttt) REVERT: e 862 PHE cc_start: 0.0439 (OUTLIER) cc_final: -0.0421 (m-10) REVERT: e 893 MET cc_start: -0.0574 (tmt) cc_final: -0.1019 (tmt) REVERT: e 963 MET cc_start: 0.1072 (ptt) cc_final: 0.0768 (ptt) REVERT: e 1068 MET cc_start: 0.2950 (ptm) cc_final: 0.2666 (ptt) REVERT: e 1086 MET cc_start: 0.6766 (pp-130) cc_final: 0.6390 (mpp) REVERT: e 1162 MET cc_start: 0.4324 (OUTLIER) cc_final: 0.4046 (ppp) REVERT: e 1250 ASP cc_start: 0.6922 (m-30) cc_final: 0.6135 (p0) REVERT: e 1309 ASP cc_start: 0.8831 (m-30) cc_final: 0.8542 (p0) REVERT: g 6 GLN cc_start: 0.8789 (mt0) cc_final: 0.8253 (mt0) REVERT: g 18 LYS cc_start: 0.9092 (tppt) cc_final: 0.8389 (tppp) REVERT: g 75 GLN cc_start: 0.8814 (mt0) cc_final: 0.8572 (mp10) REVERT: g 95 GLN cc_start: 0.8995 (tp40) cc_final: 0.8554 (tp-100) REVERT: w 63 MET cc_start: 0.7696 (pmm) cc_final: 0.7380 (pmm) REVERT: w 102 LYS cc_start: 0.8943 (mttt) cc_final: 0.8433 (mttm) REVERT: w 124 LEU cc_start: 0.9399 (mt) cc_final: 0.8937 (tm) REVERT: w 174 MET cc_start: 0.7990 (pmm) cc_final: 0.7694 (pmm) REVERT: w 210 MET cc_start: 0.4576 (mmp) cc_final: 0.3584 (mmt) REVERT: 0 10 GLU cc_start: 0.9294 (pp20) cc_final: 0.9093 (pp20) REVERT: 0 16 ARG cc_start: 0.9398 (tpp80) cc_final: 0.8459 (tpp80) REVERT: 0 20 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: 0 36 GLN cc_start: 0.8899 (tp40) cc_final: 0.8657 (mm-40) REVERT: 0 37 GLN cc_start: 0.8446 (tt0) cc_final: 0.8006 (tt0) REVERT: 0 38 MET cc_start: 0.9567 (mmm) cc_final: 0.8974 (tmm) REVERT: 0 53 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7586 (tmt) REVERT: 0 58 MET cc_start: 0.9327 (ttm) cc_final: 0.8601 (tpp) REVERT: 0 60 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8045 (mtm-85) REVERT: 0 64 ARG cc_start: 0.8967 (mtt180) cc_final: 0.8691 (ptp-110) REVERT: 0 75 LYS cc_start: 0.9348 (pttt) cc_final: 0.9118 (pttt) REVERT: v 90 TYR cc_start: 0.8213 (m-80) cc_final: 0.7963 (m-80) REVERT: v 120 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8693 (pt) outliers start: 258 outliers final: 139 residues processed: 913 average time/residue: 2.1095 time to fit residues: 2842.0180 Evaluate side-chains 866 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 704 time to evaluate : 8.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 7 GLN Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 9 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 28 GLN Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 90 GLN Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 530 GLN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 274 ARG Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 20 GLU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR 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 v residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1196 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 707 optimal weight: 7.9990 chunk 906 optimal weight: 9.9990 chunk 702 optimal weight: 2.9990 chunk 1044 optimal weight: 6.9990 chunk 693 optimal weight: 0.7980 chunk 1236 optimal weight: 40.0000 chunk 773 optimal weight: 4.9990 chunk 753 optimal weight: 8.9990 chunk 570 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN F 142 GLN G 127 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN K 85 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN b 27 GLN j 132 ASN p 59 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 397 ASN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1422 ASN ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 171 ASN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 188 ASN v 52 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 161856 Z= 0.289 Angle : 0.587 12.952 236437 Z= 0.309 Chirality : 0.038 0.298 29528 Planarity : 0.004 0.093 16477 Dihedral : 22.489 179.962 66827 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 3.06 % Allowed : 16.03 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.09), residues: 9312 helix: 1.66 (0.08), residues: 3972 sheet: 0.07 (0.15), residues: 1160 loop : -0.75 (0.09), residues: 4180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 579 HIS 0.006 0.001 HIS r 123 PHE 0.034 0.001 PHE 0 66 TYR 0.018 0.001 TYR n 10 ARG 0.013 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 7 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 966 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 735 time to evaluate : 8.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: D 180 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7345 (mtm-85) REVERT: E 68 GLN cc_start: 0.8113 (tp40) cc_final: 0.6325 (tp-100) REVERT: J 1 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8001 (ptt) REVERT: M 103 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: R 19 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8475 (ttp-170) REVERT: V 88 GLU cc_start: 0.8053 (tp30) cc_final: 0.7763 (tm-30) REVERT: W 37 CYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8494 (p) REVERT: X 10 GLN cc_start: 0.8525 (tt0) cc_final: 0.8165 (tp40) REVERT: Z 120 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7875 (mm-40) REVERT: j 74 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: n 133 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6991 (tm-30) REVERT: n 137 ASP cc_start: 0.8543 (m-30) cc_final: 0.8087 (m-30) REVERT: q 7 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: s 28 ASP cc_start: 0.8516 (p0) cc_final: 0.8257 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8231 (tp30) cc_final: 0.7912 (tp30) REVERT: s 90 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7588 (mm-40) REVERT: s 108 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8076 (pp20) REVERT: s 131 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7949 (mmm) REVERT: u 11 ASN cc_start: 0.8236 (p0) cc_final: 0.7971 (p0) REVERT: u 135 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8351 (mm) REVERT: a 32 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8240 (pp) REVERT: a 334 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8624 (p0) REVERT: a 414 MET cc_start: 0.8781 (ptp) cc_final: 0.8519 (ptm) REVERT: a 612 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8097 (tmm) REVERT: a 947 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9366 (mm) REVERT: e 125 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9211 (mm) REVERT: e 733 HIS cc_start: 0.9009 (OUTLIER) cc_final: 0.8371 (m-70) REVERT: e 755 ASN cc_start: 0.9006 (m-40) cc_final: 0.8441 (p0) REVERT: e 809 MET cc_start: 0.7889 (ttt) cc_final: 0.7440 (ttt) REVERT: e 862 PHE cc_start: 0.0328 (OUTLIER) cc_final: -0.0476 (m-10) REVERT: e 893 MET cc_start: -0.0509 (tmt) cc_final: -0.0945 (tmt) REVERT: e 963 MET cc_start: 0.1113 (ptt) cc_final: 0.0785 (ptt) REVERT: e 1068 MET cc_start: 0.3268 (ptm) cc_final: 0.2873 (ptt) REVERT: e 1086 MET cc_start: 0.6890 (pp-130) cc_final: 0.6614 (mpp) REVERT: e 1162 MET cc_start: 0.4253 (OUTLIER) cc_final: 0.3978 (ppp) REVERT: e 1309 ASP cc_start: 0.8837 (m-30) cc_final: 0.8566 (p0) REVERT: e 1336 ASN cc_start: 0.9211 (t0) cc_final: 0.8921 (p0) REVERT: g 6 GLN cc_start: 0.8726 (mt0) cc_final: 0.8237 (mt0) REVERT: g 18 LYS cc_start: 0.9096 (tppt) cc_final: 0.8385 (tppp) REVERT: g 75 GLN cc_start: 0.8805 (mt0) cc_final: 0.8568 (mp10) REVERT: g 95 GLN cc_start: 0.8999 (tp40) cc_final: 0.8552 (tp-100) REVERT: w 102 LYS cc_start: 0.8939 (mttt) cc_final: 0.8427 (mttm) REVERT: w 124 LEU cc_start: 0.9403 (mt) cc_final: 0.8914 (tm) REVERT: w 174 MET cc_start: 0.8018 (pmm) cc_final: 0.7627 (pmm) REVERT: w 210 MET cc_start: 0.4679 (mmp) cc_final: 0.3699 (mmt) REVERT: 0 16 ARG cc_start: 0.9434 (tpp80) cc_final: 0.8940 (tpp80) REVERT: 0 36 GLN cc_start: 0.8861 (tp40) cc_final: 0.8602 (mm-40) REVERT: 0 37 GLN cc_start: 0.8234 (tt0) cc_final: 0.7957 (tt0) REVERT: 0 38 MET cc_start: 0.9570 (mmm) cc_final: 0.8997 (tmm) REVERT: 0 46 ARG cc_start: 0.8314 (mmt180) cc_final: 0.8076 (mmm160) REVERT: 0 53 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7510 (tmt) REVERT: 0 60 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8081 (mtm-85) REVERT: 0 75 LYS cc_start: 0.9389 (pttt) cc_final: 0.9136 (pttt) REVERT: v 90 TYR cc_start: 0.8204 (m-80) cc_final: 0.7992 (m-80) REVERT: v 120 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8721 (pt) outliers start: 231 outliers final: 144 residues processed: 900 average time/residue: 2.1071 time to fit residues: 2792.4930 Evaluate side-chains 880 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 714 time to evaluate : 8.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain V residue 9 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 37 CYS Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 218 ILE Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 90 GLN Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 274 ARG Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 120 LEU Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 142 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 765 optimal weight: 6.9990 chunk 493 optimal weight: 10.0000 chunk 738 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 786 optimal weight: 9.9990 chunk 842 optimal weight: 0.7980 chunk 611 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 972 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 ASN F 142 GLN G 127 GLN G 134 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN T 98 GLN b 27 GLN l 5 GLN p 59 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 545 ASN ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 854 GLN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 161856 Z= 0.279 Angle : 0.589 15.787 236437 Z= 0.309 Chirality : 0.038 0.293 29528 Planarity : 0.004 0.092 16477 Dihedral : 22.464 179.771 66827 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.84 % Allowed : 16.59 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 9312 helix: 1.67 (0.08), residues: 3963 sheet: 0.04 (0.15), residues: 1157 loop : -0.71 (0.09), residues: 4192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP a 579 HIS 0.006 0.001 HIS r 123 PHE 0.026 0.001 PHE 0 66 TYR 0.023 0.001 TYR s 52 ARG 0.012 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 8 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 949 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 734 time to evaluate : 8.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: E 72 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: J 1 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7956 (ptt) REVERT: M 103 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: R 19 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8468 (ttp-170) REVERT: V 88 GLU cc_start: 0.8070 (tp30) cc_final: 0.7791 (tm-30) REVERT: W 37 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8491 (p) REVERT: X 10 GLN cc_start: 0.8525 (tt0) cc_final: 0.8239 (tp40) REVERT: Z 120 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: j 74 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: n 133 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6996 (tm-30) REVERT: n 137 ASP cc_start: 0.8560 (m-30) cc_final: 0.8082 (m-30) REVERT: q 7 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: s 28 ASP cc_start: 0.8567 (p0) cc_final: 0.8333 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8250 (tp30) cc_final: 0.7977 (tp30) REVERT: s 108 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8122 (pp20) REVERT: s 131 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: u 11 ASN cc_start: 0.8184 (p0) cc_final: 0.7927 (p0) REVERT: u 135 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8420 (mm) REVERT: a 32 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8233 (pp) REVERT: a 334 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8546 (p0) REVERT: a 414 MET cc_start: 0.8782 (ptp) cc_final: 0.8535 (ptm) REVERT: a 590 MET cc_start: 0.8703 (tmm) cc_final: 0.8453 (tmm) REVERT: a 612 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: a 699 MET cc_start: 0.8153 (tpp) cc_final: 0.7801 (tpp) REVERT: a 947 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9357 (mm) REVERT: a 996 MET cc_start: 0.9347 (mmp) cc_final: 0.8744 (mtp) REVERT: e 125 ILE cc_start: 0.9540 (OUTLIER) cc_final: 0.9209 (mm) REVERT: e 755 ASN cc_start: 0.8939 (m-40) cc_final: 0.8363 (p0) REVERT: e 809 MET cc_start: 0.7843 (ttt) cc_final: 0.7359 (ttt) REVERT: e 862 PHE cc_start: 0.0226 (OUTLIER) cc_final: -0.0521 (m-10) REVERT: e 893 MET cc_start: -0.0421 (tmt) cc_final: -0.1320 (tmt) REVERT: e 963 MET cc_start: 0.0816 (ptt) cc_final: 0.0484 (ptt) REVERT: e 1068 MET cc_start: 0.3181 (ptm) cc_final: 0.2782 (ptt) REVERT: e 1086 MET cc_start: 0.6861 (pp-130) cc_final: 0.6601 (mpp) REVERT: e 1162 MET cc_start: 0.4388 (OUTLIER) cc_final: 0.4110 (ppp) REVERT: e 1286 MET cc_start: 0.9299 (mtp) cc_final: 0.8643 (ptp) REVERT: e 1309 ASP cc_start: 0.8890 (m-30) cc_final: 0.8594 (p0) REVERT: e 1336 ASN cc_start: 0.9228 (t0) cc_final: 0.8962 (p0) REVERT: g 6 GLN cc_start: 0.8703 (mt0) cc_final: 0.8225 (mt0) REVERT: g 18 LYS cc_start: 0.9105 (tppt) cc_final: 0.8386 (tppp) REVERT: g 75 GLN cc_start: 0.8800 (mt0) cc_final: 0.8563 (mp10) REVERT: g 95 GLN cc_start: 0.8963 (tp40) cc_final: 0.8606 (tp-100) REVERT: g 140 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8458 (mp10) REVERT: w 102 LYS cc_start: 0.8945 (mttt) cc_final: 0.8440 (mttm) REVERT: w 124 LEU cc_start: 0.9402 (mt) cc_final: 0.8934 (tm) REVERT: w 174 MET cc_start: 0.8116 (pmm) cc_final: 0.7748 (pmm) REVERT: w 210 MET cc_start: 0.4539 (mmp) cc_final: 0.4010 (mmt) REVERT: 0 16 ARG cc_start: 0.9488 (tpp80) cc_final: 0.8936 (tpp80) REVERT: 0 36 GLN cc_start: 0.8871 (tp40) cc_final: 0.8648 (mm-40) REVERT: 0 37 GLN cc_start: 0.8233 (tt0) cc_final: 0.7991 (tt0) REVERT: 0 38 MET cc_start: 0.9564 (mmm) cc_final: 0.8991 (tmm) REVERT: 0 46 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8097 (mmm160) REVERT: 0 53 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7497 (tmt) REVERT: 0 60 ARG cc_start: 0.8588 (mtt180) cc_final: 0.7896 (mtm-85) REVERT: 0 64 ARG cc_start: 0.9225 (ttm110) cc_final: 0.8465 (mpp80) REVERT: 0 73 PHE cc_start: 0.9497 (m-10) cc_final: 0.9123 (m-80) REVERT: 0 75 LYS cc_start: 0.9388 (pttt) cc_final: 0.9112 (pttt) REVERT: 0 90 ASN cc_start: 0.8363 (m-40) cc_final: 0.8086 (m-40) outliers start: 215 outliers final: 149 residues processed: 886 average time/residue: 2.0863 time to fit residues: 2728.3521 Evaluate side-chains 878 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 710 time to evaluate : 8.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 9 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 37 CYS Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 338 LEU Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 218 ILE Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 110 LYS Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 32 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 530 GLN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 142 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1124 optimal weight: 7.9990 chunk 1184 optimal weight: 5.9990 chunk 1080 optimal weight: 30.0000 chunk 1152 optimal weight: 50.0000 chunk 693 optimal weight: 6.9990 chunk 502 optimal weight: 10.0000 chunk 904 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 1041 optimal weight: 5.9990 chunk 1089 optimal weight: 40.0000 chunk 1148 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN A E 47 ASN ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN b 27 GLN l 5 GLN q 157 ASN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 854 GLN ** a 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 188 ASN ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 161856 Z= 0.480 Angle : 0.679 16.563 236437 Z= 0.353 Chirality : 0.043 0.339 29528 Planarity : 0.005 0.096 16477 Dihedral : 22.452 179.478 66825 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 2.68 % Allowed : 17.05 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 9312 helix: 1.55 (0.08), residues: 3962 sheet: 0.01 (0.15), residues: 1137 loop : -0.77 (0.09), residues: 4213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP a 579 HIS 0.008 0.001 HIS l 311 PHE 0.030 0.002 PHE o 229 TYR 0.027 0.002 TYR H 83 ARG 0.015 0.001 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 9 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 911 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 708 time to evaluate : 8.399 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: B 4 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: H 33 TYR cc_start: 0.9041 (t80) cc_final: 0.8818 (t80) REVERT: J 1 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7932 (ptt) REVERT: M 103 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: Q 81 GLU cc_start: 0.7696 (mp0) cc_final: 0.7480 (pm20) REVERT: R 19 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8683 (ttp-170) REVERT: V 88 GLU cc_start: 0.8096 (tp30) cc_final: 0.7789 (tm-30) REVERT: W 37 CYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8461 (p) REVERT: X 10 GLN cc_start: 0.8593 (tt0) cc_final: 0.8330 (tp40) REVERT: Z 120 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7900 (mm-40) REVERT: j 74 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: j 142 ASP cc_start: 0.8165 (p0) cc_final: 0.7845 (p0) REVERT: q 7 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: s 28 ASP cc_start: 0.8517 (p0) cc_final: 0.8258 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8241 (tp30) cc_final: 0.7964 (tp30) REVERT: s 131 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: a 334 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8556 (p0) REVERT: a 414 MET cc_start: 0.8793 (ptp) cc_final: 0.8565 (ptm) REVERT: a 543 MET cc_start: 0.9240 (mmt) cc_final: 0.9019 (mmm) REVERT: a 612 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7986 (tmm) REVERT: a 699 MET cc_start: 0.8373 (tpp) cc_final: 0.8068 (tpp) REVERT: a 947 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9360 (mm) REVERT: a 996 MET cc_start: 0.9356 (mmp) cc_final: 0.8749 (mtp) REVERT: e 125 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9232 (mm) REVERT: e 755 ASN cc_start: 0.8892 (m-40) cc_final: 0.8310 (p0) REVERT: e 809 MET cc_start: 0.7945 (ttt) cc_final: 0.7423 (ttt) REVERT: e 862 PHE cc_start: 0.0352 (OUTLIER) cc_final: -0.0152 (m-80) REVERT: e 893 MET cc_start: -0.0409 (tmt) cc_final: -0.1321 (tmt) REVERT: e 963 MET cc_start: 0.0850 (ptt) cc_final: 0.0441 (ptt) REVERT: e 1068 MET cc_start: 0.3207 (ptm) cc_final: 0.2792 (ptt) REVERT: e 1086 MET cc_start: 0.6856 (pp-130) cc_final: 0.6590 (mpp) REVERT: e 1162 MET cc_start: 0.4223 (OUTLIER) cc_final: 0.4004 (ppp) REVERT: e 1250 ASP cc_start: 0.7686 (m-30) cc_final: 0.7378 (m-30) REVERT: e 1286 MET cc_start: 0.9223 (mtp) cc_final: 0.8565 (ptp) REVERT: e 1309 ASP cc_start: 0.8825 (m-30) cc_final: 0.8539 (p0) REVERT: e 1336 ASN cc_start: 0.9202 (t0) cc_final: 0.8939 (p0) REVERT: g 6 GLN cc_start: 0.8830 (mt0) cc_final: 0.8307 (mt0) REVERT: g 18 LYS cc_start: 0.9108 (tppt) cc_final: 0.8399 (tppp) REVERT: g 75 GLN cc_start: 0.8815 (mt0) cc_final: 0.8567 (mp10) REVERT: g 95 GLN cc_start: 0.8993 (tp40) cc_final: 0.8635 (tp-100) REVERT: g 140 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8502 (mm-40) REVERT: w 102 LYS cc_start: 0.8957 (mttt) cc_final: 0.8444 (mttm) REVERT: w 124 LEU cc_start: 0.9436 (mt) cc_final: 0.8943 (tm) REVERT: w 174 MET cc_start: 0.8211 (pmm) cc_final: 0.7836 (pmm) REVERT: w 210 MET cc_start: 0.4784 (mmp) cc_final: 0.4270 (mmt) REVERT: 0 16 ARG cc_start: 0.9478 (tpp80) cc_final: 0.9003 (tpp80) REVERT: 0 22 TYR cc_start: 0.8884 (m-80) cc_final: 0.8582 (m-10) REVERT: 0 36 GLN cc_start: 0.8809 (tp40) cc_final: 0.8569 (mm-40) REVERT: 0 38 MET cc_start: 0.9561 (mmm) cc_final: 0.9003 (tmm) REVERT: 0 46 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8088 (tpt90) REVERT: 0 53 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7573 (tmt) REVERT: 0 60 ARG cc_start: 0.8515 (mtt180) cc_final: 0.8022 (mtm-85) REVERT: 0 73 PHE cc_start: 0.9507 (m-10) cc_final: 0.9111 (m-80) REVERT: 0 75 LYS cc_start: 0.9372 (pttt) cc_final: 0.9109 (pttt) REVERT: 0 90 ASN cc_start: 0.8421 (m-40) cc_final: 0.8016 (m-40) outliers start: 203 outliers final: 146 residues processed: 850 average time/residue: 2.1147 time to fit residues: 2646.2902 Evaluate side-chains 857 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 696 time to evaluate : 8.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 21 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 120 GLU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 9 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 37 CYS Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 66 LYS Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 338 LEU Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 218 ILE Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 44 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 48 SER Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 530 GLN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1162 MET Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain g residue 218 ILE Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 756 optimal weight: 2.9990 chunk 1218 optimal weight: 30.0000 chunk 743 optimal weight: 0.9980 chunk 578 optimal weight: 10.0000 chunk 847 optimal weight: 7.9990 chunk 1278 optimal weight: 30.0000 chunk 1176 optimal weight: 40.0000 chunk 1017 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 786 optimal weight: 1.9990 chunk 624 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN A E 47 ASN F 142 GLN G 127 GLN G 134 GLN ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN P 36 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN T 98 GLN b 27 GLN l 5 GLN p 59 GLN q 157 ASN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 376 GLN ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 899 GLN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN v 52 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 161856 Z= 0.230 Angle : 0.595 17.046 236437 Z= 0.312 Chirality : 0.037 0.280 29528 Planarity : 0.004 0.092 16477 Dihedral : 22.491 179.943 66825 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 2.29 % Allowed : 17.50 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.04 % 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: 0.57 (0.09), residues: 9312 helix: 1.64 (0.08), residues: 3956 sheet: 0.02 (0.15), residues: 1152 loop : -0.72 (0.09), residues: 4204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP a 579 HIS 0.008 0.001 HIS r 123 PHE 0.033 0.001 PHE w 49 TYR 0.032 0.001 TYR s 116 ARG 0.016 0.000 ARG g 123 ********************** REFINEMENT MACRO_CYCLE 10 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 902 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 729 time to evaluate : 8.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: G 107 GLU cc_start: 0.8274 (pm20) cc_final: 0.8052 (pm20) REVERT: J 1 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7923 (ptt) REVERT: M 103 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: R 19 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8468 (ttp-170) REVERT: V 88 GLU cc_start: 0.8067 (tp30) cc_final: 0.7784 (tm-30) REVERT: X 10 GLN cc_start: 0.8564 (tt0) cc_final: 0.8305 (tp40) REVERT: X 39 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8232 (tpp80) REVERT: Z 120 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: j 74 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: q 7 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: s 28 ASP cc_start: 0.8564 (p0) cc_final: 0.8344 (OUTLIER) REVERT: s 81 GLU cc_start: 0.8217 (tp30) cc_final: 0.7970 (tp30) REVERT: s 108 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: s 131 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: u 11 ASN cc_start: 0.8135 (p0) cc_final: 0.7887 (p0) REVERT: a 334 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8519 (p0) REVERT: a 414 MET cc_start: 0.8756 (ptp) cc_final: 0.8527 (ptm) REVERT: a 590 MET cc_start: 0.8729 (tmm) cc_final: 0.8453 (tmm) REVERT: a 612 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8005 (tmm) REVERT: a 699 MET cc_start: 0.8311 (tpp) cc_final: 0.8066 (tpp) REVERT: a 947 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9334 (mm) REVERT: a 996 MET cc_start: 0.9369 (mmp) cc_final: 0.8755 (mtp) REVERT: e 125 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9214 (mm) REVERT: e 755 ASN cc_start: 0.8898 (m-40) cc_final: 0.8266 (p0) REVERT: e 809 MET cc_start: 0.7840 (ttt) cc_final: 0.7311 (ttt) REVERT: e 862 PHE cc_start: 0.0296 (OUTLIER) cc_final: -0.0199 (m-80) REVERT: e 893 MET cc_start: -0.0504 (tmt) cc_final: -0.1429 (tmt) REVERT: e 963 MET cc_start: 0.0845 (ptt) cc_final: 0.0440 (ptt) REVERT: e 1068 MET cc_start: 0.3155 (ptm) cc_final: 0.2735 (ptt) REVERT: e 1309 ASP cc_start: 0.8842 (m-30) cc_final: 0.8550 (p0) REVERT: e 1336 ASN cc_start: 0.9190 (t0) cc_final: 0.8934 (p0) REVERT: g 6 GLN cc_start: 0.8731 (mt0) cc_final: 0.8287 (mt0) REVERT: g 18 LYS cc_start: 0.9108 (tppt) cc_final: 0.8698 (tppp) REVERT: g 75 GLN cc_start: 0.8798 (mt0) cc_final: 0.8564 (mp10) REVERT: g 95 GLN cc_start: 0.8981 (tp40) cc_final: 0.8627 (tp-100) REVERT: g 123 ARG cc_start: 0.8640 (mmp80) cc_final: 0.8333 (mmm160) REVERT: g 140 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8496 (mm-40) REVERT: w 102 LYS cc_start: 0.8937 (mttt) cc_final: 0.8426 (mttm) REVERT: w 124 LEU cc_start: 0.9412 (mt) cc_final: 0.8953 (tm) REVERT: w 174 MET cc_start: 0.8157 (pmm) cc_final: 0.7791 (pmm) REVERT: w 210 MET cc_start: 0.4726 (mmp) cc_final: 0.4092 (mmt) REVERT: 0 36 GLN cc_start: 0.8799 (tp40) cc_final: 0.8560 (mt0) REVERT: 0 38 MET cc_start: 0.9562 (mmm) cc_final: 0.8974 (tmm) REVERT: 0 46 ARG cc_start: 0.8438 (mmt180) cc_final: 0.8230 (mmm160) REVERT: 0 53 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7567 (tmt) REVERT: 0 60 ARG cc_start: 0.8581 (mtt180) cc_final: 0.7950 (mtm-85) REVERT: 0 64 ARG cc_start: 0.9234 (ttm110) cc_final: 0.8465 (mpp80) REVERT: 0 73 PHE cc_start: 0.9486 (m-10) cc_final: 0.9080 (m-80) REVERT: 0 75 LYS cc_start: 0.9344 (pttt) cc_final: 0.9127 (pttt) REVERT: 0 90 ASN cc_start: 0.8323 (m-40) cc_final: 0.7854 (m-40) outliers start: 173 outliers final: 130 residues processed: 850 average time/residue: 2.1382 time to fit residues: 2675.3349 Evaluate side-chains 857 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 713 time to evaluate : 8.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 GLU Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 58 SER Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 338 LEU Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 208 MET Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain q residue 7 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 92 TYR Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 15 GLU Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 176 GLU Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 59 ASN Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 157 PHE Chi-restraints excluded: chain a residue 334 ASN Chi-restraints excluded: chain a residue 530 GLN Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 857 THR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 1013 ASP Chi-restraints excluded: chain e residue 1123 TYR Chi-restraints excluded: chain e residue 1151 PHE Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain g residue 218 ILE Chi-restraints excluded: chain w residue 15 GLU Chi-restraints excluded: chain w residue 73 ASP Chi-restraints excluded: chain w residue 144 LEU Chi-restraints excluded: chain 0 residue 53 MET Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 124 LEU Chi-restraints excluded: chain v residue 142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 808 optimal weight: 0.9990 chunk 1084 optimal weight: 50.0000 chunk 311 optimal weight: 6.9990 chunk 938 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 282 optimal weight: 0.5980 chunk 1019 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 1046 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN E 47 ASN F 142 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 134 GLN ** Q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN T 98 GLN b 27 GLN j 24 GLN l 5 GLN q 157 ASN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN ** a 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.074049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046876 restraints weight = 509496.084| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.79 r_work: 0.2661 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 161856 Z= 0.168 Angle : 0.577 17.177 236437 Z= 0.302 Chirality : 0.035 0.258 29528 Planarity : 0.004 0.091 16477 Dihedral : 22.466 179.982 66825 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 1.79 % Allowed : 18.13 % Favored : 80.08 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.04 % 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: 0.64 (0.09), residues: 9312 helix: 1.68 (0.08), residues: 3957 sheet: 0.10 (0.15), residues: 1153 loop : -0.67 (0.09), residues: 4202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 579 HIS 0.021 0.001 HIS H 40 PHE 0.031 0.001 PHE w 49 TYR 0.028 0.001 TYR s 52 ARG 0.015 0.000 ARG E 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49230.01 seconds wall clock time: 857 minutes 28.48 seconds (51448.48 seconds total)