Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 24 15:27:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq8_8597/07_2023/5uq8_8597_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 4702 5.49 5 S 130 5.16 5 C 74971 2.51 5 N 27973 2.21 5 O 40800 1.98 5 H 4 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U ARG 64": "NH1" <-> "NH2" Residue "V TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 65": "NH1" <-> "NH2" Residue "Z TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "0 ARG 32": "NH1" <-> "NH2" Residue "1 ARG 61": "NH1" <-> "NH2" Residue "1 ARG 76": "NH1" <-> "NH2" Residue "2 ARG 55": "NH1" <-> "NH2" Residue "3 ARG 55": "NH1" <-> "NH2" Residue "4 ARG 68": "NH1" <-> "NH2" Residue "8 ARG 46": "NH1" <-> "NH2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 115": "NH1" <-> "NH2" Residue "d ARG 168": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "i ARG 42": "NH1" <-> "NH2" Residue "i ARG 66": "NH1" <-> "NH2" Residue "n ARG 3": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "r ARG 42": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 148590 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 61758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2867, 61758 Classifications: {'RNA': 2867} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 289, 'rna2p_pyr': 142, 'rna3p': 7, 'rna3p_pur': 1389, 'rna3p_pyr': 1036} Link IDs: {'rna2p': 434, 'rna3p': 2432} Unresolved chain links: 1 Chain breaks: 9 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2573 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 108} Chain: "D" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2136 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1559 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1580 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 190} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 172} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1324 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 155} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 136} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1117 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "P" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1135 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "R" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "S" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 959 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "V" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "W" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 886 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 89} Chain: "Y" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Z" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1459 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "0" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 759 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 592 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "3" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 464 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} 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: "4" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 536 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "5" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 49} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 449 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 50} 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: "7" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 418 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "8" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 517 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "9" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "a" Number of atoms: 32532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1513, 32532 Classifications: {'RNA': 1513} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 90, 'rna3p': 10, 'rna3p_pur': 734, 'rna3p_pyr': 560} Link IDs: {'rna2p': 209, 'rna3p': 1303} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1825 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 219} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "c" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "d" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1668 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "e" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1133 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "f" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 816 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1229 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "h" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1088 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 127} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 966 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "j" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 710 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 88} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 25 Chain: "k" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'0TD:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "m" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 728 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 677 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "r" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "s" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 733 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 199 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 37, 'rna3p_pyr': 36} Link IDs: {'rna2p': 4, 'rna3p': 72} Chain: "C" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1718 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 13, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "x" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1180 Classifications: {'RNA': 55} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 27, 'rna3p_pyr': 20} Link IDs: {'rna2p': 8, 'rna3p': 46} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 84603 SG CYS Y 76 259.930 60.516 141.857 1.00134.89 S ATOM 84621 SG CYS Y 79 260.895 58.556 139.125 1.00139.70 S ATOM 84785 SG CYS Y 99 257.372 58.086 140.712 1.00158.89 S ATOM 84805 SG CYS Y 102 260.384 56.733 142.891 1.00154.46 S ATOM 88840 SG CYS 4 16 67.743 53.394 100.535 1.00153.77 S ATOM 88850 SG CYS 4 18 64.623 53.310 97.722 1.00154.39 S ATOM 88984 SG CYS 4 36 68.678 52.076 97.578 1.00141.84 S ATOM 89005 SG CYS 4 39 68.096 55.892 98.230 1.00149.94 S ATOM 89503 SG CYS 5 33 242.628 132.931 93.655 1.00114.14 S ATOM 89525 SG CYS 5 36 244.626 130.548 95.844 1.00122.09 S ATOM 89596 SG CYS 5 46 241.430 131.682 96.623 1.00117.87 S ATOM 89618 SG CYS 5 49 242.948 134.931 96.405 1.00120.49 S ATOM 89797 SG CYS 6 13 132.947 37.793 134.764 1.00122.59 S ATOM 89819 SG CYS 6 16 136.592 38.346 136.244 1.00126.64 S ATOM 90030 SG CYS 6 40 136.479 36.498 133.360 1.00110.32 S ATOM 90057 SG CYS 6 43 134.942 34.425 135.720 1.00118.36 S ATOM 91178 SG CYS 9 11 142.981 111.833 47.971 1.00162.27 S ATOM 91201 SG CYS 9 14 145.024 110.147 50.228 1.00162.77 S ATOM 91312 SG CYS 9 27 145.880 113.596 47.373 1.00168.25 S ATOM A0L3W SG CYS d 9 76.154 189.086 94.511 1.00102.65 S ATOM A0L7R SG CYS d 26 76.335 196.481 97.641 1.00108.91 S ATOM A0L8V SG CYS d 31 71.910 190.986 99.139 1.00111.26 S ATOM A0T4U SG CYS n 24 54.312 130.137 103.460 1.00112.59 S ATOM A0T5I SG CYS n 27 57.798 130.640 103.504 1.00108.66 S ATOM A0T8H SG CYS n 40 57.150 129.793 106.690 1.00112.38 S ATOM A0T96 SG CYS n 43 56.049 132.976 105.797 1.00111.86 S Time building chain proxies: 52.11, per 1000 atoms: 0.35 Number of scatterers: 148590 At special positions: 0 Unit cell: (272, 254, 228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 130 16.00 P 4702 15.00 O 40800 8.00 N 27973 7.00 C 74971 6.00 H 4 1.00 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: 73.04 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 d 301 " pdb="FE2 SF4 d 301 " - pdb=" SG CYS d 26 " pdb="FE1 SF4 d 301 " - pdb=" SG CYS d 9 " pdb="FE4 SF4 d 301 " - pdb=" SG CYS d 31 " pdb="FE3 SF4 d 301 " - pdb=" SG CYS d 12 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 36 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 39 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 49 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 46 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 33 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 13 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 40 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 43 " pdb=" ZN 9 101 " pdb="ZN ZN 9 101 " - pdb=" ND1 HIS 9 32 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 14 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 27 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 11 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 102 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 99 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 79 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 76 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " Number of angles added : 33 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11024 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 186 helices and 81 sheets defined 38.4% alpha, 20.0% beta 1621 base pairs and 2447 stacking pairs defined. Time for finding SS restraints: 62.02 Creating SS restraints... Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.783A pdb=" N PHE D 15 " --> pdb=" O PRO D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 removed outlier: 3.510A pdb=" N VAL D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 30 through 35' Processing helix chain 'D' and resid 132 through 137 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.728A pdb=" N SER D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 5.657A pdb=" N ILE D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 4.004A pdb=" N VAL E 59 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 60' Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.842A pdb=" N ALA E 70 " --> pdb=" O HIS E 66 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 4.682A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS E 97 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 97' Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'F' and resid 29 through 45 removed outlier: 3.552A pdb=" N LEU F 33 " --> pdb=" O ASN F 29 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 135 through 147 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 182 through 190 removed outlier: 5.722A pdb=" N GLU F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 207 Processing helix chain 'G' and resid 5 through 24 removed outlier: 4.137A pdb=" N ARG G 16 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.861A pdb=" N VAL G 31 " --> pdb=" O ASN G 27 " (cutoff:3.500A) Proline residue: G 32 - end of helix No H-bonds generated for 'chain 'G' and resid 27 through 32' Processing helix chain 'G' and resid 43 through 49 removed outlier: 6.927A pdb=" N LYS G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 65 removed outlier: 3.851A pdb=" N ALA G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 114 removed outlier: 4.442A pdb=" N LEU G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix Processing helix chain 'G' and resid 145 through 150 removed outlier: 5.313A pdb=" N ASP G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'H' and resid 58 through 81 Processing helix chain 'H' and resid 137 through 153 removed outlier: 4.213A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 27 removed outlier: 3.738A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.615A pdb=" N ARG I 33 " --> pdb=" O TYR I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.572A pdb=" N GLU I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA I 49 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG I 50 " --> pdb=" O ALA I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 73 Processing helix chain 'I' and resid 93 through 103 Processing helix chain 'I' and resid 110 through 115 removed outlier: 5.153A pdb=" N ALA I 115 " --> pdb=" O PRO I 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 95 through 108 removed outlier: 3.786A pdb=" N LEU N 99 " --> pdb=" O PRO N 95 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Proline residue: N 108 - end of helix Processing helix chain 'N' and resid 110 through 121 removed outlier: 5.172A pdb=" N LYS N 121 " --> pdb=" O PHE N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 70 removed outlier: 4.476A pdb=" N LYS N 70 " --> pdb=" O LYS N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 65 through 70' Processing helix chain 'O' and resid 104 through 110 removed outlier: 3.711A pdb=" N GLU O 108 " --> pdb=" O ARG O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 2 through 7 removed outlier: 3.773A pdb=" N LEU P 6 " --> pdb=" O LYS P 2 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG P 7 " --> pdb=" O LEU P 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 7' Processing helix chain 'P' and resid 37 through 42 removed outlier: 5.665A pdb=" N SER P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 63 removed outlier: 3.665A pdb=" N LEU P 62 " --> pdb=" O THR P 58 " (cutoff:3.500A) Proline residue: P 63 - end of helix Processing helix chain 'P' and resid 84 through 90 removed outlier: 4.868A pdb=" N ARG P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 104 Processing helix chain 'P' and resid 131 through 142 Processing helix chain 'Q' and resid 43 through 59 Processing helix chain 'Q' and resid 110 through 126 Proline residue: Q 126 - end of helix Processing helix chain 'Q' and resid 135 through 141 removed outlier: 3.556A pdb=" N GLN Q 141 " --> pdb=" O TYR Q 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 32 Processing helix chain 'R' and resid 38 through 58 removed outlier: 4.646A pdb=" N GLY R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 71 removed outlier: 3.741A pdb=" N ASP R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 88 removed outlier: 3.761A pdb=" N VAL R 76 " --> pdb=" O ASP R 72 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Proline residue: R 85 - end of helix Processing helix chain 'S' and resid 5 through 22 removed outlier: 3.880A pdb=" N THR S 21 " --> pdb=" O ARG S 17 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY S 22 " --> pdb=" O ILE S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 57 Processing helix chain 'S' and resid 61 through 81 removed outlier: 3.561A pdb=" N LEU S 80 " --> pdb=" O LYS S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 109 Processing helix chain 'T' and resid 2 through 13 removed outlier: 4.071A pdb=" N ARG T 13 " --> pdb=" O LEU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 106 removed outlier: 4.736A pdb=" N ARG T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN T 104 " --> pdb=" O TYR T 100 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU T 105 " --> pdb=" O PHE T 101 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER T 106 " --> pdb=" O ILE T 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 99 through 106' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.931A pdb=" N ARG T 115 " --> pdb=" O ARG T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 129 removed outlier: 3.802A pdb=" N GLU T 128 " --> pdb=" O ASP T 124 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG T 129 " --> pdb=" O ARG T 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 22 Processing helix chain 'U' and resid 26 through 31 removed outlier: 3.767A pdb=" N LYS U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 73 removed outlier: 3.969A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 102 Processing helix chain 'U' and resid 103 through 117 removed outlier: 3.685A pdb=" N GLN U 117 " --> pdb=" O ALA U 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.563A pdb=" N LEU W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL W 20 " --> pdb=" O LYS W 16 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG W 25 " --> pdb=" O VAL W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 41 through 60 removed outlier: 3.868A pdb=" N TYR W 45 " --> pdb=" O LYS W 41 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 9 removed outlier: 3.678A pdb=" N VAL X 7 " --> pdb=" O THR X 3 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU X 9 " --> pdb=" O TYR X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 24 removed outlier: 3.829A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE X 21 " --> pdb=" O ALA X 17 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA X 22 " --> pdb=" O TYR X 18 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU X 23 " --> pdb=" O ALA X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 47 Processing helix chain 'X' and resid 89 through 94 removed outlier: 3.511A pdb=" N GLU X 93 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY X 94 " --> pdb=" O GLU X 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 89 through 94' Processing helix chain 'Z' and resid 14 through 22 Processing helix chain 'Z' and resid 40 through 52 removed outlier: 3.590A pdb=" N GLN Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 114 Processing helix chain 'Z' and resid 179 through 187 removed outlier: 4.124A pdb=" N LEU Z 183 " --> pdb=" O ASP Z 179 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Z 184 " --> pdb=" O VAL Z 180 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU Z 185 " --> pdb=" O GLU Z 181 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU Z 186 " --> pdb=" O LYS Z 182 " (cutoff:3.500A) Processing helix chain '1' and resid 63 through 81 Proline residue: 1 68 - end of helix removed outlier: 3.877A pdb=" N TYR 1 71 " --> pdb=" O ILE 1 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS 1 78 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY 1 79 " --> pdb=" O GLU 1 75 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU 1 80 " --> pdb=" O ARG 1 76 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS 1 81 " --> pdb=" O ALA 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 98 removed outlier: 3.503A pdb=" N LEU 1 98 " --> pdb=" O LEU 1 94 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.543A pdb=" N LEU 2 16 " --> pdb=" O GLU 2 12 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 42 Processing helix chain '2' and resid 46 through 70 removed outlier: 4.663A pdb=" N ILE 2 50 " --> pdb=" O GLN 2 46 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG 2 51 " --> pdb=" O ASN 2 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP 2 52 " --> pdb=" O HIS 2 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN 2 70 " --> pdb=" O GLU 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 51 Processing helix chain '4' and resid 40 through 45 removed outlier: 4.022A pdb=" N GLY 4 45 " --> pdb=" O PRO 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 62 removed outlier: 7.155A pdb=" N GLN 4 60 " --> pdb=" O GLU 4 57 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ARG 4 61 " --> pdb=" O ARG 4 58 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG 4 62 " --> pdb=" O PHE 4 59 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 57 through 62' Processing helix chain '5' and resid 12 through 22 removed outlier: 4.758A pdb=" N HIS 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 31 Proline residue: 6 31 - end of helix Processing helix chain '7' and resid 8 through 16 Processing helix chain '7' and resid 17 through 25 removed outlier: 4.291A pdb=" N THR 7 24 " --> pdb=" O ALA 7 20 " (cutoff:3.500A) Proline residue: 7 25 - end of helix Processing helix chain '7' and resid 26 through 38 Processing helix chain '8' and resid 7 through 14 removed outlier: 3.924A pdb=" N ARG 8 13 " --> pdb=" O GLY 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 37 through 46 removed outlier: 3.998A pdb=" N ARG 8 46 " --> pdb=" O ARG 8 42 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 63 Proline residue: 8 63 - end of helix Processing helix chain '9' and resid 29 through 34 removed outlier: 3.723A pdb=" N LYS 9 33 " --> pdb=" O ASN 9 29 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN 9 34 " --> pdb=" O PRO 9 30 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 29 through 34' Processing helix chain 'b' and resid 10 through 16 removed outlier: 4.235A pdb=" N HIS b 16 " --> pdb=" O GLU b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 33 removed outlier: 3.719A pdb=" N ALA b 29 " --> pdb=" O ASN b 25 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG b 30 " --> pdb=" O PRO b 26 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR b 31 " --> pdb=" O LYS b 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE b 32 " --> pdb=" O PHE b 28 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR b 33 " --> pdb=" O ALA b 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 25 through 33' Processing helix chain 'b' and resid 44 through 63 removed outlier: 3.590A pdb=" N GLU b 49 " --> pdb=" O GLN b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 89 removed outlier: 4.276A pdb=" N VAL b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 123 removed outlier: 3.673A pdb=" N ALA b 123 " --> pdb=" O GLU b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 149 Processing helix chain 'b' and resid 150 through 156 removed outlier: 4.222A pdb=" N LEU b 154 " --> pdb=" O SER b 150 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU b 155 " --> pdb=" O GLY b 151 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS b 156 " --> pdb=" O PHE b 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 156' Processing helix chain 'b' and resid 166 through 171 Processing helix chain 'b' and resid 172 through 181 removed outlier: 3.826A pdb=" N GLU b 176 " --> pdb=" O ILE b 172 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 198 removed outlier: 3.708A pdb=" N VAL b 197 " --> pdb=" O ASP b 193 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP b 198 " --> pdb=" O PRO b 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 193 through 198' Processing helix chain 'b' and resid 207 through 227 Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.518A pdb=" N GLU c 35 " --> pdb=" O HIS c 31 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS c 45 " --> pdb=" O GLY c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.661A pdb=" N GLU c 89 " --> pdb=" O ARG c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.198A pdb=" N SER c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.970A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 28 Processing helix chain 'd' and resid 31 through 36 Processing helix chain 'd' and resid 52 through 69 removed outlier: 3.619A pdb=" N TYR d 68 " --> pdb=" O LEU d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 86 removed outlier: 5.129A pdb=" N LYS d 86 " --> pdb=" O ALA d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 100 Processing helix chain 'd' and resid 101 through 109 Processing helix chain 'd' and resid 113 through 124 removed outlier: 3.634A pdb=" N GLN d 119 " --> pdb=" O ARG d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 156 removed outlier: 3.694A pdb=" N ASN d 154 " --> pdb=" O GLU d 150 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU d 155 " --> pdb=" O LYS d 151 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 168 removed outlier: 5.200A pdb=" N GLY d 167 " --> pdb=" O GLU d 163 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 195 removed outlier: 5.257A pdb=" N ALA d 195 " --> pdb=" O ARG d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 209 removed outlier: 3.751A pdb=" N TYR d 207 " --> pdb=" O VAL d 203 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 66 Processing helix chain 'e' and resid 103 through 114 removed outlier: 3.509A pdb=" N GLY e 114 " --> pdb=" O LEU e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 142 Processing helix chain 'e' and resid 144 through 152 Processing helix chain 'f' and resid 15 through 34 Processing helix chain 'f' and resid 68 through 82 removed outlier: 3.595A pdb=" N VAL f 72 " --> pdb=" O PRO f 68 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP f 74 " --> pdb=" O ASP f 70 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG f 82 " --> pdb=" O GLU f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 3.521A pdb=" N LYS g 29 " --> pdb=" O ALA g 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE g 30 " --> pdb=" O PHE g 26 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.604A pdb=" N THR g 54 " --> pdb=" O ILE g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.764A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.564A pdb=" N ARG g 119 " --> pdb=" O ARG g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.889A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N HIS g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 Processing helix chain 'h' and resid 29 through 43 removed outlier: 3.565A pdb=" N GLU h 34 " --> pdb=" O ARG h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 107 removed outlier: 4.536A pdb=" N GLY h 106 " --> pdb=" O ARG h 102 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU h 107 " --> pdb=" O VAL h 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 102 through 107' Processing helix chain 'h' and resid 120 through 128 Processing helix chain 'i' and resid 32 through 38 Processing helix chain 'i' and resid 42 through 54 removed outlier: 4.612A pdb=" N ALA i 46 " --> pdb=" O ARG i 42 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU i 48 " --> pdb=" O VAL i 44 " (cutoff:3.500A) Proline residue: i 49 - end of helix removed outlier: 3.517A pdb=" N ALA i 52 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.534A pdb=" N ALA i 84 " --> pdb=" O GLY i 80 " (cutoff:3.500A) Proline residue: i 90 - end of helix Processing helix chain 'i' and resid 91 through 100 removed outlier: 5.044A pdb=" N LYS i 95 " --> pdb=" O ASP i 91 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU i 96 " --> pdb=" O TYR i 92 " (cutoff:3.500A) Proline residue: i 98 - end of helix Processing helix chain 'j' and resid 12 through 31 removed outlier: 3.747A pdb=" N LEU j 16 " --> pdb=" O ASP j 12 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA j 27 " --> pdb=" O ILE j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 78 through 88 removed outlier: 3.720A pdb=" N GLN j 84 " --> pdb=" O LYS j 80 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU j 88 " --> pdb=" O GLN j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 49 Processing helix chain 'k' and resid 52 through 58 removed outlier: 4.422A pdb=" N GLY k 56 " --> pdb=" O GLY k 52 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR k 57 " --> pdb=" O SER k 53 " (cutoff:3.500A) Proline residue: k 58 - end of helix No H-bonds generated for 'chain 'k' and resid 52 through 58' Processing helix chain 'k' and resid 59 through 76 Processing helix chain 'k' and resid 88 through 102 removed outlier: 4.868A pdb=" N GLU k 92 " --> pdb=" O GLY k 88 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN k 93 " --> pdb=" O ALA k 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE k 95 " --> pdb=" O ARG k 91 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG k 96 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA k 97 " --> pdb=" O GLN k 93 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER k 101 " --> pdb=" O ALA k 97 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY k 102 " --> pdb=" O LEU k 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 13 Processing helix chain 'l' and resid 116 through 121 removed outlier: 4.477A pdb=" N TYR l 120 " --> pdb=" O SER l 116 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 116 through 121' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.671A pdb=" N THR m 20 " --> pdb=" O ASP m 16 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR m 21 " --> pdb=" O VAL m 17 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.875A pdb=" N LEU m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 6.118A pdb=" N THR m 49 " --> pdb=" O VAL m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.682A pdb=" N ASN m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 3.661A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU m 73 " --> pdb=" O GLU m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 2 through 13 removed outlier: 4.832A pdb=" N LEU n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.743A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.773A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 3.629A pdb=" N ALA p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 4.054A pdb=" N LEU p 73 " --> pdb=" O THR p 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 99 removed outlier: 3.528A pdb=" N VAL q 85 " --> pdb=" O ARG q 81 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU q 96 " --> pdb=" O ARG q 92 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER q 97 " --> pdb=" O GLN q 93 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU q 98 " --> pdb=" O ASN q 94 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER q 99 " --> pdb=" O TYR q 95 " (cutoff:3.500A) Processing helix chain 'r' and resid 21 through 27 removed outlier: 3.656A pdb=" N THR r 25 " --> pdb=" O LYS r 21 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU r 26 " --> pdb=" O VAL r 22 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY r 27 " --> pdb=" O LYS r 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 21 through 27' Processing helix chain 'r' and resid 36 through 45 removed outlier: 3.906A pdb=" N PHE r 43 " --> pdb=" O VAL r 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU r 44 " --> pdb=" O LEU r 40 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 57 Processing helix chain 'r' and resid 59 through 77 removed outlier: 3.685A pdb=" N LYS r 68 " --> pdb=" O ARG r 64 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 63 through 68 removed outlier: 4.002A pdb=" N VAL s 67 " --> pdb=" O THR s 63 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY s 68 " --> pdb=" O GLU s 64 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.731A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 9 through 47 removed outlier: 3.872A pdb=" N HIS t 16 " --> pdb=" O ALA t 12 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG t 17 " --> pdb=" O LEU t 13 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN t 18 " --> pdb=" O LYS t 14 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER t 19 " --> pdb=" O ARG t 15 " (cutoff:3.500A) Processing helix chain 't' and resid 48 through 70 removed outlier: 4.420A pdb=" N GLY t 69 " --> pdb=" O LYS t 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER t 70 " --> pdb=" O ALA t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 73 through 96 removed outlier: 3.677A pdb=" N ALA t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) Processing helix chain 'u' and resid 8 through 16 Processing helix chain 'C' and resid 4 through 15 removed outlier: 4.146A pdb=" N LEU C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASP C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.534A pdb=" N ALA C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.995A pdb=" N GLU C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 removed outlier: 5.945A pdb=" N ILE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 135 Proline residue: C 133 - end of helix No H-bonds generated for 'chain 'C' and resid 129 through 135' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.707A pdb=" N ALA C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.834A pdb=" N ASP C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 2 through 5 removed outlier: 7.661A pdb=" N ALA D 2 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP D 20 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 81 through 84 removed outlier: 4.382A pdb=" N ALA D 81 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 94 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 80 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE D 75 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA D 119 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN D 115 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 128 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL D 118 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 140 through 143 removed outlier: 4.285A pdb=" N THR D 140 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN D 164 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 174 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 177 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 91 through 97 removed outlier: 5.147A pdb=" N ARG D 91 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.518A pdb=" N LYS E 2 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 10 through 15 removed outlier: 3.675A pdb=" N GLY E 10 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN E 180 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.681A pdb=" N GLN E 48 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 77 " --> pdb=" O PHE E 51 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 164 through 168 removed outlier: 4.270A pdb=" N GLU E 100 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 16 through 23 removed outlier: 8.208A pdb=" N LEU F 123 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 191 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 68 through 72 removed outlier: 3.847A pdb=" N LYS G 36 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY G 42 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLY G 154 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 16 through 19 Processing sheet with id= 12, first strand: chain 'H' and resid 41 through 46 Processing sheet with id= 13, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.233A pdb=" N THR H 129 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 94 through 98 Processing sheet with id= 15, first strand: chain 'I' and resid 17 through 21 removed outlier: 3.995A pdb=" N GLN I 17 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET I 1 " --> pdb=" O VAL I 21 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU I 35 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 76 through 81 removed outlier: 6.067A pdb=" N ILE I 138 " --> pdb=" O TYR I 130 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'N' and resid 12 through 17 removed outlier: 4.083A pdb=" N PHE N 51 " --> pdb=" O ARG N 12 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'N' and resid 72 through 76 removed outlier: 7.297A pdb=" N GLY N 81 " --> pdb=" O SER N 76 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'O' and resid 18 through 21 removed outlier: 3.817A pdb=" N THR O 6 " --> pdb=" O CYS O 21 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN O 82 " --> pdb=" O TYR O 7 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE O 86 " --> pdb=" O ALA O 11 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS O 59 " --> pdb=" O ILE O 87 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP O 37 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.562A pdb=" N ARG O 64 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP O 81 " --> pdb=" O LYS O 66 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 79 through 83 removed outlier: 3.973A pdb=" N LYS P 113 " --> pdb=" O GLN P 81 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'P' and resid 123 through 126 Processing sheet with id= 23, first strand: chain 'Q' and resid 63 through 67 removed outlier: 6.041A pdb=" N MET Q 103 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE Q 104 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP Q 31 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS Q 128 " --> pdb=" O LEU Q 37 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 72 through 75 Processing sheet with id= 25, first strand: chain 'R' and resid 33 through 37 removed outlier: 4.963A pdb=" N LEU R 111 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR R 94 " --> pdb=" O VAL R 117 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'S' and resid 34 through 41 removed outlier: 3.732A pdb=" N HIS S 34 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL S 28 " --> pdb=" O ASP S 88 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'T' and resid 40 through 47 removed outlier: 6.356A pdb=" N THR T 27 " --> pdb=" O VAL T 89 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'T' and resid 51 through 55 removed outlier: 3.873A pdb=" N ARG T 51 " --> pdb=" O THR T 62 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN T 55 " --> pdb=" O ASN T 58 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'V' and resid 11 through 15 Processing sheet with id= 30, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.844A pdb=" N LEU V 18 " --> pdb=" O ILE V 96 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU V 93 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL V 58 " --> pdb=" O LYS V 97 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL V 57 " --> pdb=" O LEU V 35 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA V 31 " --> pdb=" O VAL V 61 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'V' and resid 55 through 58 Processing sheet with id= 32, first strand: chain 'V' and resid 63 through 67 removed outlier: 4.679A pdb=" N GLN V 89 " --> pdb=" O GLY V 67 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 69 through 76 removed outlier: 4.122A pdb=" N TYR V 81 " --> pdb=" O LYS V 76 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'W' and resid 2 through 7 Processing sheet with id= 35, first strand: chain 'W' and resid 72 through 79 removed outlier: 4.585A pdb=" N THR W 100 " --> pdb=" O GLY W 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 80 through 88 removed outlier: 4.248A pdb=" N THR W 100 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG W 92 " --> pdb=" O ARG W 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'X' and resid 25 through 29 removed outlier: 3.964A pdb=" N LYS X 64 " --> pdb=" O GLY X 71 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS X 62 " --> pdb=" O ARG X 73 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP X 75 " --> pdb=" O ARG X 60 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG X 60 " --> pdb=" O ASP X 75 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS X 77 " --> pdb=" O HIS X 58 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS X 58 " --> pdb=" O LYS X 77 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA X 79 " --> pdb=" O THR X 56 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR X 56 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL X 81 " --> pdb=" O VAL X 54 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL X 54 " --> pdb=" O VAL X 81 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Y' and resid 23 through 26 removed outlier: 4.497A pdb=" N ARG Y 23 " --> pdb=" O VAL Y 15 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR Y 12 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LYS Y 71 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Y' and resid 28 through 32 Processing sheet with id= 40, first strand: chain 'Y' and resid 43 through 49 removed outlier: 5.277A pdb=" N ASN Y 43 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Y' and resid 84 through 87 removed outlier: 6.718A pdb=" N ARG Y 84 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Z' and resid 65 through 69 removed outlier: 4.204A pdb=" N GLN Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS Z 36 " --> pdb=" O ARG Z 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 75 through 78 removed outlier: 6.242A pdb=" N ASN Z 75 " --> pdb=" O GLU Z 84 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 115 through 119 removed outlier: 3.719A pdb=" N ALA Z 172 " --> pdb=" O LEU Z 150 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP Z 148 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ILE Z 146 " --> pdb=" O PRO Z 176 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 123 through 127 removed outlier: 3.693A pdb=" N ILE Z 137 " --> pdb=" O PRO Z 101 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '0' and resid 45 through 48 removed outlier: 5.921A pdb=" N VAL 0 81 " --> pdb=" O GLY 0 48 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY 0 76 " --> pdb=" O ARG 0 72 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '0' and resid 51 through 54 removed outlier: 4.318A pdb=" N THR 0 58 " --> pdb=" O GLY 0 54 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '1' and resid 32 through 35 removed outlier: 6.533A pdb=" N GLN 1 19 " --> pdb=" O THR 1 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '1' and resid 48 through 52 Processing sheet with id= 50, first strand: chain '3' and resid 32 through 38 removed outlier: 3.883A pdb=" N GLN 3 33 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '4' and resid 20 through 25 removed outlier: 3.862A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '6' and resid 21 through 25 removed outlier: 3.823A pdb=" N TYR 6 21 " --> pdb=" O LEU 6 11 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU 6 34 " --> pdb=" O GLU 6 51 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '8' and resid 22 through 25 removed outlier: 5.761A pdb=" N VAL 8 22 " --> pdb=" O LEU 8 50 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '9' and resid 14 through 19 Processing sheet with id= 55, first strand: chain 'b' and resid 68 through 72 Processing sheet with id= 56, first strand: chain 'c' and resid 54 through 59 Processing sheet with id= 57, first strand: chain 'c' and resid 164 through 171 removed outlier: 3.564A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN c 181 " --> pdb=" O LEU c 204 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'd' and resid 144 through 148 removed outlier: 6.994A pdb=" N MET d 181 " --> pdb=" O VAL d 148 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 6 through 11 removed outlier: 6.473A pdb=" N LEU e 31 " --> pdb=" O ILE e 11 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'e' and resid 78 through 83 removed outlier: 7.643A pdb=" N HIS e 78 " --> pdb=" O PRO e 93 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA e 94 " --> pdb=" O ASP e 117 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP e 117 " --> pdb=" O ALA e 94 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 28 through 36 removed outlier: 6.510A pdb=" N ARG e 40 " --> pdb=" O ASP e 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 4 through 10 removed outlier: 5.048A pdb=" N PHE f 60 " --> pdb=" O LEU f 43 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'f' and resid 44 through 48 Processing sheet with id= 64, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.278A pdb=" N ARG g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'h' and resid 22 through 26 removed outlier: 6.362A pdb=" N GLU h 22 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL h 26 " --> pdb=" O LEU h 59 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'h' and resid 82 through 85 removed outlier: 6.988A pdb=" N ILE h 111 " --> pdb=" O ILE h 134 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'i' and resid 3 through 9 Processing sheet with id= 68, first strand: chain 'j' and resid 5 through 11 removed outlier: 3.719A pdb=" N ASP j 73 " --> pdb=" O SER j 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN j 33 " --> pdb=" O ILE j 75 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'j' and resid 37 through 40 removed outlier: 4.583A pdb=" N ASN j 69 " --> pdb=" O LEU j 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'j' and resid 42 through 50 removed outlier: 3.789A pdb=" N ARG j 43 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG j 45 " --> pdb=" O LEU j 65 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'k' and resid 40 through 43 removed outlier: 4.366A pdb=" N ASN k 27 " --> pdb=" O SER k 24 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 32 through 35 removed outlier: 5.353A pdb=" N LEU l 84 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY l 88 " --> pdb=" O ARG l 97 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG l 97 " --> pdb=" O GLY l 88 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'l' and resid 39 through 44 removed outlier: 5.344A pdb=" N LYS l 54 " --> pdb=" O ILE l 70 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'p' and resid 2 through 9 removed outlier: 3.553A pdb=" N ALA p 7 " --> pdb=" O ARG p 18 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'q' and resid 4 through 9 removed outlier: 5.500A pdb=" N LYS q 4 " --> pdb=" O GLU q 61 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG q 70 " --> pdb=" O SER q 62 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'q' and resid 17 through 28 No H-bonds generated for sheet with id= 76 Processing sheet with id= 77, first strand: chain 'q' and resid 56 through 59 removed outlier: 6.200A pdb=" N VAL q 56 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 's' and resid 30 through 34 removed outlier: 3.641A pdb=" N HIS s 47 " --> pdb=" O ILE s 62 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 42 through 47 removed outlier: 4.313A pdb=" N VAL C 212 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'C' and resid 58 through 63 removed outlier: 5.824A pdb=" N VAL C 58 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'C' and resid 73 through 78 1964 hydrogen bonds defined for protein. 5775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4274 hydrogen bonds 6936 hydrogen bond angles 0 basepair planarities 1621 basepair parallelities 2447 stacking parallelities Total time for adding SS restraints: 263.17 Time building geometry restraints manager: 75.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.19: 5 1.19 - 1.45: 88333 1.45 - 1.71: 72924 1.71 - 1.97: 215 1.97 - 2.22: 19 Bond restraints: 161496 Sorted by residual: bond pdb=" C2 C a 71 " pdb=" N3 C a 71 " ideal model delta sigma weight residual 1.353 2.183 -0.830 2.00e-02 2.50e+03 1.72e+03 bond pdb=" N1 C a 71 " pdb=" C2 C a 71 " ideal model delta sigma weight residual 1.397 2.223 -0.826 2.00e-02 2.50e+03 1.71e+03 bond pdb=" O3' G a 64 " pdb=" P U a 65 " ideal model delta sigma weight residual 1.607 2.225 -0.618 1.50e-02 4.44e+03 1.70e+03 bond pdb=" N3 C a 71 " pdb=" C4 C a 71 " ideal model delta sigma weight residual 1.334 2.141 -0.807 2.00e-02 2.50e+03 1.63e+03 bond pdb=" N1 C a 71 " pdb=" C6 C a 71 " ideal model delta sigma weight residual 1.367 2.159 -0.792 2.00e-02 2.50e+03 1.57e+03 ... (remaining 161491 not shown) Histogram of bond angle deviations from ideal: 77.11 - 94.03: 28 94.03 - 110.94: 97113 110.94 - 127.85: 135833 127.85 - 144.77: 8688 144.77 - 161.68: 1 Bond angle restraints: 241663 Sorted by residual: angle pdb=" C3' G a 64 " pdb=" O3' G a 64 " pdb=" P U a 65 " ideal model delta sigma weight residual 120.20 161.68 -41.48 1.50e+00 4.44e-01 7.65e+02 angle pdb="FE1 SF4 d 301 " pdb=" S4 SF4 d 301 " pdb="FE2 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.79 -17.09 1.50e+00 4.44e-01 1.30e+02 angle pdb="FE1 SF4 d 301 " pdb=" S3 SF4 d 301 " pdb="FE2 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.38 -16.68 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE2 SF4 d 301 " pdb=" S1 SF4 d 301 " pdb="FE4 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.35 -16.65 1.50e+00 4.44e-01 1.23e+02 angle pdb="FE2 SF4 d 301 " pdb=" S3 SF4 d 301 " pdb="FE4 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.33 -16.63 1.50e+00 4.44e-01 1.23e+02 ... (remaining 241658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 82632 35.99 - 71.97: 3041 71.97 - 107.96: 349 107.96 - 143.94: 60 143.94 - 179.93: 43 Dihedral angle restraints: 86125 sinusoidal: 68946 harmonic: 17179 Sorted by residual: dihedral pdb=" C4' G a 70 " pdb=" C3' G a 70 " pdb=" C2' G a 70 " pdb=" C1' G a 70 " ideal model delta sinusoidal sigma weight residual -35.00 33.88 -68.88 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" C5' G a 70 " pdb=" C4' G a 70 " pdb=" C3' G a 70 " pdb=" O3' G a 70 " ideal model delta sinusoidal sigma weight residual 147.00 78.55 68.45 1 8.00e+00 1.56e-02 9.49e+01 dihedral pdb=" O4' U y 36 " pdb=" C1' U y 36 " pdb=" N1 U y 36 " pdb=" C2 U y 36 " ideal model delta sinusoidal sigma weight residual 200.00 24.39 175.61 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 86122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 30606 0.382 - 0.763: 0 0.763 - 1.145: 1 1.145 - 1.527: 0 1.527 - 1.908: 2 Chirality restraints: 30609 Sorted by residual: chirality pdb=" P U A2884 " pdb=" OP1 U A2884 " pdb=" OP2 U A2884 " pdb=" O5' U A2884 " both_signs ideal model delta sigma weight residual True 2.41 0.50 1.91 2.00e-01 2.50e+01 9.11e+01 chirality pdb=" P A A2225 " pdb=" OP1 A A2225 " pdb=" OP2 A A2225 " pdb=" O5' A A2225 " both_signs ideal model delta sigma weight residual True 2.41 0.58 1.83 2.00e-01 2.50e+01 8.34e+01 chirality pdb=" P U a 65 " pdb=" OP1 U a 65 " pdb=" OP2 U a 65 " pdb=" O5' U a 65 " both_signs ideal model delta sigma weight residual True 2.41 -3.19 -0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 30606 not shown) Planarity restraints: 13093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.032 2.00e-02 2.50e+03 5.74e-01 7.41e+03 pdb=" C4' OMG A2251 " 0.442 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.632 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.215 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 0.917 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.222 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.866 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " 0.032 2.00e-02 2.50e+03 5.67e-01 7.24e+03 pdb=" C4' 2MG a1207 " 0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " 0.609 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " -0.568 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " -0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " 0.910 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " 0.233 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " -0.857 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1404 " 0.053 2.00e-02 2.50e+03 5.51e-01 6.84e+03 pdb=" C4' 5MC a1404 " 0.422 2.00e-02 2.50e+03 pdb=" O4' 5MC a1404 " 0.512 2.00e-02 2.50e+03 pdb=" C3' 5MC a1404 " -0.587 2.00e-02 2.50e+03 pdb=" O3' 5MC a1404 " -0.574 2.00e-02 2.50e+03 pdb=" C2' 5MC a1404 " -0.193 2.00e-02 2.50e+03 pdb=" O2' 5MC a1404 " 0.928 2.00e-02 2.50e+03 pdb=" C1' 5MC a1404 " 0.249 2.00e-02 2.50e+03 pdb=" N1 5MC a1404 " -0.811 2.00e-02 2.50e+03 ... (remaining 13090 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.43: 1576 2.43 - 2.97: 75933 2.97 - 3.51: 223957 3.51 - 4.06: 397841 4.06 - 4.60: 476970 Nonbonded interactions: 1176277 Sorted by model distance: nonbonded pdb=" O2' A a 101 " pdb=" OP1 A a 152 " model vdw 1.881 2.200 nonbonded pdb=" O2' C a 103 " pdb=" O2' C a 174 " model vdw 1.930 2.200 nonbonded pdb=" O4' G a 102 " pdb=" O2' A a 151 " model vdw 1.934 2.200 nonbonded pdb=" O6 G a 66 " pdb=" N2 G a 97 " model vdw 1.976 2.360 nonbonded pdb=" O2' A A1496 " pdb=" O2' C A1577 " model vdw 1.986 2.200 ... (remaining 1176272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.920 Extract box with map and model: 22.660 Check model and map are aligned: 1.690 Set scattering table: 1.030 Process input model: 603.240 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 641.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 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 : 0.009 0.830 161492 Z= 0.603 Angle : 0.762 41.480 241653 Z= 0.399 Chirality : 0.041 1.908 30609 Planarity : 0.017 0.574 13093 Dihedral : 15.800 179.929 75101 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 46.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.62 % Favored : 92.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.10), residues: 5916 helix: -2.48 (0.09), residues: 1807 sheet: -2.97 (0.13), residues: 1111 loop : -1.96 (0.11), residues: 2998 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2152 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2152 time to evaluate : 6.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2152 average time/residue: 1.5333 time to fit residues: 5389.0711 Evaluate side-chains 1440 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1440 time to evaluate : 6.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 884 optimal weight: 7.9990 chunk 793 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 535 optimal weight: 10.0000 chunk 423 optimal weight: 6.9990 chunk 820 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 498 optimal weight: 10.0000 chunk 610 optimal weight: 8.9990 chunk 950 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 137 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 108 ASN G 130 ASN I 54 GLN I 105 HIS ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 27 HIS ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 HIS ** Q 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 HIS S 38 GLN T 58 ASN ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 57 ASN W 62 HIS X 82 GLN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN Z 151 HIS 0 12 ASN 0 50 ASN ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN 2 47 ASN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 HIS ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN d 125 HIS e 56 GLN e 78 HIS ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN g 86 GLN g 109 ASN g 122 HIS g 148 ASN g 153 HIS ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 22 HIS k 26 ASN k 62 GLN ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 ASN p 16 HIS s 65 ASN s 69 HIS s 83 HIS t 9 ASN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.381 161492 Z= 0.394 Angle : 0.720 29.128 241653 Z= 0.377 Chirality : 0.041 1.864 30609 Planarity : 0.007 0.136 13093 Dihedral : 16.549 179.877 63193 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 48.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.83 % Favored : 93.10 % Rotamer Outliers : 4.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.10), residues: 5916 helix: -0.55 (0.11), residues: 1948 sheet: -2.43 (0.14), residues: 1119 loop : -1.69 (0.11), residues: 2849 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1738 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1501 time to evaluate : 6.056 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 outliers start: 237 outliers final: 169 residues processed: 1602 average time/residue: 1.5218 time to fit residues: 4158.2500 Evaluate side-chains 1525 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1356 time to evaluate : 6.627 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 0 residues processed: 169 average time/residue: 1.2080 time to fit residues: 396.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 528 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 647 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 952 optimal weight: 9.9990 chunk 1028 optimal weight: 20.0000 chunk 848 optimal weight: 0.9980 chunk 944 optimal weight: 4.9990 chunk 324 optimal weight: 8.9990 chunk 764 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 GLN T 58 ASN ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 70 GLN ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 GLN ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 GLN i 124 GLN ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN m 62 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 HIS ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.380 161492 Z= 0.344 Angle : 0.645 28.087 241653 Z= 0.344 Chirality : 0.038 1.888 30609 Planarity : 0.006 0.128 13093 Dihedral : 16.317 179.421 63193 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 47.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.11), residues: 5916 helix: 0.08 (0.11), residues: 1938 sheet: -2.16 (0.14), residues: 1110 loop : -1.49 (0.11), residues: 2868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1618 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1455 time to evaluate : 6.733 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 outliers start: 163 outliers final: 102 residues processed: 1528 average time/residue: 1.4934 time to fit residues: 3887.3872 Evaluate side-chains 1477 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1375 time to evaluate : 6.631 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 1.1976 time to fit residues: 236.0357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 941 optimal weight: 10.0000 chunk 716 optimal weight: 10.0000 chunk 494 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 454 optimal weight: 4.9990 chunk 639 optimal weight: 10.0000 chunk 955 optimal weight: 9.9990 chunk 1012 optimal weight: 20.0000 chunk 499 optimal weight: 10.0000 chunk 905 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN G 58 GLN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 50 GLN ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 37 GLN ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN d 119 GLN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 201 GLN e 130 ASN f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN g 153 HIS h 82 HIS ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 HIS r 63 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.377 161492 Z= 0.470 Angle : 0.779 27.966 241653 Z= 0.404 Chirality : 0.044 2.049 30609 Planarity : 0.007 0.129 13093 Dihedral : 16.803 179.673 63193 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 52.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.16 % Favored : 91.77 % Rotamer Outliers : 4.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 5916 helix: -0.16 (0.11), residues: 1947 sheet: -2.13 (0.14), residues: 1123 loop : -1.65 (0.11), residues: 2846 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1370 time to evaluate : 6.878 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 outliers start: 226 outliers final: 170 residues processed: 1465 average time/residue: 1.4299 time to fit residues: 3554.7248 Evaluate side-chains 1462 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1292 time to evaluate : 6.258 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 0 residues processed: 170 average time/residue: 1.1859 time to fit residues: 378.7701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 842 optimal weight: 7.9990 chunk 574 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 753 optimal weight: 20.0000 chunk 417 optimal weight: 5.9990 chunk 863 optimal weight: 0.9990 chunk 699 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 516 optimal weight: 30.0000 chunk 908 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN H 147 ASN ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 ASN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN 0 70 GLN ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 201 GLN f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.369 161492 Z= 0.345 Angle : 0.657 27.980 241653 Z= 0.350 Chirality : 0.039 2.029 30609 Planarity : 0.006 0.125 13093 Dihedral : 16.451 179.913 63193 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 49.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 5916 helix: 0.15 (0.11), residues: 1956 sheet: -2.00 (0.14), residues: 1123 loop : -1.54 (0.11), residues: 2837 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1371 time to evaluate : 6.616 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 outliers start: 128 outliers final: 90 residues processed: 1433 average time/residue: 1.4475 time to fit residues: 3554.6816 Evaluate side-chains 1421 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1331 time to evaluate : 6.613 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 1.2095 time to fit residues: 209.2711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 340 optimal weight: 8.9990 chunk 911 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 594 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 1013 optimal weight: 30.0000 chunk 840 optimal weight: 20.0000 chunk 469 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 531 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 108 ASN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 47 GLN ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 201 GLN ** f 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 153 HIS i 3 GLN ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.365 161492 Z= 0.411 Angle : 0.714 28.250 241653 Z= 0.374 Chirality : 0.041 2.040 30609 Planarity : 0.006 0.127 13093 Dihedral : 16.609 179.629 63193 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 51.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.62 % Favored : 91.33 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.10), residues: 5916 helix: 0.13 (0.12), residues: 1953 sheet: -1.98 (0.15), residues: 1084 loop : -1.64 (0.11), residues: 2879 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1353 time to evaluate : 6.812 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 outliers start: 171 outliers final: 125 residues processed: 1411 average time/residue: 1.4010 time to fit residues: 3358.3570 Evaluate side-chains 1434 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1309 time to evaluate : 6.534 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 0 residues processed: 125 average time/residue: 1.0613 time to fit residues: 256.2696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 976 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 577 optimal weight: 3.9990 chunk 739 optimal weight: 20.0000 chunk 573 optimal weight: 4.9990 chunk 852 optimal weight: 20.0000 chunk 565 optimal weight: 30.0000 chunk 1009 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 615 optimal weight: 0.8980 chunk 465 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 70 GLN ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 56 GLN ** g 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 63 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.365 161492 Z= 0.317 Angle : 0.622 28.341 241653 Z= 0.334 Chirality : 0.038 2.014 30609 Planarity : 0.006 0.124 13093 Dihedral : 16.291 179.761 63193 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 49.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.08 % Favored : 92.87 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5916 helix: 0.48 (0.12), residues: 1954 sheet: -1.89 (0.14), residues: 1118 loop : -1.50 (0.11), residues: 2844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1373 time to evaluate : 6.808 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 outliers start: 71 outliers final: 50 residues processed: 1397 average time/residue: 1.4909 time to fit residues: 3560.1710 Evaluate side-chains 1375 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1325 time to evaluate : 6.581 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 1.1916 time to fit residues: 117.9058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 624 optimal weight: 1.9990 chunk 402 optimal weight: 0.0170 chunk 602 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 687 optimal weight: 10.0000 chunk 498 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 793 optimal weight: 10.0000 overall best weight: 6.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 GLN g 153 HIS ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 63 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.362 161492 Z= 0.353 Angle : 0.658 28.465 241653 Z= 0.349 Chirality : 0.039 2.035 30609 Planarity : 0.006 0.125 13093 Dihedral : 16.399 179.795 63193 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 50.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.11), residues: 5916 helix: 0.49 (0.12), residues: 1940 sheet: -1.87 (0.15), residues: 1110 loop : -1.56 (0.11), residues: 2866 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1333 time to evaluate : 6.799 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 outliers start: 97 outliers final: 73 residues processed: 1360 average time/residue: 1.4362 time to fit residues: 3338.4449 Evaluate side-chains 1375 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1302 time to evaluate : 6.621 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 1.1906 time to fit residues: 168.6222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 917 optimal weight: 10.0000 chunk 966 optimal weight: 10.0000 chunk 882 optimal weight: 7.9990 chunk 940 optimal weight: 2.9990 chunk 566 optimal weight: 20.0000 chunk 409 optimal weight: 7.9990 chunk 738 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 849 optimal weight: 4.9990 chunk 889 optimal weight: 3.9990 chunk 937 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 HIS ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 63 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.361 161492 Z= 0.327 Angle : 0.630 28.397 241653 Z= 0.336 Chirality : 0.038 2.009 30609 Planarity : 0.006 0.125 13093 Dihedral : 16.276 179.258 63193 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 50.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.11), residues: 5916 helix: 0.57 (0.12), residues: 1947 sheet: -1.86 (0.15), residues: 1104 loop : -1.48 (0.11), residues: 2865 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1343 time to evaluate : 6.731 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 outliers start: 79 outliers final: 65 residues processed: 1366 average time/residue: 1.4339 time to fit residues: 3340.5879 Evaluate side-chains 1381 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1316 time to evaluate : 6.683 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 1.1066 time to fit residues: 143.7596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 617 optimal weight: 8.9990 chunk 994 optimal weight: 8.9990 chunk 606 optimal weight: 2.9990 chunk 471 optimal weight: 5.9990 chunk 691 optimal weight: 10.0000 chunk 1043 optimal weight: 20.0000 chunk 960 optimal weight: 10.0000 chunk 830 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 509 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 70 GLN ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 40 HIS ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 HIS g 153 HIS ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.359 161492 Z= 0.337 Angle : 0.642 28.353 241653 Z= 0.342 Chirality : 0.038 2.010 30609 Planarity : 0.006 0.125 13093 Dihedral : 16.295 179.782 63193 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 50.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 5916 helix: 0.57 (0.12), residues: 1946 sheet: -1.86 (0.15), residues: 1099 loop : -1.50 (0.11), residues: 2871 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1331 time to evaluate : 6.744 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 outliers start: 44 outliers final: 29 residues processed: 1347 average time/residue: 1.4953 time to fit residues: 3442.1746 Evaluate side-chains 1344 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1315 time to evaluate : 6.797 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 1.1781 time to fit residues: 71.5713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 659 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 765 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 831 optimal weight: 6.9990 chunk 348 optimal weight: 8.9990 chunk 854 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 ASN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 GLN b 40 HIS ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** d 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** f 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 93 GLN r 63 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102436 restraints weight = 304107.269| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.11 r_work: 0.3199 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.356 161492 Z= 0.470 Angle : 0.768 28.268 241653 Z= 0.398 Chirality : 0.043 2.023 30609 Planarity : 0.007 0.128 13093 Dihedral : 16.716 178.839 63193 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 53.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.57 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.10), residues: 5916 helix: 0.11 (0.11), residues: 1955 sheet: -2.02 (0.15), residues: 1092 loop : -1.67 (0.11), residues: 2869 =============================================================================== Job complete usr+sys time: 50961.59 seconds wall clock time: 887 minutes 57.67 seconds (53277.67 seconds total)