Starting phenix.real_space_refine on Tue Mar 26 02:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unv_26634/03_2024/7unv_26634_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4606 5.49 5 Mg 595 5.21 5 S 169 5.16 5 C 75242 2.51 5 N 27704 2.21 5 O 41281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 44": "OE1" <-> "OE2" Residue "b GLU 83": "OE1" <-> "OE2" Residue "c TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "d GLU 197": "OE1" <-> "OE2" Residue "d TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "g PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 469": "OD1" <-> "OD2" Residue "x ASP 728": "OD1" <-> "OD2" Residue "x ASP 802": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "U ASP 22": "OD1" <-> "OD2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 78": "OE1" <-> "OE2" Residue "U ASP 94": "OD1" <-> "OD2" Residue "W GLU 9": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 142": "OD1" <-> "OD2" Residue "Z GLU 41": "OE1" <-> "OE2" Residue "Z PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 8": "OE1" <-> "OE2" Residue "5 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 20": "OD1" <-> "OD2" Residue "5 GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149599 Number of models: 1 Model: "" Number of chains: 85 Chain: "a" Number of atoms: 32675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 32675 Classifications: {'RNA': 1522} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 123, 'rna2p_pyr': 85, 'rna3p': 8, 'rna3p_pur': 742, 'rna3p_pyr': 563} Link IDs: {'rna2p': 209, 'rna3p': 1312} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1751 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1617 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1134 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 857 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 104} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "g" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1187 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 787 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} 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: "k" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 879 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "m" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 892 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "n" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 800 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 636 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "q" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 480 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "s" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "t" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 671 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 506 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "v" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 4275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4275 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 21, 'TRANS': 571} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 16, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "A" Number of atoms: 61891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2884, 61891 Classifications: {'RNA': 2884} Modifications used: {'5*END': 1, 'rna2p': 5, 'rna2p_pur': 276, 'rna2p_pyr': 169, 'rna3p': 8, 'rna3p_pur': 1368, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 450, 'rna3p': 2433} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 103} Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2072 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "D" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1588 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "E" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1521 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1406 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 168} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1323 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 587 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 260 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Chain: "J" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 689 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 144 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1130 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 132} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1066 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "O" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1085 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "P" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "Q" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "R" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "S" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "V" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "W" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 786 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1445 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "Y" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "Z" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 490 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "3" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 356 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 440 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "5" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "8" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Unusual residues: {' MG': 121} Classifications: {'undetermined': 121} Link IDs: {None: 120} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 455 Unusual residues: {' MG': 455} Classifications: {'undetermined': 455} Link IDs: {None: 454} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" 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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 238 Classifications: {'water': 238} Link IDs: {None: 237} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0ZSK SG CYS 3 16 125.880 18.974 163.181 1.00 80.80 S ATOM A0ZSW SG CYS 3 18 123.579 16.380 164.728 1.00 81.51 S ATOM A0ZWS SG CYS 3 37 122.525 18.346 161.588 1.00 82.78 S ATOM A0ZXD SG CYS 3 40 122.599 20.065 164.870 1.00 83.77 S ATOM A11DN SG CYS 8 11 57.429 108.602 139.748 1.00 49.72 S ATOM A11EC SG CYS 8 14 58.445 109.664 136.269 1.00 46.28 S ATOM A11HA SG CYS 8 27 56.466 112.088 138.540 1.00 46.36 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU e 152 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU e 152 " occ=0.00 residue: pdb=" N VAL e 154 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL e 154 " occ=0.00 residue: pdb=" N ALA e 155 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 155 " occ=0.00 residue: pdb=" N ALA e 156 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA e 156 " occ=0.00 residue: pdb=" N LYS e 157 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS e 157 " occ=0.00 residue: pdb=" N ARG e 158 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG e 158 " occ=0.00 residue: pdb=" N GLY e 159 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY e 159 " occ=0.00 residue: pdb=" N FME v 102 " occ=0.80 ... (8 atoms not shown) pdb=" O1 FME v 102 " occ=0.80 Time building chain proxies: 60.41, per 1000 atoms: 0.40 Number of scatterers: 149599 At special positions: 0 Unit cell: (246.5, 249.9, 272.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 169 16.00 P 4606 15.00 Mg 595 11.99 O 41281 8.00 N 27704 7.00 C 75242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.44 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 37 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 18 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " Number of angles added : 9 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11926 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 196 helices and 85 sheets defined 38.3% alpha, 20.4% beta 1516 base pairs and 2358 stacking pairs defined. Time for finding SS restraints: 80.62 Creating SS restraints... Processing helix chain 'b' and resid 6 through 13 removed outlier: 3.794A pdb=" N LEU b 10 " --> pdb=" O MET b 6 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 32 removed outlier: 3.877A pdb=" N GLY b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE b 32 " --> pdb=" O GLY b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 64 Proline residue: b 48 - end of helix removed outlier: 3.843A pdb=" N ALA b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLY b 63 " --> pdb=" O ARG b 59 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 removed outlier: 4.905A pdb=" N ILE b 79 " --> pdb=" O SER b 75 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG b 86 " --> pdb=" O GLU b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 125 removed outlier: 3.564A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR b 125 " --> pdb=" O SER b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 3.735A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.939A pdb=" N GLU b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.539A pdb=" N GLN b 226 " --> pdb=" O ILE b 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N GLY b 227 " --> pdb=" O ARG b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.673A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 48 removed outlier: 5.426A pdb=" N ALA c 30 " --> pdb=" O ARG c 26 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.685A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 5.483A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.120A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.532A 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 removed outlier: 3.749A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 4.313A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.673A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 removed outlier: 5.572A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS d 33 " --> pdb=" O ASP d 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 27 through 33' Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.148A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.159A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 removed outlier: 3.568A pdb=" N GLY d 106 " --> pdb=" O VAL d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.694A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.842A pdb=" N ASN d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.800A pdb=" N ALA d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY d 166 " --> pdb=" O CYS d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.774A pdb=" N LEU d 191 " --> pdb=" O ALA d 187 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.799A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 4.736A pdb=" N ASN e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.604A pdb=" N ASN e 147 " --> pdb=" O LYS e 143 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 156 removed outlier: 3.687A pdb=" N VAL e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA e 155 " --> pdb=" O PRO e 151 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA e 156 " --> pdb=" O GLU e 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 150 through 156' Processing helix chain 'e' and resid 159 through 164 removed outlier: 4.527A pdb=" N GLU e 163 " --> pdb=" O GLY e 159 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU e 164 " --> pdb=" O LYS e 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 164' Processing helix chain 'f' and resid 16 through 33 removed outlier: 4.530A pdb=" N GLY f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL f 22 " --> pdb=" O VAL f 18 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU f 30 " --> pdb=" O THR f 26 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 removed outlier: 5.059A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.796A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 111 removed outlier: 4.317A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG g 111 " --> pdb=" O PHE g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.924A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.800A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA g 145 " --> pdb=" O VAL g 141 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.753A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.655A pdb=" N ALA h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.016A pdb=" N GLY i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 56 Proline residue: i 51 - end of helix removed outlier: 3.637A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.536A pdb=" N GLU i 89 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU i 92 " --> pdb=" O ILE i 88 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.690A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 88 removed outlier: 4.417A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 82 through 88' Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.064A pdb=" N GLY k 51 " --> pdb=" O SER k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.685A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 78 removed outlier: 4.123A pdb=" N GLU k 76 " --> pdb=" O GLN k 72 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR k 77 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY k 78 " --> pdb=" O ALA k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.676A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN k 101 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS k 103 " --> pdb=" O ALA k 99 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.566A pdb=" N TYR l 117 " --> pdb=" O GLY l 113 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 21 removed outlier: 4.061A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.803A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY m 38 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.534A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.038A pdb=" N ASP m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.918A pdb=" N LEU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.605A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.836A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.533A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.503A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN n 51 " --> pdb=" O ALA n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 3.988A pdb=" N LEU n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARG n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.937A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.135A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.710A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.866A 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 53 through 64 Processing helix chain 'p' and resid 68 through 81 Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.054A pdb=" N ALA r 31 " --> pdb=" O ASN r 27 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.539A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.668A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA r 66 " --> pdb=" O ALA r 62 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.591A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.557A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA s 76 " --> pdb=" O GLY s 72 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 removed outlier: 3.966A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 88 removed outlier: 3.623A pdb=" N THR t 88 " --> pdb=" O LYS t 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 4.184A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU u 16 " --> pdb=" O PHE u 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.904A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 63 removed outlier: 4.241A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) Processing helix chain 'x' and resid 268 through 277 Processing helix chain 'x' and resid 279 through 291 removed outlier: 3.635A pdb=" N VAL x 283 " --> pdb=" O LYS x 279 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET x 290 " --> pdb=" O PHE x 286 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY x 291 " --> pdb=" O MET x 287 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 313 removed outlier: 3.752A pdb=" N ALA x 305 " --> pdb=" O ASP x 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY x 313 " --> pdb=" O ALA x 309 " (cutoff:3.500A) Processing helix chain 'x' and resid 322 through 333 removed outlier: 3.864A pdb=" N GLU x 326 " --> pdb=" O ASN x 322 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER x 331 " --> pdb=" O GLN x 327 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU x 332 " --> pdb=" O LEU x 328 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS x 333 " --> pdb=" O ALA x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 354 through 364 removed outlier: 3.780A pdb=" N LEU x 358 " --> pdb=" O GLY x 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU x 359 " --> pdb=" O LYS x 355 " (cutoff:3.500A) Processing helix chain 'x' and resid 402 through 413 removed outlier: 4.126A pdb=" N ALA x 412 " --> pdb=" O ARG x 408 " (cutoff:3.500A) Processing helix chain 'x' and resid 427 through 441 Processing helix chain 'x' and resid 458 through 469 removed outlier: 4.790A pdb=" N LYS x 462 " --> pdb=" O PRO x 458 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN x 463 " --> pdb=" O ASP x 459 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU x 468 " --> pdb=" O GLY x 464 " (cutoff:3.500A) Processing helix chain 'x' and resid 491 through 502 removed outlier: 3.739A pdb=" N GLN x 502 " --> pdb=" O ALA x 498 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 635 Processing helix chain 'x' and resid 648 through 663 removed outlier: 3.864A pdb=" N SER x 660 " --> pdb=" O GLN x 656 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY x 661 " --> pdb=" O GLY x 657 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU x 662 " --> pdb=" O SER x 658 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY x 663 " --> pdb=" O LEU x 659 " (cutoff:3.500A) Processing helix chain 'x' and resid 680 through 691 removed outlier: 3.507A pdb=" N SER x 690 " --> pdb=" O LEU x 686 " (cutoff:3.500A) Processing helix chain 'x' and resid 702 through 713 removed outlier: 4.442A pdb=" N GLY x 713 " --> pdb=" O VAL x 709 " (cutoff:3.500A) Processing helix chain 'x' and resid 721 through 737 removed outlier: 3.704A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY x 735 " --> pdb=" O LYS x 731 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N MET x 736 " --> pdb=" O ALA x 732 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU x 737 " --> pdb=" O LEU x 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.609A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.032A pdb=" N LEU C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.174A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.006A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.997A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 261 through 269 removed outlier: 6.500A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 269' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.061A pdb=" N SER C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.508A pdb=" N THR D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.969A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.504A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.129A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 removed outlier: 4.026A pdb=" N ALA E 103 " --> pdb=" O MET E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.736A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.571A pdb=" N ALA E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.604A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 removed outlier: 3.720A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 11 removed outlier: 3.613A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 removed outlier: 3.896A pdb=" N GLN F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.873A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.536A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.608A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.513A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.786A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.803A pdb=" N PHE G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 52 through 72 removed outlier: 3.791A pdb=" N ALA H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 21 removed outlier: 5.013A pdb=" N LYS I 9 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 48 removed outlier: 4.243A pdb=" N GLU I 44 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG I 46 " --> pdb=" O ARG I 42 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU I 47 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 removed outlier: 3.709A pdb=" N LYS I 61 " --> pdb=" O ASN I 57 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG I 62 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 76 removed outlier: 4.644A pdb=" N ASN I 73 " --> pdb=" O PHE I 69 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 104 removed outlier: 5.143A pdb=" N ARG I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.982A pdb=" N LYS J 40 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE J 42 " --> pdb=" O PHE J 38 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN J 43 " --> pdb=" O CYS J 39 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 82 removed outlier: 4.062A pdb=" N LEU J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 114 removed outlier: 3.705A pdb=" N LYS J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 4.288A pdb=" N ARG J 127 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR J 128 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE J 129 " --> pdb=" O ALA J 125 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 4.146A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.332A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.924A pdb=" N LYS L 121 " --> pdb=" O ASP L 117 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.560A pdb=" N ALA M 118 " --> pdb=" O ILE M 114 " (cutoff:3.500A) Proline residue: M 119 - end of helix Processing helix chain 'M' and resid 103 through 108 removed outlier: 4.553A pdb=" N THR M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 Processing helix chain 'N' and resid 68 through 75 removed outlier: 4.375A pdb=" N MET N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASP N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 68 through 75' Processing helix chain 'N' and resid 78 through 83 removed outlier: 3.660A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA N 83 " --> pdb=" O THR N 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 83' Processing helix chain 'N' and resid 91 through 99 removed outlier: 3.529A pdb=" N LYS N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 4.088A pdb=" N GLY N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 6.113A pdb=" N ILE O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 4.178A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.526A pdb=" N VAL P 26 " --> pdb=" O GLN P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 57 removed outlier: 3.639A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 4.800A pdb=" N GLU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 Processing helix chain 'P' and resid 72 through 88 removed outlier: 4.328A pdb=" N PHE P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN P 81 " --> pdb=" O GLY P 77 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS P 85 " --> pdb=" O ASN P 81 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 23 removed outlier: 5.337A pdb=" N GLU Q 6 " --> pdb=" O SER Q 2 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 85 removed outlier: 3.542A pdb=" N GLU Q 79 " --> pdb=" O GLN Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 113 Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.692A pdb=" N GLN R 8 " --> pdb=" O LYS R 4 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU R 12 " --> pdb=" O GLN R 8 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 105 removed outlier: 4.995A pdb=" N ARG R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 105' Processing helix chain 'S' and resid 7 through 22 removed outlier: 3.750A pdb=" N LYS S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.998A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 3.999A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 3.524A pdb=" N ALA S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.669A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 117 removed outlier: 3.684A pdb=" N SER S 116 " --> pdb=" O LYS S 112 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 25 removed outlier: 3.996A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP U 22 " --> pdb=" O ARG U 18 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.745A pdb=" N ASN U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.787A pdb=" N GLU U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL U 50 " --> pdb=" O ILE U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.531A pdb=" N LEU U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 2 through 10 removed outlier: 3.916A pdb=" N VAL V 6 " --> pdb=" O ASN V 2 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE V 7 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS V 8 " --> pdb=" O GLU V 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU V 10 " --> pdb=" O VAL V 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 2 through 10' Processing helix chain 'V' and resid 16 through 26 removed outlier: 3.582A pdb=" N ASP V 24 " --> pdb=" O THR V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 50 Processing helix chain 'W' and resid 65 through 70 removed outlier: 4.328A pdb=" N VAL W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ALA W 70 " --> pdb=" O VAL W 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 65 through 70' Processing helix chain 'X' and resid 15 through 25 Processing helix chain 'X' and resid 46 through 56 removed outlier: 3.693A pdb=" N LYS X 52 " --> pdb=" O ARG X 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 122 removed outlier: 3.647A pdb=" N GLN X 122 " --> pdb=" O VAL X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 161 through 166 removed outlier: 3.652A pdb=" N LEU X 165 " --> pdb=" O HIS X 161 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS X 166 " --> pdb=" O LEU X 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 161 through 166' Processing helix chain 'X' and resid 173 through 179 removed outlier: 5.362A pdb=" N ALA X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY X 179 " --> pdb=" O GLN X 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 63 removed outlier: 3.505A pdb=" N ARG Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 75 Processing helix chain '1' and resid 2 through 10 removed outlier: 3.546A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 3.839A pdb=" N GLU 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 61 removed outlier: 4.572A pdb=" N LEU 1 43 " --> pdb=" O GLN 1 39 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG 1 48 " --> pdb=" O SER 1 44 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.590A pdb=" N LEU 2 26 " --> pdb=" O CYS 2 22 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.754A pdb=" N MET 2 46 " --> pdb=" O GLU 2 42 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 removed outlier: 4.174A pdb=" N THR 3 45 " --> pdb=" O HIS 3 41 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.623A pdb=" N ARG 4 16 " --> pdb=" O ALA 4 12 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 4 17 " --> pdb=" O ARG 4 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER 4 18 " --> pdb=" O ASP 4 14 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 removed outlier: 3.620A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.517A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.709A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 36 removed outlier: 4.812A pdb=" N MET 7 35 " --> pdb=" O ILE 7 31 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR 7 36 " --> pdb=" O LEU 7 32 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 31 through 36' Processing helix chain '7' and resid 37 through 45 removed outlier: 3.804A pdb=" N ARG 7 44 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY 7 45 " --> pdb=" O ARG 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 62 removed outlier: 4.830A pdb=" N ALA 7 55 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG 7 56 " --> pdb=" O SER 7 52 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 89 through 92 Processing sheet with id= 2, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.674A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.559A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS c 204 " --> pdb=" O ASP c 181 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU c 206 " --> pdb=" O ARG c 179 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ARG c 179 " --> pdb=" O GLU c 206 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 140 through 144 removed outlier: 4.006A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL d 143 " --> pdb=" O GLY d 180 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N TRP d 170 " --> pdb=" O LYS d 183 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 18 through 26 removed outlier: 6.815A pdb=" N ARG e 46 " --> pdb=" O ASP e 42 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 85 through 89 removed outlier: 4.044A pdb=" N GLN e 98 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU e 125 " --> pdb=" O GLN e 98 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'f' and resid 38 through 43 removed outlier: 4.875A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU f 61 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU f 88 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'g' and resid 73 through 79 removed outlier: 3.536A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.116A pdb=" N THR h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN h 58 " --> pdb=" O SER h 52 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP h 48 " --> pdb=" O GLU h 62 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.704A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE h 103 " --> pdb=" O LEU h 126 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 12, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.152A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'k' and resid 29 through 36 removed outlier: 3.537A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.255A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.581A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'p' and resid 4 through 11 removed outlier: 3.930A pdb=" N GLY p 37 " --> pdb=" O LEU p 19 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ARG p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'q' and resid 10 through 14 Processing sheet with id= 18, first strand: chain 'q' and resid 22 through 34 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 's' and resid 30 through 33 removed outlier: 4.242A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'x' and resid 259 through 263 removed outlier: 3.892A pdb=" N ILE x 263 " --> pdb=" O LYS x 317 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'x' and resid 379 through 385 removed outlier: 3.732A pdb=" N THR x 396 " --> pdb=" O VAL x 347 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY x 349 " --> pdb=" O THR x 396 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE x 415 " --> pdb=" O VAL x 344 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL x 446 " --> pdb=" O PRO x 480 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL x 482 " --> pdb=" O VAL x 446 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'x' and resid 522 through 526 removed outlier: 6.843A pdb=" N THR x 534 " --> pdb=" O VAL x 521 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG x 517 " --> pdb=" O GLN x 538 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY x 516 " --> pdb=" O VAL x 594 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP x 590 " --> pdb=" O VAL x 520 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET x 547 " --> pdb=" O VAL x 595 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL x 550 " --> pdb=" O ASN x 553 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'x' and resid 666 through 672 removed outlier: 7.371A pdb=" N LEU x 644 " --> pdb=" O VAL x 672 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY x 673 " --> pdb=" O ILE x 642 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'x' and resid 716 through 719 Processing sheet with id= 25, first strand: chain 'x' and resid 739 through 746 removed outlier: 5.538A pdb=" N SER x 739 " --> pdb=" O ALA x 837 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU x 741 " --> pdb=" O GLU x 835 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLU x 835 " --> pdb=" O LEU x 741 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU x 743 " --> pdb=" O LYS x 833 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS x 833 " --> pdb=" O GLU x 743 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE x 745 " --> pdb=" O PHE x 831 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE x 831 " --> pdb=" O ILE x 745 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE x 748 " --> pdb=" O THR x 769 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY x 765 " --> pdb=" O ARG x 752 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'x' and resid 771 through 774 removed outlier: 6.629A pdb=" N GLY x 771 " --> pdb=" O ALA x 808 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'x' and resid 789 through 792 removed outlier: 3.644A pdb=" N PHE x 789 " --> pdb=" O VAL x 781 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY x 791 " --> pdb=" O ILE x 779 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'x' and resid 794 through 798 Processing sheet with id= 29, first strand: chain 'x' and resid 338 through 341 removed outlier: 5.565A pdb=" N VAL x 339 " --> pdb=" O LYS x 509 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU x 507 " --> pdb=" O ARG x 341 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'x' and resid 534 through 538 removed outlier: 3.674A pdb=" N VAL x 537 " --> pdb=" O ILE x 575 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE x 575 " --> pdb=" O VAL x 537 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'x' and resid 641 through 646 Processing sheet with id= 32, first strand: chain 'x' and resid 763 through 769 removed outlier: 4.193A pdb=" N MET x 810 " --> pdb=" O VAL x 768 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'x' and resid 779 through 783 Processing sheet with id= 34, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 35, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.751A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 116 through 119 removed outlier: 5.346A pdb=" N ILE C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.012A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ALA C 170 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.589A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.123A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY D 199 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP D 200 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 37 through 40 removed outlier: 3.572A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASP D 94 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.535A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 25 through 30 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'D' and resid 48 through 52 Processing sheet with id= 44, first strand: chain 'D' and resid 105 through 108 removed outlier: 5.465A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.319A pdb=" N MET E 1 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU E 3 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 11 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 5 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'E' and resid 41 through 46 removed outlier: 7.479A pdb=" N GLY E 41 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER E 90 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA E 86 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.769A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 149 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.771A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE F 85 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL F 89 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.615A pdb=" N GLU G 34 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY G 28 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 82 through 89 removed outlier: 3.540A pdb=" N ARG G 85 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 52, first strand: chain 'H' and resid 16 through 21 removed outlier: 4.554A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET H 1 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'I' and resid 80 through 85 removed outlier: 3.948A pdb=" N ALA I 28 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL I 26 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL I 27 " --> pdb=" O LYS I 109 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP I 29 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU I 107 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'J' and resid 9 through 14 removed outlier: 3.693A pdb=" N ILE J 9 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE J 59 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE J 58 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR J 60 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR J 68 " --> pdb=" O THR J 60 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'L' and resid 14 through 19 Processing sheet with id= 56, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.511A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.336A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 38 through 41 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.545A pdb=" N TYR O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'O' and resid 31 through 37 removed outlier: 7.735A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA O 128 " --> pdb=" O THR O 37 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'P' and resid 33 through 36 removed outlier: 5.383A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 50 through 53 removed outlier: 3.739A pdb=" N ALA Q 50 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 39 through 46 removed outlier: 6.557A pdb=" N THR R 26 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER R 84 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 50 through 53 removed outlier: 3.730A pdb=" N ALA R 50 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER R 58 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.717A pdb=" N LEU T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.847A pdb=" N GLU T 18 " --> pdb=" O ILE T 98 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU T 95 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR T 60 " --> pdb=" O THR T 99 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU T 31 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 57 through 60 Processing sheet with id= 68, first strand: chain 'T' and resid 65 through 68 Processing sheet with id= 69, first strand: chain 'T' and resid 71 through 78 removed outlier: 4.212A pdb=" N HIS T 83 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'U' and resid 2 through 8 removed outlier: 5.135A pdb=" N SER U 100 " --> pdb=" O GLY U 79 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 73 " --> pdb=" O LYS U 106 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'V' and resid 28 through 32 removed outlier: 4.696A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP V 78 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS V 63 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL V 57 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 39 through 44 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'W' and resid 81 through 84 removed outlier: 7.379A pdb=" N ARG W 81 " --> pdb=" O LYS W 96 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG W 93 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS W 100 " --> pdb=" O PHE W 95 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'X' and resid 72 through 75 removed outlier: 5.138A pdb=" N SER X 42 " --> pdb=" O ARG X 11 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA X 92 " --> pdb=" O PRO X 30 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA X 79 " --> pdb=" O ASP X 93 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'X' and resid 125 through 129 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 'X' and resid 132 through 138 removed outlier: 7.274A pdb=" N SER X 132 " --> pdb=" O LEU X 109 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Y' and resid 29 through 32 removed outlier: 5.052A pdb=" N GLN Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY Y 65 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER Y 81 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE Y 82 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Y' and resid 34 through 37 removed outlier: 4.032A pdb=" N ASN Y 35 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU Y 59 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLY Y 50 " --> pdb=" O LYS Y 62 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.704A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '2' and resid 32 through 38 removed outlier: 4.287A pdb=" N HIS 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL 2 6 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL 2 37 " --> pdb=" O VAL 2 4 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS 2 5 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '3' and resid 12 through 16 No H-bonds generated for sheet with id= 81 Processing sheet with id= 82, first strand: chain '4' and resid 28 through 31 removed outlier: 3.533A pdb=" N GLU 4 35 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '5' and resid 16 through 22 removed outlier: 6.359A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '7' and resid 21 through 24 removed outlier: 6.252A pdb=" N LEU 7 21 " --> pdb=" O LEU 7 49 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '8' and resid 14 through 19 removed outlier: 4.610A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) 1973 hydrogen bonds defined for protein. 5838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3842 hydrogen bonds 6062 hydrogen bond angles 0 basepair planarities 1516 basepair parallelities 2358 stacking parallelities Total time for adding SS restraints: 260.71 Time building geometry restraints manager: 65.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27299 1.33 - 1.46: 65033 1.46 - 1.58: 59364 1.58 - 1.70: 9202 1.70 - 1.83: 298 Bond restraints: 161196 Sorted by residual: bond pdb=" C4 5MU A1926 " pdb=" C5 5MU A1926 " ideal model delta sigma weight residual 1.802 1.478 0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.482 0.320 2.00e-02 2.50e+03 2.57e+02 bond pdb=" N1 5MU A1926 " pdb=" C6 5MU A1926 " ideal model delta sigma weight residual 1.635 1.333 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" N1 5MU v 54 " pdb=" C6 5MU v 54 " ideal model delta sigma weight residual 1.635 1.337 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2' GCP x 902 " pdb=" C3' GCP x 902 " ideal model delta sigma weight residual 1.241 1.512 -0.271 2.00e-02 2.50e+03 1.84e+02 ... (remaining 161191 not shown) Histogram of bond angle deviations from ideal: 81.05 - 92.79: 3 92.79 - 104.53: 20164 104.53 - 116.27: 120434 116.27 - 128.00: 92014 128.00 - 139.74: 7900 Bond angle restraints: 240515 Sorted by residual: angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP1 U A1095 " ideal model delta sigma weight residual 108.00 81.05 26.95 3.00e+00 1.11e-01 8.07e+01 angle pdb=" O4' A v 76 " pdb=" C1' A v 76 " pdb=" N9 A v 76 " ideal model delta sigma weight residual 108.20 120.44 -12.24 1.50e+00 4.44e-01 6.65e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP2 U A1095 " ideal model delta sigma weight residual 108.00 83.77 24.23 3.00e+00 1.11e-01 6.52e+01 angle pdb=" C1' 2MA A2490 " pdb=" N9 2MA A2490 " pdb=" C8 2MA A2490 " ideal model delta sigma weight residual 106.32 126.51 -20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" C1' OMG A2238 " pdb=" N9 OMG A2238 " pdb=" C4 OMG A2238 " ideal model delta sigma weight residual 108.29 127.25 -18.96 3.00e+00 1.11e-01 3.99e+01 ... (remaining 240510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 91165 35.93 - 71.85: 10443 71.85 - 107.78: 1174 107.78 - 143.71: 34 143.71 - 179.63: 40 Dihedral angle restraints: 102856 sinusoidal: 84314 harmonic: 18542 Sorted by residual: dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual 180.00 -106.11 -73.89 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" O4' U A2100 " pdb=" C1' U A2100 " pdb=" N1 U A2100 " pdb=" C2 U A2100 " ideal model delta sinusoidal sigma weight residual 200.00 20.55 179.45 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1913 " pdb=" C1' U A1913 " pdb=" N1 U A1913 " pdb=" C2 U A1913 " ideal model delta sinusoidal sigma weight residual 200.00 30.20 169.80 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 102853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.394: 30623 0.394 - 0.788: 1 0.788 - 1.182: 0 1.182 - 1.576: 0 1.576 - 1.970: 1 Chirality restraints: 30625 Sorted by residual: chirality pdb=" P U A1095 " pdb=" OP1 U A1095 " pdb=" OP2 U A1095 " pdb=" O5' U A1095 " both_signs ideal model delta sigma weight residual True 2.41 0.44 1.97 2.00e-01 2.50e+01 9.70e+01 chirality pdb=" C1' A v 76 " pdb=" O4' A v 76 " pdb=" C2' A v 76 " pdb=" N9 A v 76 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" C1' A A 973 " pdb=" O4' A A 973 " pdb=" C2' A A 973 " pdb=" N9 A A 973 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 30622 not shown) Planarity restraints: 13447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1510 " 0.063 2.00e-02 2.50e+03 5.98e-01 8.06e+03 pdb=" C4' 2MG a1510 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG a1510 " 0.610 2.00e-02 2.50e+03 pdb=" C3' 2MG a1510 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1510 " -0.642 2.00e-02 2.50e+03 pdb=" C2' 2MG a1510 " -0.171 2.00e-02 2.50e+03 pdb=" O2' 2MG a1510 " 0.987 2.00e-02 2.50e+03 pdb=" C1' 2MG a1510 " 0.225 2.00e-02 2.50e+03 pdb=" N9 2MG a1510 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2485 " -0.056 2.00e-02 2.50e+03 5.81e-01 7.61e+03 pdb=" C4' OMC A2485 " -0.433 2.00e-02 2.50e+03 pdb=" O4' OMC A2485 " -0.590 2.00e-02 2.50e+03 pdb=" C3' OMC A2485 " 0.596 2.00e-02 2.50e+03 pdb=" O3' OMC A2485 " 0.614 2.00e-02 2.50e+03 pdb=" C2' OMC A2485 " 0.186 2.00e-02 2.50e+03 pdb=" O2' OMC A2485 " -0.961 2.00e-02 2.50e+03 pdb=" C1' OMC A2485 " -0.229 2.00e-02 2.50e+03 pdb=" N1 OMC A2485 " 0.873 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2056 " -0.073 2.00e-02 2.50e+03 5.80e-01 7.57e+03 pdb=" C4' 7MG A2056 " -0.422 2.00e-02 2.50e+03 pdb=" O4' 7MG A2056 " -0.530 2.00e-02 2.50e+03 pdb=" C3' 7MG A2056 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 7MG A2056 " 0.635 2.00e-02 2.50e+03 pdb=" C2' 7MG A2056 " 0.164 2.00e-02 2.50e+03 pdb=" O2' 7MG A2056 " -0.992 2.00e-02 2.50e+03 pdb=" C1' 7MG A2056 " -0.236 2.00e-02 2.50e+03 pdb=" N9 7MG A2056 " 0.858 2.00e-02 2.50e+03 ... (remaining 13444 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 731 2.38 - 3.01: 73401 3.01 - 3.64: 251497 3.64 - 4.27: 433589 4.27 - 4.90: 583647 Nonbonded interactions: 1342865 Sorted by model distance: nonbonded pdb=" OP2 C A1144 " pdb="MG MG A3449 " model vdw 1.751 2.170 nonbonded pdb="MG MG A3035 " pdb=" O HOH A3530 " model vdw 1.889 2.170 nonbonded pdb=" N7 G A1641 " pdb="MG MG A3397 " model vdw 1.895 2.250 nonbonded pdb=" N7 G A1833 " pdb="MG MG A3416 " model vdw 1.895 2.250 nonbonded pdb=" N7 G a 499 " pdb="MG MG a3108 " model vdw 1.895 2.250 ... (remaining 1342860 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=0.00 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: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.120 Extract box with map and model: 30.220 Check model and map are aligned: 1.570 Set scattering table: 0.950 Process input model: 594.790 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.350 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:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 651.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 161196 Z= 0.309 Angle : 0.624 26.947 240515 Z= 0.319 Chirality : 0.039 1.970 30625 Planarity : 0.019 0.598 13447 Dihedral : 22.907 179.632 90930 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.63 % Favored : 92.95 % Rotamer: Outliers : 0.16 % Allowed : 0.54 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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 (0.10), residues: 6429 helix: -0.24 (0.12), residues: 1939 sheet: -0.22 (0.15), residues: 1281 loop : -1.73 (0.10), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP d 170 HIS 0.014 0.001 HIS P 16 PHE 0.029 0.001 PHE x 481 TYR 0.026 0.002 TYR e 139 ARG 0.008 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1768 time to evaluate : 6.965 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: d 36 ASN cc_start: 0.8102 (m110) cc_final: 0.7652 (m110) REVERT: f 65 GLU cc_start: 0.6713 (tt0) cc_final: 0.5818 (mp0) REVERT: f 74 LEU cc_start: 0.8340 (pp) cc_final: 0.7931 (pt) REVERT: h 9 ASP cc_start: 0.8063 (t70) cc_final: 0.7854 (t0) REVERT: h 23 THR cc_start: 0.9103 (p) cc_final: 0.8742 (p) REVERT: m 75 MET cc_start: 0.6677 (tmm) cc_final: 0.6307 (OUTLIER) REVERT: m 76 ASN cc_start: 0.7870 (m-40) cc_final: 0.6719 (m-40) REVERT: u 19 PHE cc_start: 0.8233 (t80) cc_final: 0.7792 (t80) REVERT: u 23 CYS cc_start: 0.6678 (m) cc_final: 0.6074 (m) REVERT: X 100 ASP cc_start: 0.8090 (p0) cc_final: 0.7701 (p0) REVERT: X 112 ILE cc_start: 0.9201 (pt) cc_final: 0.8764 (pt) REVERT: 1 4 ASN cc_start: 0.7790 (m110) cc_final: 0.7525 (m110) outliers start: 8 outliers final: 8 residues processed: 1774 average time/residue: 2.2018 time to fit residues: 5597.1914 Evaluate side-chains 1452 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1445 time to evaluate : 6.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain x residue 469 ASP Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain R residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 920 optimal weight: 2.9990 chunk 826 optimal weight: 7.9990 chunk 458 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 557 optimal weight: 20.0000 chunk 441 optimal weight: 6.9990 chunk 854 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 519 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 989 optimal weight: 9.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 ASN c 69 HIS c 118 GLN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN d 41 HIS ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN g 28 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN l 46 ASN l 73 ASN ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN o 37 ASN t 34 ASN x 297 ASN x 457 ASN x 463 ASN x 621 HIS x 668 GLN x 776 ASN C 22 GLN C 61 HIS C 115 GLN C 261 ASN D 126 ASN D 130 GLN E 2 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN M 56 GLN N 55 GLN ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 GLN U 61 ASN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 ASN X 113 ASN X 129 HIS Y 40 GLN 2 18 ASN 6 16 HIS 6 26 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 161196 Z= 0.500 Angle : 0.751 27.460 240515 Z= 0.398 Chirality : 0.046 1.932 30625 Planarity : 0.007 0.146 13447 Dihedral : 23.256 179.852 78928 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.72 % Favored : 91.90 % Rotamer: Outliers : 4.49 % Allowed : 17.94 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.21 (0.10), residues: 6429 helix: 0.28 (0.11), residues: 2026 sheet: -0.30 (0.14), residues: 1298 loop : -1.78 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP n 101 HIS 0.019 0.001 HIS P 16 PHE 0.029 0.002 PHE x 481 TYR 0.028 0.002 TYR x 554 ARG 0.011 0.001 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1479 time to evaluate : 7.141 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: f 65 GLU cc_start: 0.6923 (tt0) cc_final: 0.5994 (mp0) REVERT: f 74 LEU cc_start: 0.8164 (pp) cc_final: 0.6444 (pp) REVERT: h 9 ASP cc_start: 0.8057 (t70) cc_final: 0.7851 (t0) REVERT: h 48 ASP cc_start: 0.7790 (t70) cc_final: 0.7473 (t70) REVERT: l 94 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8098 (mtt180) REVERT: m 76 ASN cc_start: 0.7988 (m-40) cc_final: 0.7015 (m-40) REVERT: n 3 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8010 (mtpt) REVERT: u 25 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8354 (mmtt) REVERT: C 68 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7751 (mtp180) REVERT: C 133 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7322 (ptp90) REVERT: C 187 GLU cc_start: 0.7260 (tp30) cc_final: 0.7021 (tp30) REVERT: E 73 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8463 (mmt90) REVERT: L 37 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (ttt180) REVERT: O 59 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (pttm) REVERT: R 90 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7779 (mtm180) REVERT: X 100 ASP cc_start: 0.8170 (p0) cc_final: 0.7743 (p0) REVERT: 1 2 LYS cc_start: 0.8419 (tppp) cc_final: 0.7836 (tppp) REVERT: 1 9 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8673 (mmtp) REVERT: 1 32 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9060 (tttm) REVERT: 8 9 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8518 (mtpm) outliers start: 226 outliers final: 105 residues processed: 1560 average time/residue: 2.1130 time to fit residues: 4794.6544 Evaluate side-chains 1537 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1422 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 118 GLN Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 205 SER Chi-restraints excluded: chain e residue 12 TYR Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 111 LYS Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 91 HIS Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 50 LYS Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 48 LYS Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 527 LYS Chi-restraints excluded: chain x residue 566 LYS Chi-restraints excluded: chain x residue 580 LEU Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 37 ASP Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 32 LYS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 8 residue 9 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 550 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 823 optimal weight: 0.0270 chunk 674 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 991 optimal weight: 1.9990 chunk 1071 optimal weight: 0.9990 chunk 883 optimal weight: 3.9990 chunk 983 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 795 optimal weight: 0.7980 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 65 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 HIS c 139 GLN d 41 HIS d 100 ASN ** d 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN h 4 GLN h 50 GLN j 15 HIS j 58 ASN l 73 ASN l 112 GLN o 35 ASN o 62 GLN p 66 GLN t 70 ASN ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 322 ASN x 399 HIS C 22 GLN C 163 GLN D 126 ASN D 164 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN G 56 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN N 54 GLN N 58 HIS N 99 ASN O 98 GLN R 30 GLN R 39 GLN R 42 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN X 9 GLN X 113 ASN 6 16 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 161196 Z= 0.149 Angle : 0.624 26.924 240515 Z= 0.336 Chirality : 0.037 1.964 30625 Planarity : 0.006 0.134 13447 Dihedral : 23.208 179.831 78922 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.22 % Favored : 93.39 % Rotamer: Outliers : 3.47 % Allowed : 21.81 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.10), residues: 6429 helix: 0.75 (0.12), residues: 2032 sheet: 0.02 (0.15), residues: 1247 loop : -1.65 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP n 42 HIS 0.008 0.001 HIS f 58 PHE 0.023 0.001 PHE F 114 TYR 0.018 0.001 TYR c 42 ARG 0.010 0.000 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1539 time to evaluate : 6.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 42 ASN cc_start: 0.7854 (t0) cc_final: 0.7011 (m-40) REVERT: f 65 GLU cc_start: 0.6712 (tt0) cc_final: 0.5911 (mp0) REVERT: g 13 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4214 (tm) REVERT: h 48 ASP cc_start: 0.7873 (t70) cc_final: 0.7492 (t70) REVERT: m 66 GLU cc_start: 0.8013 (mp0) cc_final: 0.7756 (mp0) REVERT: o 58 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7329 (ttp80) REVERT: p 1 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7590 (pmm) REVERT: C 133 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7243 (ptp90) REVERT: C 187 GLU cc_start: 0.7176 (tp30) cc_final: 0.6894 (tp30) REVERT: C 252 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: F 121 SER cc_start: 0.6444 (OUTLIER) cc_final: 0.6157 (t) REVERT: R 38 ARG cc_start: 0.7319 (mtp-110) cc_final: 0.7091 (mtp180) REVERT: R 90 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7711 (mtm180) REVERT: T 19 PHE cc_start: 0.8157 (m-80) cc_final: 0.7955 (m-80) REVERT: X 100 ASP cc_start: 0.8047 (p0) cc_final: 0.7724 (p0) REVERT: 1 9 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8540 (mmtp) REVERT: 1 32 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8903 (tttm) REVERT: 8 9 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8553 (mtpm) outliers start: 175 outliers final: 64 residues processed: 1599 average time/residue: 2.1317 time to fit residues: 4968.5449 Evaluate side-chains 1509 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1435 time to evaluate : 6.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 40 ASP Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 774 HIS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 7 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 113 ASN Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 141 LYS Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 32 LYS Chi-restraints excluded: chain 1 residue 44 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 8 residue 9 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 979 optimal weight: 8.9990 chunk 745 optimal weight: 10.0000 chunk 514 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 473 optimal weight: 8.9990 chunk 665 optimal weight: 50.0000 chunk 995 optimal weight: 5.9990 chunk 1053 optimal weight: 2.9990 chunk 519 optimal weight: 10.0000 chunk 943 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 65 ASN c 118 GLN c 123 GLN c 139 GLN d 41 HIS d 100 ASN ** d 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN e 78 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN h 50 GLN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN l 73 ASN l 112 GLN m 14 HIS ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 91 HIS o 35 ASN t 3 ASN x 327 GLN C 163 GLN D 173 GLN E 61 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN N 99 ASN O 98 GLN R 30 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN W 103 GLN 1 59 GLN 5 22 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 161196 Z= 0.423 Angle : 0.705 27.414 240515 Z= 0.374 Chirality : 0.043 1.943 30625 Planarity : 0.007 0.154 13447 Dihedral : 23.126 179.968 78915 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.33 % Favored : 92.32 % Rotamer: Outliers : 4.64 % Allowed : 23.92 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.10), residues: 6429 helix: 0.77 (0.12), residues: 2048 sheet: -0.20 (0.14), residues: 1306 loop : -1.63 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP g 103 HIS 0.012 0.001 HIS P 16 PHE 0.029 0.002 PHE u 19 TYR 0.027 0.002 TYR m 23 ARG 0.013 0.001 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1683 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1449 time to evaluate : 7.009 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: e 78 ASN cc_start: 0.8634 (t0) cc_final: 0.8362 (t0) REVERT: g 13 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4490 (tm) REVERT: h 9 ASP cc_start: 0.8041 (t70) cc_final: 0.7758 (t0) REVERT: i 129 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8738 (ttpt) REVERT: j 48 ARG cc_start: 0.8585 (mmt-90) cc_final: 0.8059 (mmt90) REVERT: l 94 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8039 (mtt180) REVERT: m 66 GLU cc_start: 0.8223 (mp0) cc_final: 0.7845 (mp0) REVERT: o 58 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7368 (ttp80) REVERT: p 1 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7465 (pmm) REVERT: C 68 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7741 (mtp180) REVERT: C 133 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7545 (ptp90) REVERT: C 252 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: G 115 TYR cc_start: 0.8562 (t80) cc_final: 0.8338 (t80) REVERT: L 136 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: O 59 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8024 (pttm) REVERT: R 38 ARG cc_start: 0.7358 (mtp-110) cc_final: 0.7073 (mtp180) REVERT: R 90 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7689 (mtm180) REVERT: X 100 ASP cc_start: 0.8101 (p0) cc_final: 0.7721 (p0) REVERT: Z 71 LEU cc_start: 0.9270 (mt) cc_final: 0.8676 (mp) REVERT: Z 74 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7308 (ttp80) REVERT: 1 9 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8564 (mmtp) REVERT: 8 9 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8570 (mtpm) outliers start: 234 outliers final: 126 residues processed: 1537 average time/residue: 2.1210 time to fit residues: 4775.3355 Evaluate side-chains 1557 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1419 time to evaluate : 9.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 205 SER Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 61 LEU Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 766 CYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 136 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 90 LYS Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 99 THR Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 74 ARG Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Chi-restraints excluded: chain 8 residue 9 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 877 optimal weight: 40.0000 chunk 598 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 784 optimal weight: 2.9990 chunk 434 optimal weight: 3.9990 chunk 899 optimal weight: 4.9990 chunk 728 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 537 optimal weight: 40.0000 chunk 945 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 ASN c 118 GLN c 123 GLN c 139 GLN d 41 HIS d 100 ASN ** d 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN h 4 GLN i 50 GLN l 46 ASN l 73 ASN l 112 GLN m 14 HIS o 35 ASN p 73 GLN t 3 ASN t 13 GLN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 61 GLN N 99 ASN O 98 GLN R 30 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN X 9 GLN 1 59 GLN 5 41 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 161196 Z= 0.350 Angle : 0.683 27.342 240515 Z= 0.365 Chirality : 0.041 1.948 30625 Planarity : 0.006 0.147 13447 Dihedral : 23.126 179.928 78915 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.22 % Favored : 92.42 % Rotamer: Outliers : 4.68 % Allowed : 25.43 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.10), residues: 6429 helix: 0.88 (0.12), residues: 2043 sheet: -0.19 (0.14), residues: 1320 loop : -1.63 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP g 103 HIS 0.010 0.001 HIS P 16 PHE 0.025 0.001 PHE F 114 TYR 0.023 0.002 TYR i 7 ARG 0.015 0.000 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1460 time to evaluate : 7.006 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: f 65 GLU cc_start: 0.6957 (tt0) cc_final: 0.5987 (mp0) REVERT: g 13 LEU cc_start: 0.5300 (OUTLIER) cc_final: 0.4799 (tm) REVERT: h 9 ASP cc_start: 0.7974 (t70) cc_final: 0.7700 (t0) REVERT: h 48 ASP cc_start: 0.7765 (t70) cc_final: 0.6868 (t70) REVERT: l 94 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8017 (mtt180) REVERT: o 58 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7343 (ttp80) REVERT: x 756 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6239 (pmm150) REVERT: C 68 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7717 (mtp180) REVERT: C 133 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7421 (ptp90) REVERT: C 187 GLU cc_start: 0.7192 (tp30) cc_final: 0.6861 (tp30) REVERT: C 252 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: D 161 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8345 (mtt) REVERT: F 121 SER cc_start: 0.6711 (OUTLIER) cc_final: 0.6388 (t) REVERT: L 1 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6848 (ttt) REVERT: M 90 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7767 (mtmt) REVERT: N 76 GLU cc_start: 0.7931 (pt0) cc_final: 0.7565 (pt0) REVERT: N 111 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7419 (ptp) REVERT: O 59 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7955 (pttm) REVERT: Q 82 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7994 (mppt) REVERT: R 38 ARG cc_start: 0.7330 (mtp-110) cc_final: 0.7092 (mtp180) REVERT: R 90 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7701 (mtm180) REVERT: X 100 ASP cc_start: 0.7998 (p0) cc_final: 0.7725 (p0) REVERT: Z 71 LEU cc_start: 0.9272 (mt) cc_final: 0.8735 (mp) REVERT: Z 74 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: 1 9 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8559 (mmtp) outliers start: 236 outliers final: 136 residues processed: 1556 average time/residue: 2.0894 time to fit residues: 4758.1979 Evaluate side-chains 1585 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1433 time to evaluate : 6.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 61 LEU Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 653 GLU Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 756 ARG Chi-restraints excluded: chain x residue 766 CYS Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 8 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 90 LYS Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 99 THR Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 74 ARG Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 354 optimal weight: 2.9990 chunk 948 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 618 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 1054 optimal weight: 7.9990 chunk 875 optimal weight: 20.0000 chunk 488 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 348 optimal weight: 0.0370 chunk 553 optimal weight: 30.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 65 ASN c 139 GLN d 41 HIS d 100 ASN d 196 ASN e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN l 73 ASN m 14 HIS ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN o 62 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 GLN ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN x 327 GLN C 163 GLN F 24 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 98 GLN R 15 ASN R 30 GLN V 3 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN ** 1 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 31 GLN 1 59 GLN 5 41 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 161196 Z= 0.340 Angle : 0.686 27.335 240515 Z= 0.365 Chirality : 0.041 1.948 30625 Planarity : 0.006 0.144 13447 Dihedral : 23.118 179.912 78915 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.51 % Favored : 92.14 % Rotamer: Outliers : 4.92 % Allowed : 26.64 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 6429 helix: 0.92 (0.12), residues: 2041 sheet: -0.23 (0.14), residues: 1310 loop : -1.63 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP g 103 HIS 0.009 0.001 HIS P 16 PHE 0.035 0.002 PHE u 19 TYR 0.028 0.002 TYR x 819 ARG 0.016 0.000 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1447 time to evaluate : 7.159 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: f 1 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.2316 (ppp) REVERT: h 9 ASP cc_start: 0.8034 (t70) cc_final: 0.7742 (t0) REVERT: l 94 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8020 (mtt180) REVERT: o 58 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: s 70 LYS cc_start: 0.8101 (tppp) cc_final: 0.7879 (tppp) REVERT: t 78 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8531 (mtm-85) REVERT: u 25 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8085 (mmtt) REVERT: x 756 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6267 (pmm150) REVERT: C 68 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7714 (mtp180) REVERT: C 87 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7794 (mtt90) REVERT: C 108 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7857 (ttmm) REVERT: C 133 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7409 (ptp90) REVERT: C 252 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: D 161 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: E 172 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: F 121 SER cc_start: 0.6735 (OUTLIER) cc_final: 0.6378 (t) REVERT: F 142 ASP cc_start: 0.6947 (t70) cc_final: 0.6570 (t70) REVERT: G 175 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7358 (pmtt) REVERT: N 76 GLU cc_start: 0.7909 (pt0) cc_final: 0.7623 (pt0) REVERT: N 111 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7283 (ptp) REVERT: O 59 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7895 (pttm) REVERT: Q 14 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8301 (ttmt) REVERT: Q 82 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8136 (mppt) REVERT: R 38 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.7113 (mtp180) REVERT: R 90 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7452 (mtm180) REVERT: U 27 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8170 (mttm) REVERT: X 100 ASP cc_start: 0.8025 (p0) cc_final: 0.7734 (p0) REVERT: 1 9 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8560 (mmtp) outliers start: 248 outliers final: 150 residues processed: 1552 average time/residue: 2.1249 time to fit residues: 4825.1485 Evaluate side-chains 1588 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1418 time to evaluate : 6.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 76 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 653 GLU Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 756 ARG Chi-restraints excluded: chain x residue 766 CYS Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 56 ASN Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 1016 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 770 optimal weight: 3.9990 chunk 596 optimal weight: 10.0000 chunk 887 optimal weight: 0.9980 chunk 588 optimal weight: 10.0000 chunk 1050 optimal weight: 7.9990 chunk 657 optimal weight: 40.0000 chunk 640 optimal weight: 7.9990 chunk 485 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 ASN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN c 139 GLN d 41 HIS d 100 ASN d 196 ASN e 20 ASN e 78 ASN e 147 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN l 73 ASN m 14 HIS ** n 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN p 73 GLN ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN N 99 ASN O 98 GLN R 30 GLN X 9 GLN 1 31 GLN 1 59 GLN 5 41 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 161196 Z= 0.402 Angle : 0.715 27.454 240515 Z= 0.379 Chirality : 0.043 1.942 30625 Planarity : 0.007 0.144 13447 Dihedral : 23.117 179.693 78915 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.53 % Favored : 92.14 % Rotamer: Outliers : 5.08 % Allowed : 27.33 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.10), residues: 6429 helix: 0.90 (0.12), residues: 2042 sheet: -0.23 (0.14), residues: 1283 loop : -1.68 (0.11), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP n 42 HIS 0.010 0.001 HIS P 16 PHE 0.025 0.002 PHE F 114 TYR 0.031 0.002 TYR m 23 ARG 0.017 0.001 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1700 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1444 time to evaluate : 7.054 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: d 100 ASN cc_start: 0.8755 (t0) cc_final: 0.8520 (t0) REVERT: d 196 ASN cc_start: 0.7878 (t0) cc_final: 0.7652 (t160) REVERT: e 66 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7273 (tm-30) REVERT: e 96 TYR cc_start: 0.8880 (t80) cc_final: 0.8659 (t80) REVERT: g 13 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5129 (tm) REVERT: h 4 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8062 (mm-40) REVERT: h 9 ASP cc_start: 0.8018 (t70) cc_final: 0.7741 (t0) REVERT: l 94 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (mtt180) REVERT: m 66 GLU cc_start: 0.8137 (mp0) cc_final: 0.7875 (mp0) REVERT: o 58 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7343 (ttp80) REVERT: p 19 LEU cc_start: 0.8937 (mp) cc_final: 0.8718 (mp) REVERT: t 78 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8392 (mtm-85) REVERT: u 25 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8248 (mmtt) REVERT: x 756 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6199 (pmm150) REVERT: C 68 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7750 (mtp180) REVERT: C 87 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7786 (mtt90) REVERT: C 108 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7794 (ttmm) REVERT: C 133 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7402 (ptp90) REVERT: C 252 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: D 161 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: E 172 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: F 121 SER cc_start: 0.6779 (OUTLIER) cc_final: 0.6430 (t) REVERT: G 175 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7366 (pmtt) REVERT: N 76 GLU cc_start: 0.7894 (pt0) cc_final: 0.7658 (pt0) REVERT: N 111 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7289 (ptp) REVERT: O 59 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7953 (pttm) REVERT: Q 14 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8333 (ttmt) REVERT: Q 82 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8198 (mppt) REVERT: R 90 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7663 (mtm180) REVERT: U 27 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8223 (mttm) REVERT: X 100 ASP cc_start: 0.8063 (p0) cc_final: 0.7761 (p0) REVERT: 1 9 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8553 (mmtp) REVERT: 4 13 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8180 (ptt90) outliers start: 256 outliers final: 164 residues processed: 1550 average time/residue: 2.1227 time to fit residues: 4815.0536 Evaluate side-chains 1608 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1422 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 76 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 98 GLN Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 22 LYS Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain t residue 78 ARG Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 415 ILE Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 653 GLU Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 756 ARG Chi-restraints excluded: chain x residue 766 CYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 99 THR Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 13 ARG Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 649 optimal weight: 4.9990 chunk 419 optimal weight: 10.0000 chunk 627 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 667 optimal weight: 10.0000 chunk 715 optimal weight: 5.9990 chunk 519 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 825 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 ASN ** c 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN c 139 GLN d 41 HIS d 198 ASN e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN j 58 ASN l 73 ASN m 14 HIS ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN o 62 GLN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 66 GLN ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN t 13 GLN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 98 GLN R 15 ASN R 30 GLN V 90 GLN 1 31 GLN 1 59 GLN 5 41 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 161196 Z= 0.365 Angle : 0.706 27.403 240515 Z= 0.375 Chirality : 0.042 1.945 30625 Planarity : 0.007 0.143 13447 Dihedral : 23.119 179.490 78915 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.44 % Favored : 92.22 % Rotamer: Outliers : 5.06 % Allowed : 27.95 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.10), residues: 6429 helix: 0.92 (0.12), residues: 2041 sheet: -0.28 (0.14), residues: 1307 loop : -1.66 (0.11), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 101 HIS 0.008 0.001 HIS P 16 PHE 0.033 0.002 PHE u 19 TYR 0.028 0.002 TYR i 7 ARG 0.018 0.001 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1708 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1453 time to evaluate : 6.269 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: f 22 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7735 (p) REVERT: g 13 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5074 (tm) REVERT: h 9 ASP cc_start: 0.7997 (t70) cc_final: 0.7705 (t0) REVERT: l 94 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8062 (mtt180) REVERT: m 66 GLU cc_start: 0.8113 (mp0) cc_final: 0.7806 (mp0) REVERT: n 3 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8039 (mtpt) REVERT: o 58 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7337 (ttp80) REVERT: q 18 ASP cc_start: 0.7838 (p0) cc_final: 0.7469 (p0) REVERT: u 25 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8239 (mmtt) REVERT: x 756 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6277 (pmm150) REVERT: C 68 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7725 (mtp180) REVERT: C 87 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7778 (mtt90) REVERT: C 108 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (ttmm) REVERT: C 133 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7419 (ptp90) REVERT: C 252 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: D 161 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8417 (mtt) REVERT: E 172 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: F 121 SER cc_start: 0.6792 (OUTLIER) cc_final: 0.6428 (t) REVERT: G 175 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7378 (pmtt) REVERT: L 60 GLU cc_start: 0.7849 (pm20) cc_final: 0.7597 (pm20) REVERT: N 76 GLU cc_start: 0.7884 (pt0) cc_final: 0.7643 (pt0) REVERT: N 111 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7271 (ptp) REVERT: O 59 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7953 (pttm) REVERT: Q 82 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8137 (mppt) REVERT: R 90 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7456 (mtm180) REVERT: U 27 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8217 (mttm) REVERT: X 100 ASP cc_start: 0.8086 (p0) cc_final: 0.7773 (p0) REVERT: 1 9 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8542 (mmtp) REVERT: 4 13 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8167 (ptt90) outliers start: 255 outliers final: 163 residues processed: 1558 average time/residue: 2.1327 time to fit residues: 4893.4289 Evaluate side-chains 1605 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1421 time to evaluate : 6.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 36 ASN Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 157 GLN Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 38 THR Chi-restraints excluded: chain e residue 76 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 98 GLN Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain o residue 13 ASN Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 61 LEU Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 52 THR Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 469 ASP Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 653 GLU Chi-restraints excluded: chain x residue 669 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 756 ARG Chi-restraints excluded: chain x residue 766 CYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 113 SER Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 38 SER Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 99 THR Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 13 ARG Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 955 optimal weight: 10.0000 chunk 1006 optimal weight: 10.0000 chunk 918 optimal weight: 4.9990 chunk 979 optimal weight: 6.9990 chunk 589 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 768 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 884 optimal weight: 0.8980 chunk 925 optimal weight: 1.9990 chunk 975 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 ASN c 139 GLN d 41 HIS ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 196 ASN e 20 ASN e 78 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN m 14 HIS ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN p 66 GLN p 73 GLN t 13 GLN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 98 GLN R 15 ASN R 30 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN X 9 GLN 1 31 GLN 1 59 GLN 5 41 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 161196 Z= 0.161 Angle : 0.674 26.923 240515 Z= 0.359 Chirality : 0.038 1.964 30625 Planarity : 0.006 0.142 13447 Dihedral : 23.184 179.851 78915 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.00 % Favored : 92.67 % Rotamer: Outliers : 3.18 % Allowed : 29.91 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.10), residues: 6429 helix: 0.96 (0.12), residues: 2040 sheet: -0.17 (0.14), residues: 1259 loop : -1.58 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP n 42 HIS 0.007 0.001 HIS s 43 PHE 0.034 0.001 PHE c 130 TYR 0.033 0.002 TYR c 184 ARG 0.017 0.000 ARG x 602 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1460 time to evaluate : 6.899 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: e 66 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7208 (tp30) REVERT: f 65 GLU cc_start: 0.6826 (tt0) cc_final: 0.5975 (mp0) REVERT: g 13 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5271 (tm) REVERT: h 9 ASP cc_start: 0.7926 (t70) cc_final: 0.7633 (t0) REVERT: h 124 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6895 (tm-30) REVERT: m 66 GLU cc_start: 0.8050 (mp0) cc_final: 0.7722 (mp0) REVERT: n 3 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7971 (mtpt) REVERT: o 58 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7342 (ttp80) REVERT: s 44 MET cc_start: 0.7614 (pmm) cc_final: 0.7260 (pmt) REVERT: C 68 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7695 (mtp180) REVERT: C 87 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7687 (mtt90) REVERT: C 133 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7355 (ptp90) REVERT: C 252 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: F 121 SER cc_start: 0.6512 (OUTLIER) cc_final: 0.6147 (t) REVERT: L 60 GLU cc_start: 0.7769 (pm20) cc_final: 0.7541 (pm20) REVERT: M 105 GLU cc_start: 0.7717 (mp0) cc_final: 0.7498 (mp0) REVERT: N 76 GLU cc_start: 0.7837 (pt0) cc_final: 0.7607 (pt0) REVERT: N 111 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7277 (ptp) REVERT: O 59 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7900 (pttm) REVERT: Q 76 LEU cc_start: 0.9045 (tp) cc_final: 0.8774 (tp) REVERT: Q 82 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8058 (mppt) REVERT: R 38 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7173 (mtp180) REVERT: R 90 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7407 (mtm180) REVERT: X 100 ASP cc_start: 0.8006 (p0) cc_final: 0.7735 (p0) REVERT: 8 9 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8633 (mtpm) outliers start: 160 outliers final: 99 residues processed: 1534 average time/residue: 2.1210 time to fit residues: 4762.6295 Evaluate side-chains 1548 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1437 time to evaluate : 6.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 157 GLN Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 76 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 123 ASN Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 120 LYS Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 18 ASP Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 415 ILE Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 460 ASN Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 8 residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 642 optimal weight: 8.9990 chunk 1035 optimal weight: 4.9990 chunk 631 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 719 optimal weight: 8.9990 chunk 1085 optimal weight: 10.0000 chunk 999 optimal weight: 5.9990 chunk 864 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 667 optimal weight: 10.0000 chunk 530 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 65 ASN c 123 GLN c 139 GLN d 41 HIS d 100 ASN e 20 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN p 66 GLN ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN t 34 ASN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 98 GLN R 15 ASN R 30 GLN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 113 ASN 1 31 GLN 1 59 GLN 5 41 GLN 6 16 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 161196 Z= 0.489 Angle : 0.765 27.613 240515 Z= 0.402 Chirality : 0.045 1.934 30625 Planarity : 0.007 0.145 13447 Dihedral : 23.105 179.983 78915 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.89 % Favored : 91.77 % Rotamer: Outliers : 2.90 % Allowed : 30.81 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6429 helix: 0.84 (0.12), residues: 2043 sheet: -0.33 (0.14), residues: 1286 loop : -1.66 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 170 HIS 0.011 0.001 HIS P 16 PHE 0.033 0.002 PHE c 130 TYR 0.039 0.002 TYR H 25 ARG 0.015 0.001 ARG e 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12858 Ramachandran restraints generated. 6429 Oldfield, 0 Emsley, 6429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1439 time to evaluate : 7.006 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: d 167 ARG cc_start: 0.7049 (tpp-160) cc_final: 0.6734 (tpm-80) REVERT: g 13 LEU cc_start: 0.5808 (OUTLIER) cc_final: 0.5577 (tm) REVERT: h 4 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8100 (mm-40) REVERT: h 9 ASP cc_start: 0.8025 (t70) cc_final: 0.7734 (t0) REVERT: j 48 ARG cc_start: 0.8708 (mmt90) cc_final: 0.7948 (mmt90) REVERT: l 94 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8063 (mtt180) REVERT: n 3 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: o 58 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: p 19 LEU cc_start: 0.8956 (mp) cc_final: 0.8675 (mp) REVERT: x 756 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6254 (pmm150) REVERT: C 68 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7760 (mtp180) REVERT: C 87 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7816 (mtt90) REVERT: C 133 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7441 (ptp90) REVERT: C 252 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: N 76 GLU cc_start: 0.7906 (pt0) cc_final: 0.7634 (pt0) REVERT: N 111 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7275 (ptp) REVERT: O 59 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7979 (pttm) REVERT: Q 82 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8179 (mppt) REVERT: R 90 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7533 (mtm180) REVERT: X 100 ASP cc_start: 0.8145 (p0) cc_final: 0.7814 (p0) REVERT: 8 9 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8619 (mttm) outliers start: 146 outliers final: 115 residues processed: 1506 average time/residue: 2.1227 time to fit residues: 4676.2738 Evaluate side-chains 1541 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1412 time to evaluate : 6.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 42 ASN Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 211 GLN Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 36 ASN Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 149 SER Chi-restraints excluded: chain d residue 157 GLN Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 76 ASP Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 162 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain i residue 68 VAL Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 117 ARG Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain t residue 13 GLN Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain t residue 87 SER Chi-restraints excluded: chain u residue 23 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 415 ILE Chi-restraints excluded: chain x residue 446 VAL Chi-restraints excluded: chain x residue 469 ASP Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 737 LEU Chi-restraints excluded: chain x residue 756 ARG Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 92 GLU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 59 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 82 LYS Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain T residue 34 ASP Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain X residue 75 VAL Chi-restraints excluded: chain X residue 142 ASP Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain 2 residue 18 ASN Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain 4 residue 33 THR Chi-restraints excluded: chain 4 residue 45 ASP Chi-restraints excluded: chain 5 residue 13 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 29 SER Chi-restraints excluded: chain 7 residue 52 SER Chi-restraints excluded: chain 8 residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 686 optimal weight: 5.9990 chunk 921 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 797 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 chunk 240 optimal weight: 2.9990 chunk 866 optimal weight: 50.0000 chunk 362 optimal weight: 8.9990 chunk 889 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 159 optimal weight: 0.4980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 65 ASN c 139 GLN d 41 HIS d 100 ASN d 196 ASN d 198 ASN e 20 ASN e 78 ASN e 147 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 35 ASN ** p 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 66 GLN p 73 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN t 34 ASN C 163 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 ASN O 98 GLN R 15 ASN R 30 GLN X 9 GLN 1 31 GLN 1 59 GLN 5 41 GLN 6 16 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.056615 restraints weight = 295858.229| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 1.16 r_work: 0.2547 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 161196 Z= 0.188 Angle : 0.678 27.117 240515 Z= 0.359 Chirality : 0.037 1.963 30625 Planarity : 0.006 0.143 13447 Dihedral : 23.132 179.652 78915 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.78 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 31.46 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.10), residues: 6429 helix: 0.97 (0.12), residues: 2042 sheet: -0.24 (0.14), residues: 1285 loop : -1.57 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP n 42 HIS 0.006 0.001 HIS s 52 PHE 0.036 0.001 PHE 4 47 TYR 0.032 0.002 TYR m 23 ARG 0.018 0.000 ARG j 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 64908.21 seconds wall clock time: 1118 minutes 23.26 seconds (67103.26 seconds total)