Starting phenix.real_space_refine on Tue Mar 26 09:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unw_26635/03_2024/7unw_26635_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.063 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 796 5.21 5 S 167 5.16 5 C 75304 2.51 5 N 27719 2.21 5 O 41351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 175": "OE1" <-> "OE2" Residue "b GLU 219": "OE1" <-> "OE2" Residue "c TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "d PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "i TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 4": "OE1" <-> "OE2" Residue "o ASP 68": "OD1" <-> "OD2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "q ASP 18": "OD1" <-> "OD2" Residue "q ASP 21": "OD1" <-> "OD2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 15": "OE1" <-> "OE2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 414": "OD1" <-> "OD2" Residue "x ASP 683": "OD1" <-> "OD2" Residue "x TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "L GLU 9": "OE1" <-> "OE2" Residue "L ASP 19": "OD1" <-> "OD2" Residue "L ASP 49": "OD1" <-> "OD2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P ASP 117": "OD1" <-> "OD2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T ASP 34": "OD1" <-> "OD2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X GLU 135": "OE1" <-> "OE2" Residue "Y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 60": "OD1" <-> "OD2" Residue "2 GLU 36": "OE1" <-> "OE2" Residue "8 ASP 20": "OD1" <-> "OD2" Residue "8 GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149945 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': 122, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 743, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1314} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1747 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "c" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1650 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 201} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "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: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 793 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} 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': 6, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 11, 'rna3p': 64} 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: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4288 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 48} Link IDs: {'PTRANS': 21, 'TRANS': 571} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 11, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 99 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': 275, 'rna2p_pyr': 169, 'rna3p': 8, 'rna3p_pur': 1369, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 449, 'rna3p': 2434} 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': 7, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 102} 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: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1403 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 168} 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: "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: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 682 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "J" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 673 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 136 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: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} 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: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Unusual residues: {' MG': 213} Classifications: {'undetermined': 213} Link IDs: {None: 212} Chain: "e" 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: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 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: "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: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 549 Unusual residues: {' MG': 549} Classifications: {'undetermined': 549} Link IDs: {None: 548} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "N" 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: "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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" 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: "7" 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: "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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" 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: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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 A0ZV0 SG CYS 3 16 125.010 19.157 163.613 1.00 77.79 S ATOM A0ZVC SG CYS 3 18 122.786 16.304 164.718 1.00 77.30 S ATOM A0ZZ8 SG CYS 3 37 121.715 18.564 161.887 1.00 82.96 S ATOM A0ZZT SG CYS 3 40 121.550 19.892 165.333 1.00 83.38 S ATOM A11G3 SG CYS 8 11 56.155 108.483 139.584 1.00 46.21 S ATOM A11GS SG CYS 8 14 57.607 109.623 136.256 1.00 39.25 S ATOM A11JQ SG CYS 8 27 55.618 112.016 138.465 1.00 38.58 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 101 " occ=0.80 ... (8 atoms not shown) pdb=" O1 FME v 101 " occ=0.80 Time building chain proxies: 60.80, per 1000 atoms: 0.41 Number of scatterers: 149945 At special positions: 0 Unit cell: (246.5, 250.75, 273.7, 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 167 16.00 P 4606 15.00 Mg 796 11.99 O 41351 8.00 N 27719 7.00 C 75304 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: 61.47 Conformation dependent library (CDL) restraints added in 7.4 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 18 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " 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: 193 helices and 84 sheets defined 38.0% alpha, 20.3% beta 1517 base pairs and 2427 stacking pairs defined. Time for finding SS restraints: 78.28 Creating SS restraints... Processing helix chain 'b' and resid 6 through 13 removed outlier: 3.523A pdb=" N LEU b 10 " --> pdb=" O MET b 6 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.393A pdb=" N GLY b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 63 removed outlier: 3.764A pdb=" N LEU b 47 " --> pdb=" O LEU b 43 " (cutoff:3.500A) Proline residue: b 48 - end of helix removed outlier: 3.743A pdb=" N ALA b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLY b 63 " --> pdb=" O ARG b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 removed outlier: 5.132A pdb=" N ILE b 79 " --> pdb=" O SER b 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU b 82 " --> pdb=" O LYS b 78 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG b 86 " --> pdb=" O GLU b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.885A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.634A pdb=" N ARG b 170 " --> pdb=" O VAL b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 226 removed outlier: 3.912A pdb=" N GLN b 226 " --> pdb=" O ILE b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.599A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.165A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 95 removed outlier: 3.581A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN c 94 " --> pdb=" O ASP c 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET c 95 " --> pdb=" O LEU c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.179A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.875A 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: 3.550A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.818A pdb=" N ALA c 133 " --> pdb=" O MET c 129 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.969A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 removed outlier: 5.752A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS d 32 " --> pdb=" O LEU d 28 " (cutoff:3.500A) removed outlier: 3.586A 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: 4.971A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.069A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.987A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 5.282A pdb=" N ASN d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.822A pdb=" N ALA d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU d 161 " --> pdb=" O GLN d 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY d 166 " --> pdb=" O CYS d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 3.616A pdb=" N LEU d 191 " --> pdb=" O ALA d 187 " (cutoff:3.500A) removed outlier: 5.328A 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: 4.226A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 3.627A pdb=" N ARG e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.733A 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: 3.665A pdb=" N ASN e 147 " --> pdb=" O LYS e 143 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 156 removed outlier: 3.674A pdb=" N VAL e 154 " --> pdb=" O ALA e 150 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA e 155 " --> pdb=" O PRO e 151 " (cutoff:3.500A) removed outlier: 4.479A 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: 4.730A pdb=" N GLU e 163 " --> pdb=" O GLY e 159 " (cutoff:3.500A) removed outlier: 6.849A 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 17 through 33 removed outlier: 4.508A pdb=" N LYS f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU f 30 " --> pdb=" O THR f 26 " (cutoff:3.500A) removed outlier: 4.306A 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 Processing helix chain 'g' and resid 35 through 54 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 4.626A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG g 111 " --> pdb=" O PHE g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 4.040A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.560A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.571A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.712A 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: 3.527A pdb=" N PHE i 39 " --> pdb=" O LEU i 35 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 56 removed outlier: 3.675A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.584A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 4.270A 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: 3.556A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 88 removed outlier: 5.177A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.860A pdb=" N GLY k 51 " --> pdb=" O SER k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 60 removed outlier: 4.146A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix No H-bonds generated for 'chain 'k' and resid 54 through 60' Processing helix chain 'k' and resid 61 through 76 removed outlier: 4.489A pdb=" N GLU k 76 " --> pdb=" O GLN k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.712A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.788A 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 'm' and resid 14 through 22 removed outlier: 4.703A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.463A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY m 38 " --> pdb=" O CYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.768A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.034A 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: 3.719A pdb=" N ASP m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLN m 55 " --> pdb=" O GLU m 51 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.799A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET m 81 " --> pdb=" O ILE m 77 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.780A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.779A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.528A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 52 removed outlier: 3.940A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 56 through 61 removed outlier: 3.908A pdb=" N LEU n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.682A 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: 3.799A pdb=" N LEU n 84 " --> pdb=" O SER n 80 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.628A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.644A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.907A 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 removed outlier: 3.530A pdb=" N GLY p 64 " --> pdb=" O TRP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 81 removed outlier: 3.616A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.596A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.531A pdb=" N LEU r 65 " --> pdb=" O ARG r 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA r 66 " --> pdb=" O ALA r 62 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.838A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 68 removed outlier: 3.883A pdb=" N VAL s 67 " --> pdb=" O ASN s 63 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY s 68 " --> pdb=" O GLU s 64 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.505A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 4.738A 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 42 removed outlier: 4.071A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.608A pdb=" N THR t 88 " --> pdb=" O LYS t 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.810A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU u 16 " --> pdb=" O PHE u 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 36 removed outlier: 3.651A pdb=" N ARG u 35 " --> pdb=" O GLU u 31 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 63 removed outlier: 3.768A pdb=" N ARG u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) removed outlier: 4.646A 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: 3.564A pdb=" N VAL x 283 " --> pdb=" O LYS x 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY x 291 " --> pdb=" O MET x 287 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 313 removed outlier: 3.670A pdb=" N ALA x 305 " --> pdb=" O ASP x 301 " (cutoff:3.500A) Processing helix chain 'x' and resid 322 through 332 Processing helix chain 'x' and resid 354 through 364 removed outlier: 3.646A pdb=" N LEU x 358 " --> pdb=" O GLY x 354 " (cutoff:3.500A) Processing helix chain 'x' and resid 402 through 414 removed outlier: 3.824A pdb=" N ALA x 412 " --> pdb=" O ARG x 408 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR x 413 " --> pdb=" O GLY x 409 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP x 414 " --> pdb=" O ALA x 410 " (cutoff:3.500A) Processing helix chain 'x' and resid 427 through 441 Processing helix chain 'x' and resid 458 through 469 removed outlier: 5.078A pdb=" N LYS x 462 " --> pdb=" O PRO x 458 " (cutoff:3.500A) Processing helix chain 'x' and resid 491 through 503 removed outlier: 3.558A pdb=" N GLN x 502 " --> pdb=" O ALA x 498 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA x 503 " --> pdb=" O VAL x 499 " (cutoff:3.500A) Processing helix chain 'x' and resid 597 through 635 Processing helix chain 'x' and resid 648 through 663 removed outlier: 3.683A pdb=" N GLU x 653 " --> pdb=" O ARG x 649 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA x 654 " --> pdb=" O GLY x 650 " (cutoff:3.500A) removed outlier: 3.653A 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: 4.470A pdb=" N LEU x 662 " --> pdb=" O SER x 658 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLY x 663 " --> pdb=" O LEU x 659 " (cutoff:3.500A) Processing helix chain 'x' and resid 680 through 691 Processing helix chain 'x' and resid 702 through 713 removed outlier: 4.360A pdb=" N GLY x 713 " --> pdb=" O VAL x 709 " (cutoff:3.500A) Processing helix chain 'x' and resid 721 through 737 removed outlier: 3.767A pdb=" N ILE x 725 " --> pdb=" O VAL x 721 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET x 736 " --> pdb=" O ALA x 732 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU x 737 " --> pdb=" O LEU x 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.050A pdb=" N LEU C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.725A 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: 3.939A 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: 3.974A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.102A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.327A 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: 6.553A pdb=" N ASP C 265 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.509A 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: 4.215A pdb=" N SER C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.662A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.060A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.603A 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 23 through 39 removed outlier: 4.022A pdb=" N ARG E 39 " --> pdb=" O MET E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.176A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.836A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.449A pdb=" N ALA E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.622A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.977A pdb=" N ILE F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 11 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix removed outlier: 4.002A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.596A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.511A pdb=" N SER F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.908A pdb=" N ALA F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LYS F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.670A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.553A pdb=" N ASN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.847A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.784A pdb=" N PHE G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.520A 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 removed outlier: 3.585A pdb=" N ARG H 51 " --> pdb=" O PHE H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 71 removed outlier: 3.759A pdb=" N LYS H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU H 66 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 22 removed outlier: 5.907A pdb=" N ILE I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL I 12 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL I 15 " --> pdb=" O ILE I 11 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 48 removed outlier: 4.187A pdb=" N GLU I 44 " --> pdb=" O GLY I 40 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG I 46 " --> pdb=" O ARG I 42 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU I 47 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.641A pdb=" N VAL I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 104 removed outlier: 6.741A pdb=" N ARG I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY I 102 " --> pdb=" O GLU I 98 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN I 103 " --> pdb=" O PHE I 99 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 25 removed outlier: 3.881A pdb=" N VAL J 24 " --> pdb=" O PRO J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 removed outlier: 3.896A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS J 39 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS J 40 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN J 43 " --> pdb=" O CYS J 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR J 46 " --> pdb=" O PHE J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 85 Processing helix chain 'J' and resid 103 through 114 removed outlier: 5.002A pdb=" N GLU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 137 removed outlier: 3.982A pdb=" N ARG J 127 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER J 132 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET J 136 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.947A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.541A pdb=" N ALA L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.352A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.974A pdb=" N LYS L 121 " --> pdb=" O ASP L 117 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.536A pdb=" N LEU M 117 " --> pdb=" O LYS M 113 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.512A pdb=" N LEU M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.563A pdb=" N LEU N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 75 removed outlier: 4.482A pdb=" N MET N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG N 74 " --> pdb=" O LYS N 70 " (cutoff:3.500A) removed outlier: 5.743A 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: 3.756A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.668A 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: 3.629A pdb=" N LYS N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 4.072A pdb=" N GLY N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 6.058A pdb=" N ILE O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.517A pdb=" N ALA O 119 " --> pdb=" O ARG O 115 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU O 120 " --> pdb=" O GLU O 116 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.932A 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 Processing helix chain 'P' and resid 37 through 57 removed outlier: 3.637A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 3.731A pdb=" N LYS P 56 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.506A pdb=" N ARG P 71 " --> pdb=" O PHE P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 88 removed outlier: 4.320A pdb=" N PHE P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN P 81 " --> pdb=" O GLY P 77 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS P 85 " --> pdb=" O ASN P 81 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 23 removed outlier: 3.657A pdb=" N ARG Q 8 " --> pdb=" O LYS Q 4 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Q 13 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 85 removed outlier: 3.663A pdb=" N ALA Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.929A 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: 3.522A pdb=" N GLN R 8 " --> pdb=" O LYS R 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU R 12 " --> pdb=" O GLN R 8 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN R 13 " --> pdb=" O ILE R 9 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 105 removed outlier: 4.914A pdb=" N ARG R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 3.886A 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 6 through 22 removed outlier: 3.648A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.050A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.871A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.122A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.663A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 117 removed outlier: 4.304A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 25 removed outlier: 3.989A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.518A pdb=" N LEU U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.890A pdb=" N GLU U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 50 " --> pdb=" O ILE U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.703A pdb=" N LEU U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 5.809A 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: 3.796A pdb=" N VAL V 6 " --> pdb=" O ASN V 2 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE V 7 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS V 8 " --> pdb=" O GLU V 4 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) removed outlier: 4.769A 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: 3.591A 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: 4.219A pdb=" N VAL W 69 " --> pdb=" O HIS W 65 " (cutoff:3.500A) removed outlier: 5.557A 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 removed outlier: 3.636A pdb=" N ARG X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 56 removed outlier: 3.533A pdb=" N GLU X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 122 Processing helix chain 'X' and resid 161 through 166 removed outlier: 3.710A pdb=" N LEU X 165 " --> pdb=" O HIS X 161 " (cutoff:3.500A) removed outlier: 5.613A 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: 5.209A pdb=" N ALA X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY X 179 " --> pdb=" O GLN X 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 63 Processing helix chain 'Z' and resid 64 through 75 Processing helix chain '1' and resid 2 through 10 removed outlier: 3.541A pdb=" N LEU 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS 1 9 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N SER 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 35 removed outlier: 3.605A pdb=" N GLU 1 16 " --> pdb=" O GLU 1 12 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 61 removed outlier: 4.687A pdb=" N SER 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 1 47 " --> pdb=" O LEU 1 43 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.550A pdb=" N LEU 2 26 " --> pdb=" O CYS 2 22 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 4.275A pdb=" N MET 2 46 " --> pdb=" O GLU 2 42 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA 2 50 " --> pdb=" O MET 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 removed outlier: 3.788A pdb=" N THR 3 45 " --> pdb=" O HIS 3 41 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.542A pdb=" N SER 4 18 " --> pdb=" O ASP 4 14 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.384A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.417A 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: 3.586A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 36 removed outlier: 4.896A pdb=" N MET 7 35 " --> pdb=" O ILE 7 31 " (cutoff:3.500A) removed outlier: 5.679A 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: 4.052A pdb=" N ARG 7 44 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY 7 45 " --> pdb=" O ARG 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 62 removed outlier: 5.063A pdb=" N ALA 7 55 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) removed outlier: 5.361A 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 removed outlier: 3.800A pdb=" N GLY b 71 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.822A 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: 3.540A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS c 204 " --> pdb=" O ASP c 181 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU c 206 " --> pdb=" O ARG c 179 " (cutoff:3.500A) removed outlier: 8.135A 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: 4.042A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 13 through 17 removed outlier: 6.700A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 85 through 89 removed outlier: 3.907A pdb=" N GLN e 98 " --> pdb=" O LEU e 125 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU e 125 " --> pdb=" O GLN e 98 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 34 through 41 Processing sheet with id= 8, first strand: chain 'f' and resid 38 through 43 removed outlier: 4.259A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG f 92 " --> pdb=" O HIS f 3 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU f 5 " --> pdb=" O MET f 90 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 72 through 78 removed outlier: 7.202A pdb=" N LEU g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.780A pdb=" N THR h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER h 29 " --> pdb=" O PRO h 57 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN h 58 " --> pdb=" O SER h 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP h 48 " --> pdb=" O GLU h 62 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.799A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE h 103 " --> pdb=" O LEU h 126 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'i' and resid 5 through 11 removed outlier: 5.591A pdb=" N LYS i 27 " --> pdb=" O PHE i 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE i 63 " --> pdb=" O LYS i 27 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.993A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'k' and resid 42 through 45 removed outlier: 3.685A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS k 106 " --> pdb=" O LYS k 80 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL k 84 " --> pdb=" O ALA k 108 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.261A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.594A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'p' and resid 4 through 11 removed outlier: 3.924A pdb=" N PHE p 16 " --> pdb=" O GLY p 9 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY p 37 " --> pdb=" O LEU p 19 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG p 49 " --> pdb=" O ASN p 40 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'q' and resid 10 through 14 removed outlier: 7.811A pdb=" N GLY q 59 " --> pdb=" O ALA q 85 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA q 85 " --> pdb=" O GLY q 59 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 22 through 34 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 's' and resid 30 through 33 Processing sheet with id= 21, first strand: chain 'x' and resid 379 through 385 removed outlier: 3.884A pdb=" N THR x 396 " --> pdb=" O VAL x 347 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY x 349 " --> pdb=" O THR x 396 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE x 415 " --> pdb=" O VAL x 344 " (cutoff:3.500A) removed outlier: 3.554A 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: 6.647A pdb=" N THR x 534 " --> pdb=" O VAL x 521 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG x 517 " --> pdb=" O GLN x 538 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY x 516 " --> pdb=" O VAL x 594 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP x 590 " --> pdb=" O VAL x 520 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'x' and resid 547 through 550 removed outlier: 6.293A pdb=" N VAL x 550 " --> pdb=" O ASN x 553 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'x' and resid 666 through 672 removed outlier: 7.537A pdb=" N LEU x 644 " --> pdb=" O VAL x 672 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY x 673 " --> pdb=" O ILE x 642 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY x 675 " --> pdb=" O LEU x 644 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'x' and resid 716 through 719 Processing sheet with id= 26, first strand: chain 'x' and resid 739 through 746 removed outlier: 6.803A pdb=" N ASP x 740 " --> pdb=" O VAL x 836 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG x 742 " --> pdb=" O VAL x 834 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL x 830 " --> pdb=" O LEU x 746 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY x 765 " --> pdb=" O ARG x 752 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'x' and resid 771 through 774 removed outlier: 6.675A pdb=" N GLY x 771 " --> pdb=" O ALA x 808 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA x 808 " --> pdb=" O GLY x 771 " (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 533 through 538 removed outlier: 4.300A pdb=" N ILE x 575 " --> pdb=" O VAL x 537 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'x' and resid 641 through 646 Processing sheet with id= 31, first strand: chain 'x' and resid 761 through 768 removed outlier: 4.846A pdb=" N ALA x 762 " --> pdb=" O VAL x 816 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL x 816 " --> pdb=" O ALA x 762 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET x 810 " --> pdb=" O VAL x 768 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'x' and resid 779 through 783 Processing sheet with id= 33, first strand: chain 'C' and resid 2 through 6 removed outlier: 5.618A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.824A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 116 through 119 removed outlier: 5.359A pdb=" N ILE C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.955A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 171 through 176 removed outlier: 3.918A 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: 5.654A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 96 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 5.388A 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: 3.996A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 199 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN D 105 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 177 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.646A pdb=" N GLU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR D 46 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.258A 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 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 'E' and resid 1 through 5 removed outlier: 4.111A pdb=" N MET E 1 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 3 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL E 5 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.749A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 149 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.568A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE F 85 " --> pdb=" O LEU F 40 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL F 89 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.804A pdb=" N LEU G 24 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU G 35 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G 26 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 42 through 46 Processing sheet with id= 49, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.922A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 51, first strand: chain 'H' and resid 17 through 21 removed outlier: 4.402A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET H 1 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'I' and resid 50 through 54 removed outlier: 3.964A pdb=" N PHE I 84 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA I 28 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA I 83 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL I 26 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA I 25 " --> pdb=" O ALA I 112 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 9 through 12 removed outlier: 4.035A pdb=" N LEU J 11 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'L' and resid 14 through 19 Processing sheet with id= 55, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.422A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.340A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 38 through 41 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.644A pdb=" N TYR O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'O' and resid 31 through 37 removed outlier: 7.848A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA O 128 " --> pdb=" O THR O 37 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'P' and resid 33 through 36 removed outlier: 5.452A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 50 through 53 removed outlier: 3.661A pdb=" N ALA Q 50 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'R' and resid 39 through 46 removed outlier: 6.508A pdb=" N THR R 26 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER R 84 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 50 through 54 removed outlier: 3.594A pdb=" N ALA R 50 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG R 54 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N SER R 58 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.782A pdb=" N LEU T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.937A pdb=" N GLU T 18 " --> pdb=" O ILE T 98 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU T 95 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR T 60 " --> pdb=" O THR T 99 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU T 31 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'T' and resid 57 through 60 removed outlier: 3.745A pdb=" N GLY T 100 " --> pdb=" O THR T 60 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 65 through 68 Processing sheet with id= 68, first strand: chain 'T' and resid 71 through 78 removed outlier: 3.581A pdb=" N ARG T 78 " --> pdb=" O HIS T 83 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS T 83 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'U' and resid 2 through 8 removed outlier: 4.807A pdb=" N SER U 100 " --> pdb=" O GLY U 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR U 73 " --> pdb=" O LYS U 106 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'V' and resid 28 through 32 removed outlier: 4.652A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP V 78 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS V 63 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL V 57 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'W' and resid 39 through 44 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'W' and resid 81 through 84 removed outlier: 7.424A pdb=" N ARG W 81 " --> pdb=" O LYS W 96 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG W 93 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS W 100 " --> pdb=" O PHE W 95 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'X' and resid 72 through 75 removed outlier: 5.046A pdb=" N SER X 42 " --> pdb=" O ARG X 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA X 92 " --> pdb=" O PRO X 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA X 79 " --> pdb=" O ASP X 93 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'X' and resid 125 through 130 removed outlier: 6.962A pdb=" N VAL X 184 " --> pdb=" O THR X 130 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA X 185 " --> pdb=" O VAL X 160 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN X 158 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'X' and resid 132 through 138 removed outlier: 7.114A pdb=" N SER X 132 " --> pdb=" O LEU X 109 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Y' and resid 29 through 32 removed outlier: 5.025A pdb=" N GLN Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER Y 81 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE Y 82 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Y' and resid 37 through 40 removed outlier: 4.550A pdb=" N GLN Y 40 " --> pdb=" O HIS Y 57 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS Y 57 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 12 through 19 removed outlier: 4.661A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG Z 45 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '2' and resid 32 through 38 removed outlier: 4.305A pdb=" N HIS 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS 2 5 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '3' and resid 12 through 16 removed outlier: 4.019A pdb=" N GLU 3 13 " --> pdb=" O LYS 3 30 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '4' and resid 28 through 31 removed outlier: 3.946A pdb=" N GLU 4 35 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '5' and resid 16 through 22 removed outlier: 7.338A pdb=" N ILE 5 44 " --> pdb=" O SER 5 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 5 47 " --> pdb=" O ILE 5 30 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '7' and resid 21 through 24 removed outlier: 6.430A pdb=" N LEU 7 21 " --> pdb=" O LEU 7 49 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '8' and resid 14 through 19 removed outlier: 3.648A pdb=" N ILE 8 22 " --> pdb=" O ARG 8 19 " (cutoff:3.500A) 1991 hydrogen bonds defined for protein. 5883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3838 hydrogen bonds 6044 hydrogen bond angles 0 basepair planarities 1517 basepair parallelities 2427 stacking parallelities Total time for adding SS restraints: 387.06 Time building geometry restraints manager: 66.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 23413 1.33 - 1.45: 67625 1.45 - 1.58: 60752 1.58 - 1.70: 9202 1.70 - 1.83: 295 Bond restraints: 161287 Sorted by residual: bond pdb=" C4 5MU A1926 " pdb=" C5 5MU A1926 " ideal model delta sigma weight residual 1.802 1.473 0.329 2.00e-02 2.50e+03 2.71e+02 bond pdb=" C4 5MU v 54 " pdb=" C5 5MU v 54 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.60e+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 1.340 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' GCP x 902 " pdb=" C3' GCP x 902 " ideal model delta sigma weight residual 1.241 1.508 -0.267 2.00e-02 2.50e+03 1.78e+02 ... (remaining 161282 not shown) Histogram of bond angle deviations from ideal: 71.71 - 85.09: 3 85.09 - 98.47: 6 98.47 - 111.86: 107200 111.86 - 125.24: 115818 125.24 - 138.62: 17600 Bond angle restraints: 240627 Sorted by residual: angle pdb=" O3' C v 75 " pdb=" P A v 76 " pdb=" OP2 A v 76 " ideal model delta sigma weight residual 108.00 71.71 36.29 3.00e+00 1.11e-01 1.46e+02 angle pdb=" O3' C v 75 " pdb=" P A v 76 " pdb=" OP1 A v 76 " ideal model delta sigma weight residual 108.00 135.60 -27.60 3.00e+00 1.11e-01 8.46e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP1 U A1095 " ideal model delta sigma weight residual 108.00 81.53 26.47 3.00e+00 1.11e-01 7.79e+01 angle pdb=" N ILE F 106 " pdb=" CA ILE F 106 " pdb=" C ILE F 106 " ideal model delta sigma weight residual 113.71 105.75 7.96 9.50e-01 1.11e+00 7.01e+01 angle pdb=" O3' C A1094 " pdb=" P U A1095 " pdb=" OP2 U A1095 " ideal model delta sigma weight residual 108.00 83.53 24.47 3.00e+00 1.11e-01 6.65e+01 ... (remaining 240622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 91242 35.88 - 71.76: 10452 71.76 - 107.64: 1154 107.64 - 143.52: 32 143.52 - 179.40: 41 Dihedral angle restraints: 102921 sinusoidal: 84379 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 -106.21 -73.79 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA LEU T 51 " pdb=" C LEU T 51 " pdb=" N PRO T 52 " pdb=" CA PRO T 52 " ideal model delta harmonic sigma weight residual -180.00 -126.11 -53.89 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" O4' U A 836 " pdb=" C1' U A 836 " pdb=" N1 U A 836 " pdb=" C2 U A 836 " ideal model delta sinusoidal sigma weight residual -160.00 14.55 -174.55 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 102918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.395: 30626 0.395 - 0.791: 0 0.791 - 1.186: 0 1.186 - 1.581: 0 1.581 - 1.976: 1 Chirality restraints: 30627 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 0.43 1.98 2.00e-01 2.50e+01 9.76e+01 chirality pdb=" CB VAL O 94 " pdb=" CA VAL O 94 " pdb=" CG1 VAL O 94 " pdb=" CG2 VAL O 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C3' G a 806 " pdb=" C4' G a 806 " pdb=" O3' G a 806 " pdb=" C2' G a 806 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 30624 not shown) Planarity restraints: 13463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1510 " 0.062 2.00e-02 2.50e+03 5.94e-01 7.95e+03 pdb=" C4' 2MG a1510 " 0.430 2.00e-02 2.50e+03 pdb=" O4' 2MG a1510 " 0.586 2.00e-02 2.50e+03 pdb=" C3' 2MG a1510 " -0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG a1510 " -0.641 2.00e-02 2.50e+03 pdb=" C2' 2MG a1510 " -0.164 2.00e-02 2.50e+03 pdb=" O2' 2MG a1510 " 0.993 2.00e-02 2.50e+03 pdb=" C1' 2MG a1510 " 0.232 2.00e-02 2.50e+03 pdb=" N9 2MG a1510 " -0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU v 54 " -0.053 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 5MU v 54 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 5MU v 54 " -0.632 2.00e-02 2.50e+03 pdb=" C3' 5MU v 54 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 5MU v 54 " 0.622 2.00e-02 2.50e+03 pdb=" C2' 5MU v 54 " 0.187 2.00e-02 2.50e+03 pdb=" O2' 5MU v 54 " -0.950 2.00e-02 2.50e+03 pdb=" C1' 5MU v 54 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MU v 54 " 0.905 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2056 " -0.084 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 7MG A2056 " -0.418 2.00e-02 2.50e+03 pdb=" O4' 7MG A2056 " -0.520 2.00e-02 2.50e+03 pdb=" C3' 7MG A2056 " 0.601 2.00e-02 2.50e+03 pdb=" O3' 7MG A2056 " 0.659 2.00e-02 2.50e+03 pdb=" C2' 7MG A2056 " 0.152 2.00e-02 2.50e+03 pdb=" O2' 7MG A2056 " -1.022 2.00e-02 2.50e+03 pdb=" C1' 7MG A2056 " -0.231 2.00e-02 2.50e+03 pdb=" N9 7MG A2056 " 0.865 2.00e-02 2.50e+03 ... (remaining 13460 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 1147 2.48 - 3.09: 92428 3.09 - 3.69: 267731 3.69 - 4.30: 420608 4.30 - 4.90: 566147 Nonbonded interactions: 1348061 Sorted by model distance: nonbonded pdb="MG MG A2933 " pdb=" O HOH A3508 " model vdw 1.876 2.170 nonbonded pdb=" N7 G A 370 " pdb="MG MG A3305 " model vdw 1.894 2.250 nonbonded pdb=" N7 A a 858 " pdb="MG MG a3202 " model vdw 1.895 2.250 nonbonded pdb=" N7 A a 872 " pdb="MG MG a3208 " model vdw 1.895 2.250 nonbonded pdb=" N7 G A2825 " pdb="MG MG A3422 " model vdw 1.895 2.250 ... (remaining 1348056 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: 9.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 31.610 Check model and map are aligned: 1.720 Set scattering table: 1.080 Process input model: 711.190 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 771.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.329 161287 Z= 0.396 Angle : 0.678 36.293 240627 Z= 0.345 Chirality : 0.042 1.976 30627 Planarity : 0.019 0.594 13463 Dihedral : 22.869 179.404 90995 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.84 % Favored : 92.83 % Rotamer: Outliers : 0.02 % Allowed : 0.34 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 6429 helix: -0.18 (0.12), residues: 1976 sheet: -0.21 (0.15), residues: 1264 loop : -1.49 (0.10), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 83 HIS 0.018 0.001 HIS P 16 PHE 0.035 0.002 PHE e 142 TYR 0.024 0.002 TYR d 204 ARG 0.011 0.001 ARG E 73 *********************** 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 1691 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1690 time to evaluate : 6.578 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: b 91 TYR cc_start: 0.7926 (p90) cc_final: 0.7717 (p90) REVERT: f 71 LEU cc_start: 0.8746 (tp) cc_final: 0.8452 (tp) REVERT: o 4 SER cc_start: 0.8294 (m) cc_final: 0.8071 (p) REVERT: G 104 SER cc_start: 0.8128 (m) cc_final: 0.7555 (m) REVERT: R 8 GLN cc_start: 0.7677 (tm-30) cc_final: 0.6712 (tm-30) REVERT: R 66 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7376 (t) REVERT: X 52 LYS cc_start: 0.8721 (tppt) cc_final: 0.8139 (tppt) REVERT: X 112 ILE cc_start: 0.8611 (pt) cc_final: 0.8017 (pt) REVERT: X 142 ASP cc_start: 0.7880 (p0) cc_final: 0.7503 (p0) REVERT: 2 36 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6772 (mm-30) outliers start: 1 outliers final: 3 residues processed: 1691 average time/residue: 2.3305 time to fit residues: 5556.1501 Evaluate side-chains 1391 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1387 time to evaluate : 6.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 112 ASP Chi-restraints excluded: chain c residue 196 ILE Chi-restraints excluded: chain x residue 288 PHE Chi-restraints excluded: chain R residue 66 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 920 optimal weight: 9.9990 chunk 826 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 557 optimal weight: 50.0000 chunk 441 optimal weight: 8.9990 chunk 854 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 519 optimal weight: 10.0000 chunk 635 optimal weight: 10.0000 chunk 989 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 42 ASN b 168 HIS ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 140 ASN c 152 GLN d 152 GLN d 198 ASN e 133 ASN f 63 ASN g 148 ASN h 18 GLN h 58 GLN h 85 GLN j 23 GLN j 58 ASN k 24 HIS l 25 GLN l 59 ASN l 73 ASN l 75 GLN l 112 GLN m 58 ASN o 40 GLN r 52 GLN t 3 ASN ** x 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 538 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 261 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 40 GLN F 127 ASN G 59 GLN G 143 GLN H 14 ASN M 89 ASN N 2 GLN N 55 GLN O 98 GLN P 89 ASN R 7 GLN R 8 GLN U 61 ASN V 2 ASN V 90 GLN W 39 ASN W 99 GLN X 158 GLN Y 40 GLN 1 58 ASN 1 59 GLN 2 18 ASN 6 26 ASN 6 29 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 161287 Z= 0.411 Angle : 0.709 26.470 240627 Z= 0.377 Chirality : 0.043 1.973 30627 Planarity : 0.007 0.142 13463 Dihedral : 23.236 179.889 78924 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.17 % Favored : 92.47 % Rotamer: Outliers : 3.32 % Allowed : 16.92 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -0.89 (0.10), residues: 6429 helix: 0.49 (0.12), residues: 2041 sheet: -0.15 (0.15), residues: 1255 loop : -1.51 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 83 HIS 0.015 0.001 HIS P 16 PHE 0.027 0.002 PHE e 142 TYR 0.017 0.002 TYR m 23 ARG 0.008 0.001 ARG E 73 *********************** 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 1600 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1432 time to evaluate : 6.767 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 71 LEU cc_start: 0.8805 (tp) cc_final: 0.8380 (tp) REVERT: o 58 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7725 (tmt90) REVERT: t 44 LEU cc_start: 0.8271 (tt) cc_final: 0.8017 (tt) REVERT: x 366 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7597 (ptmm) REVERT: G 160 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (mtpt) REVERT: H 11 ASN cc_start: 0.7818 (p0) cc_final: 0.7596 (p0) REVERT: N 111 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7724 (ptt) REVERT: R 4 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7854 (tmmm) REVERT: T 21 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: X 112 ILE cc_start: 0.8773 (pt) cc_final: 0.8570 (pt) REVERT: X 142 ASP cc_start: 0.7895 (p0) cc_final: 0.7530 (p0) outliers start: 168 outliers final: 73 residues processed: 1478 average time/residue: 2.1892 time to fit residues: 4638.3859 Evaluate side-chains 1444 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1365 time to evaluate : 6.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 772 MET Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 28 GLN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain 2 residue 49 LYS Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 550 optimal weight: 7.9990 chunk 307 optimal weight: 0.8980 chunk 823 optimal weight: 0.9990 chunk 674 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 991 optimal weight: 0.9990 chunk 1071 optimal weight: 8.9990 chunk 883 optimal weight: 0.9980 chunk 983 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 795 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 152 GLN d 198 ASN h 18 GLN h 58 GLN j 23 GLN l 25 GLN l 59 ASN l 75 GLN l 112 GLN p 66 GLN x 463 ASN C 115 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 GLN O 98 GLN P 89 ASN R 7 GLN S 101 ASN U 61 ASN V 90 GLN W 39 ASN W 99 GLN X 67 ASN Y 29 GLN 1 13 GLN 1 58 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 161287 Z= 0.146 Angle : 0.616 26.688 240627 Z= 0.333 Chirality : 0.036 1.979 30627 Planarity : 0.006 0.126 13463 Dihedral : 23.210 179.131 78917 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.08 % Favored : 93.61 % Rotamer: Outliers : 2.93 % Allowed : 20.74 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.10), residues: 6429 helix: 0.89 (0.12), residues: 2046 sheet: 0.02 (0.15), residues: 1239 loop : -1.40 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 170 HIS 0.003 0.000 HIS N 17 PHE 0.014 0.001 PHE b 50 TYR 0.024 0.001 TYR m 86 ARG 0.026 0.000 ARG q 57 *********************** 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 1609 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1461 time to evaluate : 6.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 105 GLU cc_start: 0.7691 (tp30) cc_final: 0.7480 (tp30) REVERT: d 47 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6236 (ppp80) REVERT: d 126 ASN cc_start: 0.7790 (m-40) cc_final: 0.7476 (m-40) REVERT: o 40 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: u 31 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6773 (tp30) REVERT: L 1 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6223 (ttt) REVERT: R 4 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7756 (tmmm) REVERT: R 8 GLN cc_start: 0.7881 (tm-30) cc_final: 0.6543 (tm-30) REVERT: T 21 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8384 (mttp) REVERT: X 142 ASP cc_start: 0.7878 (p0) cc_final: 0.7544 (p0) REVERT: Y 70 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6689 (pm20) outliers start: 148 outliers final: 65 residues processed: 1508 average time/residue: 2.1917 time to fit residues: 4750.2123 Evaluate side-chains 1467 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1396 time to evaluate : 6.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 47 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 28 GLN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain 1 residue 16 GLU Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 979 optimal weight: 9.9990 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: 40.0000 chunk 995 optimal weight: 9.9990 chunk 1053 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 943 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 109 GLN ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 140 ASN c 152 GLN d 198 ASN e 71 ASN h 58 GLN j 23 GLN j 58 ASN k 28 ASN l 59 ASN l 75 GLN l 112 GLN n 33 ASN p 66 GLN t 3 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 127 ASN G 23 GLN G 45 GLN N 2 GLN N 93 GLN O 98 GLN P 89 ASN R 7 GLN T 43 ASN U 61 ASN V 2 ASN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 77 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 ASN W 99 GLN Y 46 HIS 1 13 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 161287 Z= 0.581 Angle : 0.765 26.233 240627 Z= 0.402 Chirality : 0.048 1.971 30627 Planarity : 0.007 0.148 13463 Dihedral : 23.121 179.869 78917 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.45 % Favored : 92.21 % Rotamer: Outliers : 4.76 % Allowed : 22.00 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % 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: -0.65 (0.10), residues: 6429 helix: 0.86 (0.12), residues: 2059 sheet: -0.13 (0.14), residues: 1298 loop : -1.47 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP n 101 HIS 0.015 0.001 HIS P 16 PHE 0.030 0.002 PHE c 34 TYR 0.023 0.002 TYR x 554 ARG 0.011 0.001 ARG f 92 *********************** 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 1620 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1379 time to evaluate : 6.737 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: d 47 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6209 (ppp80) REVERT: e 14 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: e 71 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8062 (p0) REVERT: o 40 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: p 73 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7036 (tm-30) REVERT: x 366 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7607 (ptmm) REVERT: E 73 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8523 (mmt180) REVERT: H 11 ASN cc_start: 0.8071 (p0) cc_final: 0.7768 (p0) REVERT: L 1 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6344 (ttt) REVERT: N 111 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7413 (ptp) REVERT: R 4 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7899 (tmmm) REVERT: T 21 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: X 142 ASP cc_start: 0.7897 (p0) cc_final: 0.7552 (p0) REVERT: Y 11 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6733 (ptp90) REVERT: 2 5 LYS cc_start: 0.8402 (mptt) cc_final: 0.7429 (mmtm) REVERT: 5 29 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8382 (mtpp) outliers start: 241 outliers final: 127 residues processed: 1471 average time/residue: 2.1702 time to fit residues: 4603.6354 Evaluate side-chains 1495 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1356 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 47 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain o residue 40 GLN 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 50 LEU Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain x residue 672 VAL Chi-restraints excluded: chain x residue 824 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 28 GLN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 93 ASP Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 877 optimal weight: 50.0000 chunk 598 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 784 optimal weight: 4.9990 chunk 434 optimal weight: 6.9990 chunk 899 optimal weight: 3.9990 chunk 728 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 537 optimal weight: 30.0000 chunk 945 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 140 ASN c 152 GLN d 198 ASN ** e 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN j 23 GLN j 58 ASN l 25 GLN l 59 ASN l 75 GLN l 112 GLN p 66 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN N 2 GLN O 98 GLN P 89 ASN R 7 GLN T 43 ASN U 61 ASN ** V 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 90 GLN W 39 ASN W 99 GLN 1 13 GLN 1 59 GLN 2 38 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.157 161287 Z= 0.385 Angle : 0.692 26.269 240627 Z= 0.369 Chirality : 0.042 1.982 30627 Planarity : 0.006 0.140 13463 Dihedral : 23.135 179.319 78917 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.86 % Favored : 92.81 % Rotamer: Outliers : 4.27 % Allowed : 23.65 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 6429 helix: 0.98 (0.12), residues: 2050 sheet: -0.08 (0.14), residues: 1270 loop : -1.47 (0.11), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP n 101 HIS 0.010 0.001 HIS P 16 PHE 0.019 0.001 PHE D 118 TYR 0.024 0.002 TYR m 86 ARG 0.014 0.000 ARG d 167 *********************** 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 1614 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1398 time to evaluate : 6.901 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: d 47 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6260 (ppp80) REVERT: e 14 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: o 40 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: x 366 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7638 (ptmm) REVERT: x 388 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6840 (mtp85) REVERT: E 73 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8458 (mmt180) REVERT: G 160 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: L 1 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6347 (ttt) REVERT: N 111 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7453 (ptp) REVERT: R 90 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6966 (mtm-85) REVERT: R 95 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8358 (mttm) REVERT: T 21 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: X 142 ASP cc_start: 0.7831 (p0) cc_final: 0.7486 (p0) REVERT: Y 11 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6721 (ptp90) REVERT: Z 10 LYS cc_start: 0.8335 (mttm) cc_final: 0.8115 (mttt) REVERT: 1 1 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7630 (tpp) REVERT: 2 5 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7518 (mmtm) outliers start: 216 outliers final: 124 residues processed: 1497 average time/residue: 2.1762 time to fit residues: 4691.0173 Evaluate side-chains 1505 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1366 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 47 ARG Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN 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 q residue 8 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 3 GLN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 16 GLU Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 2 residue 5 LYS Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 8 LYS Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 354 optimal weight: 5.9990 chunk 948 optimal weight: 9.9990 chunk 208 optimal weight: 0.0970 chunk 618 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 1054 optimal weight: 0.8980 chunk 875 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 553 optimal weight: 20.0000 overall best weight: 4.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN c 140 ASN c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN e 71 ASN e 98 GLN h 58 GLN j 23 GLN j 58 ASN l 25 GLN l 59 ASN l 112 GLN p 66 GLN t 3 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 GLN O 98 GLN P 89 ASN R 7 GLN T 43 ASN U 61 ASN V 90 GLN W 39 ASN W 99 GLN 1 13 GLN 1 59 GLN 2 38 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.006 0.091 161287 Z= 0.338 Angle : 0.679 26.332 240627 Z= 0.363 Chirality : 0.041 1.981 30627 Planarity : 0.006 0.138 13463 Dihedral : 23.119 179.943 78917 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.88 % Favored : 92.81 % Rotamer: Outliers : 4.27 % Allowed : 24.99 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % 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: -0.53 (0.10), residues: 6429 helix: 1.02 (0.12), residues: 2053 sheet: -0.03 (0.15), residues: 1269 loop : -1.45 (0.11), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 96 HIS 0.008 0.001 HIS s 43 PHE 0.034 0.001 PHE c 34 TYR 0.027 0.002 TYR s 80 ARG 0.015 0.000 ARG d 167 *********************** 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 1630 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1414 time to evaluate : 6.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 14 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: f 1 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.3810 (pp-130) REVERT: o 40 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: x 366 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7649 (ptmm) REVERT: x 388 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6844 (mtp85) REVERT: E 73 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8406 (mmt180) REVERT: F 130 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6497 (ptm) REVERT: G 160 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: L 1 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6359 (ttt) REVERT: N 111 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7470 (ptp) REVERT: R 4 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8028 (tmmm) REVERT: R 90 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6956 (mtm-85) REVERT: R 95 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8310 (mttm) REVERT: T 21 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8355 (mttp) REVERT: U 27 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7956 (mttm) REVERT: X 142 ASP cc_start: 0.7797 (p0) cc_final: 0.7463 (p0) REVERT: Y 11 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6723 (ptp90) REVERT: Y 70 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: 1 1 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7638 (tpp) outliers start: 216 outliers final: 140 residues processed: 1503 average time/residue: 2.2924 time to fit residues: 5032.6048 Evaluate side-chains 1533 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1375 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 116 ASP Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN 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 q residue 8 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 80 SER Chi-restraints excluded: chain t residue 83 ILE Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 8 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 1016 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 770 optimal weight: 0.6980 chunk 596 optimal weight: 10.0000 chunk 887 optimal weight: 1.9990 chunk 588 optimal weight: 10.0000 chunk 1050 optimal weight: 2.9990 chunk 657 optimal weight: 40.0000 chunk 640 optimal weight: 7.9990 chunk 485 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN h 58 GLN j 23 GLN j 58 ASN l 25 GLN l 59 ASN l 112 GLN p 66 GLN t 13 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 GLN O 98 GLN P 89 ASN R 7 GLN T 43 ASN U 61 ASN V 90 GLN W 99 GLN 1 13 GLN 1 39 GLN 1 59 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 161287 Z= 0.322 Angle : 0.675 26.333 240627 Z= 0.361 Chirality : 0.040 1.982 30627 Planarity : 0.006 0.138 13463 Dihedral : 23.101 179.704 78917 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.92 % Favored : 92.77 % Rotamer: Outliers : 4.17 % Allowed : 26.31 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % 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: -0.51 (0.10), residues: 6429 helix: 1.03 (0.12), residues: 2053 sheet: 0.01 (0.15), residues: 1259 loop : -1.45 (0.11), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 96 HIS 0.007 0.001 HIS s 43 PHE 0.022 0.001 PHE x 607 TYR 0.027 0.002 TYR s 80 ARG 0.017 0.000 ARG d 167 *********************** 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 1621 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1410 time to evaluate : 6.634 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: f 1 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.3759 (pp-130) REVERT: h 18 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8214 (tp-100) REVERT: k 20 ILE cc_start: 0.8165 (pt) cc_final: 0.7747 (mp) REVERT: o 40 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: x 366 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7687 (ptmm) REVERT: x 388 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6817 (mtp85) REVERT: E 73 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8428 (mmt180) REVERT: F 130 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6495 (ptm) REVERT: G 160 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8509 (mtpt) REVERT: L 1 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6361 (ttt) REVERT: N 111 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7479 (ptp) REVERT: R 4 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8020 (tmmm) REVERT: R 90 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6950 (mtm-85) REVERT: R 95 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8310 (mttm) REVERT: T 21 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: U 27 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7985 (mttm) REVERT: X 142 ASP cc_start: 0.7808 (p0) cc_final: 0.7460 (p0) REVERT: Y 11 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6729 (ptp90) REVERT: Y 70 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: 2 5 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7648 (mptt) REVERT: 2 36 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6685 (mm-30) outliers start: 211 outliers final: 146 residues processed: 1504 average time/residue: 2.2028 time to fit residues: 4776.8664 Evaluate side-chains 1521 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1358 time to evaluate : 6.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain h residue 18 GLN Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 20 THR Chi-restraints excluded: chain p residue 31 ARG Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 21 LYS Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain 1 residue 16 GLU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 5 residue 18 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 8 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 649 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 627 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 667 optimal weight: 10.0000 chunk 715 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 825 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 215 ASN c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN j 23 GLN j 58 ASN l 25 GLN l 59 ASN l 112 GLN p 66 GLN t 3 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 GLN O 98 GLN P 89 ASN R 7 GLN T 43 ASN V 77 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN 1 13 GLN 1 59 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 161287 Z= 0.413 Angle : 0.711 26.198 240627 Z= 0.378 Chirality : 0.043 1.983 30627 Planarity : 0.006 0.142 13463 Dihedral : 23.087 179.413 78917 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.09 % Favored : 92.61 % Rotamer: Outliers : 4.25 % Allowed : 27.18 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 6429 helix: 0.98 (0.12), residues: 2057 sheet: -0.09 (0.14), residues: 1286 loop : -1.47 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 96 HIS 0.008 0.001 HIS P 16 PHE 0.041 0.002 PHE c 34 TYR 0.034 0.002 TYR s 80 ARG 0.017 0.001 ARG d 167 *********************** 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 1582 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1367 time to evaluate : 6.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 154 MET cc_start: 0.7508 (ppp) cc_final: 0.7231 (ppp) REVERT: d 165 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6959 (ttm-80) REVERT: f 1 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.3777 (pp-130) REVERT: f 98 GLU cc_start: 0.8167 (mp0) cc_final: 0.7920 (mp0) REVERT: m 103 LYS cc_start: 0.8624 (tttt) cc_final: 0.8401 (ttmt) REVERT: o 4 SER cc_start: 0.8461 (p) cc_final: 0.8233 (p) REVERT: o 40 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7770 (mp10) REVERT: u 48 LYS cc_start: 0.8255 (mptm) cc_final: 0.8045 (mptm) REVERT: x 366 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7766 (ptmm) REVERT: x 388 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6812 (mtp85) REVERT: E 73 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8458 (mmt180) REVERT: F 130 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6548 (ptm) REVERT: G 160 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8531 (mtpt) REVERT: L 1 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6374 (ttt) REVERT: N 111 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7487 (ptp) REVERT: R 4 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8076 (tmmm) REVERT: R 90 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6971 (mtm-85) REVERT: R 95 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: U 27 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8005 (mttm) REVERT: X 142 ASP cc_start: 0.7820 (p0) cc_final: 0.7475 (p0) REVERT: Y 11 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6751 (ptp90) REVERT: Z 10 LYS cc_start: 0.8357 (mttm) cc_final: 0.8143 (mttm) REVERT: Z 41 GLU cc_start: 0.7339 (tp30) cc_final: 0.7027 (tp30) REVERT: 1 1 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7679 (tpp) REVERT: 2 5 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7863 (mptt) outliers start: 215 outliers final: 153 residues processed: 1464 average time/residue: 2.1965 time to fit residues: 4631.7917 Evaluate side-chains 1519 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1350 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 165 ARG Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 88 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 54 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 31 ARG Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 25 ASP Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 595 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain x residue 672 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 49 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 130 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain Q residue 51 SER Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 75 GLN Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 18 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 10 LYS Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 5 residue 18 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 51 LYS Chi-restraints excluded: chain 8 residue 8 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 955 optimal weight: 7.9990 chunk 1006 optimal weight: 6.9990 chunk 918 optimal weight: 4.9990 chunk 979 optimal weight: 0.6980 chunk 589 optimal weight: 10.0000 chunk 426 optimal weight: 3.9990 chunk 768 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 884 optimal weight: 1.9990 chunk 925 optimal weight: 1.9990 chunk 975 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 5 ASN ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN j 23 GLN j 58 ASN l 25 GLN l 59 ASN l 112 GLN p 66 GLN t 13 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN L 58 ASN N 2 GLN O 98 GLN P 89 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN V 90 GLN W 99 GLN 1 13 GLN 1 59 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 161287 Z= 0.169 Angle : 0.671 26.656 240627 Z= 0.358 Chirality : 0.038 1.986 30627 Planarity : 0.006 0.139 13463 Dihedral : 23.186 179.416 78917 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.52 % Favored : 93.17 % Rotamer: Outliers : 3.04 % Allowed : 28.73 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.10), residues: 6429 helix: 1.03 (0.12), residues: 2050 sheet: -0.01 (0.15), residues: 1270 loop : -1.39 (0.11), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 83 HIS 0.007 0.001 HIS k 22 PHE 0.019 0.001 PHE x 607 TYR 0.042 0.002 TYR s 80 ARG 0.018 0.001 ARG 4 51 *********************** 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 1556 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1402 time to evaluate : 6.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 154 MET cc_start: 0.7533 (ppp) cc_final: 0.7290 (ppp) REVERT: e 14 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: f 1 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.3893 (pp-130) REVERT: m 103 LYS cc_start: 0.8598 (tttt) cc_final: 0.8375 (ttmt) REVERT: o 4 SER cc_start: 0.8417 (p) cc_final: 0.8206 (p) REVERT: o 40 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: x 366 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7709 (ptmm) REVERT: x 388 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6727 (mtp85) REVERT: E 73 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8329 (mmt180) REVERT: L 1 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6343 (ttt) REVERT: R 4 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8048 (tmmm) REVERT: U 27 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (mttm) REVERT: X 142 ASP cc_start: 0.7701 (p0) cc_final: 0.7374 (p0) REVERT: 1 1 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7485 (tpt) outliers start: 154 outliers final: 107 residues processed: 1474 average time/residue: 2.1894 time to fit residues: 4654.1245 Evaluate side-chains 1500 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1383 time to evaluate : 6.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 118 VAL Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 54 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 q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 36 THR Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 288 PHE Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 63 VAL 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 7 VAL Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 16 GLU Chi-restraints excluded: chain 1 residue 19 LEU Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 5 residue 3 GLU Chi-restraints excluded: chain 5 residue 18 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 642 optimal weight: 7.9990 chunk 1035 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 719 optimal weight: 8.9990 chunk 1085 optimal weight: 9.9990 chunk 999 optimal weight: 10.0000 chunk 864 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 667 optimal weight: 10.0000 chunk 530 optimal weight: 7.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 25 GLN l 59 ASN l 77 HIS l 112 GLN p 66 GLN t 3 ASN ** t 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN F 63 GLN G 45 GLN N 2 GLN O 98 GLN P 89 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN V 77 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN 1 13 GLN 1 39 GLN 1 59 GLN 2 38 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.110 161287 Z= 0.585 Angle : 0.786 26.013 240627 Z= 0.412 Chirality : 0.048 1.980 30627 Planarity : 0.007 0.148 13463 Dihedral : 23.076 179.992 78917 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.58 % Favored : 92.10 % Rotamer: Outliers : 2.97 % Allowed : 29.32 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.05 % 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: -0.66 (0.10), residues: 6429 helix: 0.87 (0.12), residues: 2054 sheet: -0.13 (0.14), residues: 1286 loop : -1.50 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP s 34 HIS 0.011 0.001 HIS P 16 PHE 0.040 0.002 PHE c 34 TYR 0.042 0.002 TYR s 80 ARG 0.016 0.001 ARG d 167 ********************** 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 1508 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1358 time to evaluate : 6.696 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: b 154 MET cc_start: 0.7537 (ppp) cc_final: 0.7255 (ppp) REVERT: c 105 GLU cc_start: 0.7637 (tp30) cc_final: 0.7283 (tp30) REVERT: e 14 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: f 1 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.3816 (pp-130) REVERT: m 103 LYS cc_start: 0.8661 (tttt) cc_final: 0.8428 (ttmt) REVERT: o 4 SER cc_start: 0.8495 (p) cc_final: 0.7049 (p) REVERT: o 40 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: x 366 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7787 (ptmm) REVERT: x 388 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6815 (mtp85) REVERT: E 73 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8531 (mmt180) REVERT: L 1 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.6339 (ttt) REVERT: R 4 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8083 (tmmm) REVERT: R 95 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: U 27 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: X 142 ASP cc_start: 0.7863 (p0) cc_final: 0.7499 (p0) outliers start: 150 outliers final: 104 residues processed: 1429 average time/residue: 2.1643 time to fit residues: 4460.9787 Evaluate side-chains 1460 residues out of total 5296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1346 time to evaluate : 6.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 28 ASN Chi-restraints excluded: chain c residue 41 GLU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 190 ASP Chi-restraints excluded: chain e residue 14 GLU Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 35 ASN Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain o residue 8 LYS Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 40 GLN 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 50 LEU Chi-restraints excluded: chain q residue 8 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 23 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 63 THR Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain x residue 322 ASN Chi-restraints excluded: chain x residue 366 LYS Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 388 ARG Chi-restraints excluded: chain x residue 416 VAL Chi-restraints excluded: chain x residue 550 VAL Chi-restraints excluded: chain x residue 595 VAL Chi-restraints excluded: chain x residue 603 GLU Chi-restraints excluded: chain x residue 658 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 9 ASP Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 95 LYS Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain U residue 27 LYS Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain V residue 2 ASN Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 74 THR Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 5 residue 18 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1090 random chunks: chunk 686 optimal weight: 3.9990 chunk 921 optimal weight: 0.0010 chunk 264 optimal weight: 5.9990 chunk 797 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 chunk 866 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 889 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 overall best weight: 2.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 152 GLN ** d 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 ASN ** j 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 25 GLN l 59 ASN l 112 GLN p 66 GLN t 13 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 89 ASN ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 43 ASN W 99 GLN X 113 ASN 1 13 GLN 1 59 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.053496 restraints weight = 290198.659| |-----------------------------------------------------------------------------| r_work (start): 0.2543 rms_B_bonded: 1.16 r_work: 0.2389 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2321 r_free = 0.2321 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.2321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 161287 Z= 0.226 Angle : 0.674 26.410 240627 Z= 0.360 Chirality : 0.039 1.988 30627 Planarity : 0.006 0.131 13463 Dihedral : 23.127 179.068 78917 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.56 % Favored : 93.14 % Rotamer: Outliers : 2.75 % Allowed : 29.91 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % 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: -0.51 (0.10), residues: 6429 helix: 1.01 (0.12), residues: 2048 sheet: 0.03 (0.15), residues: 1259 loop : -1.44 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.006 0.001 HIS k 22 PHE 0.033 0.001 PHE x 288 TYR 0.033 0.002 TYR s 80 ARG 0.017 0.000 ARG 4 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 63925.44 seconds wall clock time: 1102 minutes 34.85 seconds (66154.85 seconds total)