Starting phenix.real_space_refine on Fri May 17 14:52:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu6_42561/05_2024/8uu6_42561_updated.pdb" } resolution = 3.3 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= 0.001 sd= 1.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 4 6.06 5 P 4614 5.49 5 Mg 98 5.21 5 S 104 5.16 5 C 67884 2.51 5 N 25406 2.21 5 O 38812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ASP 19": "OD1" <-> "OD2" Residue "d TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "d PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 196": "OE1" <-> "OE2" Residue "e GLU 13": "OE1" <-> "OE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 67": "OD1" <-> "OD2" Residue "e ASP 153": "OD1" <-> "OD2" Residue "f TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "j GLU 23": "OE1" <-> "OE2" Residue "k ASP 36": "OD1" <-> "OD2" Residue "l TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 32": "OE1" <-> "OE2" Residue "m ASP 61": "OD1" <-> "OD2" Residue "q PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "L TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L GLU 99": "OE1" <-> "OE2" Residue "L TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "M GLU 120": "OE1" <-> "OE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "O GLU 31": "OE1" <-> "OE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 95": "OD1" <-> "OD2" Residue "R GLU 7": "OE1" <-> "OE2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "S ASP 111": "OD1" <-> "OD2" Residue "T GLU 19": "OE1" <-> "OE2" Residue "T ASP 31": "OD1" <-> "OD2" Residue "V ASP 5": "OD1" <-> "OD2" Residue "V GLU 14": "OE1" <-> "OE2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "Y PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 55": "OD1" <-> "OD2" Residue "3 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 38": "OE1" <-> "OE2" Residue "4 GLU 29": "OE1" <-> "OE2" Residue "5 ASP 14": "OD1" <-> "OD2" Residue "8 GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 136923 Number of models: 1 Model: "" Number of chains: 62 Chain: "a" Number of atoms: 32515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1516, 32515 Classifications: {'RNA': 1516} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 82, 'rna3p_pur': 748, 'rna3p_pyr': 574} Link IDs: {'rna2p': 194, 'rna3p': 1321} Chain breaks: 3 Chain: "b" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1228 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 302 Chain: "c" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1395 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 3, 'TRANS': 199} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 150 Chain: "d" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1429 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 191} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "e" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1087 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 149} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "f" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 652 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 91} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "g" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1015 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 136} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "h" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 929 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "i" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 920 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "j" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 714 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "k" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 681 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "l" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 935 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "m" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 780 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "n" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 463 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "o" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 635 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG%COO:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "p" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 641 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "q" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 558 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "r" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 449 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "s" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 502 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "t" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 493 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "x" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1591 Classifications: {'RNA': 74} Modifications used: {'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 62385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2904, 62385 Classifications: {'RNA': 2904} Modifications used: {'rna2p_pur': 307, 'rna2p_pyr': 149, 'rna3p_pur': 1398, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 456, 'rna3p': 2447} Chain breaks: 3 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2428 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2059 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 258} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1545 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1515 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 8, 'TRANS': 196} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1142 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 82 Chain: "G" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1085 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 150} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "L" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1084 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 914 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1022 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "O" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1025 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 952 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 701 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Chain: "R" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 843 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 37 Chain: "S" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "U" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 843 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 724 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 735 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 549 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 439 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 57} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 58} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 529 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "4" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "5" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 380 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "6" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 361 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "8" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "a" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' MG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Unusual residues: {' MG': 78} Classifications: {'undetermined': 78} Link IDs: {None: 77} 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: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44448 SG CYS n 24 115.246 175.918 54.721 1.00 74.20 S ATOM 44474 SG CYS n 27 115.089 172.101 55.578 1.00 73.47 S ATOM 44571 SG CYS n 40 118.123 174.396 56.863 1.00 71.83 S ATOM 44596 SG CYS n 43 117.384 173.058 53.380 1.00 72.22 S ATOM A0R2K SG CYS 4 30 84.898 40.935 194.668 1.00127.87 S ATOM A0R34 SG CYS 4 33 88.254 42.166 196.123 1.00128.97 S ATOM A0R5F SG CYS 4 43 87.968 41.657 192.404 1.00126.13 S ATOM A0R61 SG CYS 4 46 88.185 38.765 194.671 1.00129.71 S ATOM A0R9Q SG CYS 5 9 132.379 187.508 174.415 1.00126.13 S ATOM A0RAC SG CYS 5 12 133.616 187.446 178.064 1.00126.12 S ATOM A0RFB SG CYS 5 36 129.929 186.649 177.336 1.00118.14 S ATOM A0S8W SG CYS 8 11 43.615 125.627 127.418 1.00129.25 S ATOM A0S9K SG CYS 8 14 44.903 124.139 130.587 1.00128.25 S ATOM A0SCG SG CYS 8 27 42.765 121.972 128.232 1.00128.25 S Time building chain proxies: 52.51, per 1000 atoms: 0.38 Number of scatterers: 136923 At special positions: 0 Unit cell: (223.55, 245.65, 276.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 1 19.00 S 104 16.00 P 4614 15.00 Mg 98 11.99 O 38812 8.00 N 25406 7.00 C 67884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.81 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 15 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9660 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: 150 helices and 68 sheets defined 36.4% alpha, 18.4% beta 1587 base pairs and 2358 stacking pairs defined. Time for finding SS restraints: 70.86 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 27 through 32 removed outlier: 3.794A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 27 through 32' Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.605A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA b 61 " --> pdb=" O MET b 57 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER b 62 " --> pdb=" O ARG b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.970A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 123 removed outlier: 4.122A pdb=" N LYS b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS b 115 " --> pdb=" O ILE b 111 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 116 " --> pdb=" O GLN b 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 4.094A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU b 140 " --> pdb=" O LEU b 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 removed outlier: 3.941A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.515A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 226 removed outlier: 3.513A pdb=" N MET b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 154 removed outlier: 4.004A pdb=" N LYS b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP b 153 " --> pdb=" O GLY b 150 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.906A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 45 removed outlier: 4.191A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP c 40 " --> pdb=" O LEU c 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.145A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 77' Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.619A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU c 93 " --> pdb=" O ASN c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.561A pdb=" N GLU c 124 " --> pdb=" O ALA c 120 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.036A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET c 141 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA c 143 " --> pdb=" O ARG c 139 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.514A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY d 16 " --> pdb=" O SER d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 60 removed outlier: 3.734A pdb=" N LYS d 54 " --> pdb=" O GLN d 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU d 57 " --> pdb=" O GLU d 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG d 58 " --> pdb=" O LYS d 54 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 79 removed outlier: 3.691A pdb=" N PHE d 68 " --> pdb=" O THR d 64 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLN d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 3.528A pdb=" N PHE d 86 " --> pdb=" O HIS d 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.812A pdb=" N LEU d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.946A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS d 116 " --> pdb=" O GLN d 112 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.662A pdb=" N ALA d 152 " --> pdb=" O ASN d 148 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 5.497A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 5.378A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE d 197 " --> pdb=" O PHE d 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 3.809A pdb=" N ARG e 62 " --> pdb=" O PRO e 58 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS e 63 " --> pdb=" O ASP e 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU e 66 " --> pdb=" O ARG e 62 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP e 67 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN e 71 " --> pdb=" O ASP e 67 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 removed outlier: 4.087A pdb=" N ALA e 114 " --> pdb=" O GLY e 110 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL e 115 " --> pdb=" O PRO e 111 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU e 116 " --> pdb=" O VAL e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 149 removed outlier: 3.539A pdb=" N VAL e 138 " --> pdb=" O PRO e 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG e 139 " --> pdb=" O ILE e 135 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS e 146 " --> pdb=" O ILE e 142 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN e 147 " --> pdb=" O ASP e 143 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS e 149 " --> pdb=" O ILE e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 159 removed outlier: 3.881A pdb=" N VAL e 154 " --> pdb=" O ASN e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 166 removed outlier: 3.786A pdb=" N LEU e 165 " --> pdb=" O THR e 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 35 removed outlier: 3.763A pdb=" N ALA f 22 " --> pdb=" O ASP f 18 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU f 25 " --> pdb=" O LYS f 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE f 30 " --> pdb=" O ARG f 26 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU f 31 " --> pdb=" O PHE f 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR f 32 " --> pdb=" O ASP f 28 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY f 35 " --> pdb=" O LEU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 84 removed outlier: 3.696A pdb=" N ASN f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS f 82 " --> pdb=" O ASP f 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 4.245A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET g 30 " --> pdb=" O LEU g 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.831A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE g 42 " --> pdb=" O LYS g 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU g 43 " --> pdb=" O SER g 39 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN g 52 " --> pdb=" O ASP g 48 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU g 53 " --> pdb=" O ILE g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.653A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.672A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.578A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN g 129 " --> pdb=" O MET g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 144 removed outlier: 3.562A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS g 142 " --> pdb=" O ARG g 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.809A pdb=" N PHE h 10 " --> pdb=" O PRO h 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA h 17 " --> pdb=" O ARG h 13 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.941A pdb=" N GLU h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU h 40 " --> pdb=" O ILE h 36 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.693A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 40 Proline residue: i 40 - end of helix Processing helix chain 'i' and resid 41 through 56 removed outlier: 3.806A pdb=" N ARG i 45 " --> pdb=" O PHE i 41 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE i 48 " --> pdb=" O LEU i 44 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.768A pdb=" N ALA i 54 " --> pdb=" O GLN i 50 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.772A pdb=" N GLN i 75 " --> pdb=" O GLY i 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA i 76 " --> pdb=" O TYR i 72 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA i 86 " --> pdb=" O GLY i 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU i 88 " --> pdb=" O ALA i 84 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 94 through 102 removed outlier: 4.773A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.635A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER j 21 " --> pdb=" O ILE j 17 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.938A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.601A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 60 removed outlier: 4.755A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 3.792A 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 78 removed outlier: 3.688A pdb=" N MET k 65 " --> pdb=" O PHE k 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU k 76 " --> pdb=" O LYS k 72 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.518A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 4.055A pdb=" N LYS l 10 " --> pdb=" O GLN l 6 " (cutoff:3.500A) Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 21 through 26 removed outlier: 4.213A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 126 through 131 removed outlier: 5.307A pdb=" N TYR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.143A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.643A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS m 31 " --> pdb=" O LYS m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 5.923A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY m 54 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS m 64 " --> pdb=" O LEU m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 84 removed outlier: 3.572A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG m 79 " --> pdb=" O LEU m 75 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE m 81 " --> pdb=" O ILE m 77 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.539A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 4.219A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 13 removed outlier: 4.976A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 4.151A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY n 51 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.595A pdb=" N ALA o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 47 removed outlier: 3.565A pdb=" N VAL o 31 " --> pdb=" O VAL o 27 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS o 46 " --> pdb=" O HIS o 42 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS o 47 " --> pdb=" O VAL o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.571A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN o 65 " --> pdb=" O GLY o 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU o 66 " --> pdb=" O HIS o 62 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR o 69 " --> pdb=" O ASN o 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 4.606A pdb=" N LYS o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 6.075A pdb=" N THR p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.573A pdb=" N LYS p 87 " --> pdb=" O PHE p 83 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU p 88 " --> pdb=" O HIS p 84 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY p 89 " --> pdb=" O ASN p 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 20 Processing helix chain 'r' and resid 29 through 38 removed outlier: 4.132A pdb=" N LYS r 35 " --> pdb=" O GLU r 31 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N SER r 38 " --> pdb=" O LYS r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.673A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 70 removed outlier: 4.008A pdb=" N ARG r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS r 58 " --> pdb=" O LYS r 54 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET r 69 " --> pdb=" O ARG r 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA r 70 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 removed outlier: 3.661A pdb=" N LYS s 17 " --> pdb=" O ASP s 13 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 5.067A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 42 removed outlier: 3.572A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU t 15 " --> pdb=" O VAL t 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG t 17 " --> pdb=" O THR t 13 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET t 28 " --> pdb=" O GLN t 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE t 35 " --> pdb=" O ALA t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 64 removed outlier: 3.536A pdb=" N LYS t 55 " --> pdb=" O VAL t 51 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS t 56 " --> pdb=" O GLU t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 4.239A pdb=" N LYS t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.009A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.471A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.311A 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 266 through 271 removed outlier: 4.194A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'D' and resid 57 through 62 removed outlier: 4.038A pdb=" N SER D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN 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: 3.880A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.553A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.605A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.741A pdb=" N LYS E 117 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.860A pdb=" N PHE E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 169 removed outlier: 4.078A pdb=" N LEU E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 5.271A pdb=" N ASP E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.805A pdb=" N VAL E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 removed outlier: 4.688A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 46 through 62 removed outlier: 5.103A pdb=" N LEU F 50 " --> pdb=" O ASN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.737A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.066A pdb=" N SER F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.951A pdb=" N GLU G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'L' and resid 25 through 39 removed outlier: 4.660A pdb=" N GLU L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 98 through 111 removed outlier: 3.821A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Proline residue: L 111 - end of helix Processing helix chain 'L' and resid 113 through 123 removed outlier: 3.821A pdb=" N LYS L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.352A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 110' Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.717A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix No H-bonds generated for 'chain 'N' and resid 56 through 62' Processing helix chain 'N' and resid 78 through 84 removed outlier: 4.216A pdb=" N LEU N 82 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 84' Processing helix chain 'N' and resid 92 through 100 Processing helix chain 'N' and resid 129 through 140 removed outlier: 3.759A pdb=" N GLY N 140 " --> pdb=" O ILE N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 4.216A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.637A pdb=" N HIS O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 4.160A 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 9 through 28 removed outlier: 3.538A pdb=" N ASP P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 54 removed outlier: 4.953A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL P 43 " --> pdb=" O GLU P 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU P 45 " --> pdb=" O ARG P 41 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 66 removed outlier: 3.923A pdb=" N PHE P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 107 removed outlier: 3.752A pdb=" N VAL P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA P 103 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Proline residue: P 104 - end of helix removed outlier: 3.769A pdb=" N ALA P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 5.142A pdb=" N LYS Q 21 " --> pdb=" O ARG Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 88 removed outlier: 5.288A pdb=" N ALA Q 72 " --> pdb=" O SER Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 4.679A pdb=" N GLY Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 10 removed outlier: 4.522A pdb=" N ASP R 6 " --> pdb=" O ASN R 2 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU R 7 " --> pdb=" O LYS R 3 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 removed outlier: 4.394A pdb=" N LEU R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 99 through 104' Processing helix chain 'S' and resid 7 through 22 removed outlier: 6.705A pdb=" N ARG S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 4.665A pdb=" N HIS S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 39 through 73 removed outlier: 3.970A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP S 73 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 102 Processing helix chain 'S' and resid 103 through 118 removed outlier: 3.607A pdb=" N ALA S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 removed outlier: 4.093A pdb=" N ILE U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG U 30 " --> pdb=" O ILE U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 45 removed outlier: 3.679A pdb=" N ALA U 39 " --> pdb=" O GLY U 35 " (cutoff:3.500A) Proline residue: U 45 - end of helix Processing helix chain 'U' and resid 48 through 66 Processing helix chain 'V' and resid 2 through 8 removed outlier: 3.601A pdb=" N ILE V 7 " --> pdb=" O ALA V 3 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LYS V 8 " --> pdb=" O ARG V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 removed outlier: 4.416A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.743A pdb=" N VAL V 38 " --> pdb=" O THR V 34 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS V 39 " --> pdb=" O LYS V 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 69 removed outlier: 4.593A pdb=" N VAL W 68 " --> pdb=" O HIS W 64 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N MET W 69 " --> pdb=" O VAL W 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.870A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 removed outlier: 3.879A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 3 through 8' Processing helix chain '1' and resid 10 through 35 removed outlier: 5.907A pdb=" N ILE 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP 1 16 " --> pdb=" O THR 1 12 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 61 removed outlier: 4.325A pdb=" N ARG 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU 1 61 " --> pdb=" O VAL 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 removed outlier: 3.622A pdb=" N LYS 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL 2 50 " --> pdb=" O MET 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 78 removed outlier: 4.387A pdb=" N ARG 3 73 " --> pdb=" O GLY 3 69 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE 3 74 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR 3 78 " --> pdb=" O PHE 3 74 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 5.041A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix No H-bonds generated for 'chain '5' and resid 22 through 27' Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.149A pdb=" N THR 6 24 " --> pdb=" O THR 6 20 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 removed outlier: 3.599A pdb=" N LYS 6 37 " --> pdb=" O SER 6 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY 6 38 " --> pdb=" O ARG 6 34 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.578A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE 7 14 " --> pdb=" O SER 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.208A pdb=" N LYS 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 removed outlier: 3.789A pdb=" N ARG 7 45 " --> pdb=" O LYS 7 41 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 5.676A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N MET 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 15 through 18 removed outlier: 6.163A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TYR b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 67 through 71 removed outlier: 4.130A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU b 161 " --> pdb=" O PRO b 182 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE b 184 " --> pdb=" O LEU b 161 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 53 through 58 removed outlier: 4.301A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL c 63 " --> pdb=" O ARG c 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'c' and resid 166 through 170 removed outlier: 3.770A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP c 200 " --> pdb=" O LYS c 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 164 through 167 removed outlier: 8.251A pdb=" N TYR d 164 " --> pdb=" O ASN d 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 13 through 17 removed outlier: 4.550A pdb=" N GLY e 41 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR e 35 " --> pdb=" O ASN e 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR e 18 " --> pdb=" O LEU e 37 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 85 through 89 removed outlier: 5.520A pdb=" N GLU e 94 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA e 100 " --> pdb=" O ASP e 123 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP e 123 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL e 124 " --> pdb=" O GLY e 105 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 33 through 41 Processing sheet with id= 9, first strand: chain 'f' and resid 41 through 44 removed outlier: 6.655A pdb=" N TYR f 61 " --> pdb=" O TRP f 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR f 9 " --> pdb=" O HIS f 62 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR f 5 " --> pdb=" O LEU f 66 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS f 4 " --> pdb=" O GLU f 95 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG f 89 " --> pdb=" O ILE f 10 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'f' and resid 45 through 49 removed outlier: 4.203A pdb=" N GLY f 45 " --> pdb=" O TYR f 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR f 61 " --> pdb=" O GLY f 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY f 59 " --> pdb=" O ARG f 47 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG f 57 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'g' and resid 72 through 77 removed outlier: 6.483A pdb=" N LEU g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.055A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.796A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.054A pdb=" N TYR i 6 " --> pdb=" O LEU i 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL i 19 " --> pdb=" O GLY i 8 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL i 16 " --> pdb=" O HIS i 68 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS i 68 " --> pdb=" O VAL i 16 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 35 through 38 removed outlier: 6.838A pdb=" N SER j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS j 11 " --> pdb=" O ASP j 97 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.911A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'j' and resid 44 through 53 removed outlier: 3.843A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER j 61 " --> pdb=" O ARG j 53 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'k' and resid 30 through 35 removed outlier: 3.903A pdb=" N THR k 81 " --> pdb=" O GLU k 17 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'l' and resid 42 through 46 removed outlier: 3.548A pdb=" N LYS l 43 " --> pdb=" O ILE l 95 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.523A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'p' and resid 6 through 11 Processing sheet with id= 22, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.411A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG q 62 " --> pdb=" O LEU q 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'q' and resid 21 through 32 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 's' and resid 30 through 33 removed outlier: 3.827A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL s 51 " --> pdb=" O VAL s 58 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.748A pdb=" N ARG C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 116 through 119 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.352A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 91 through 96 removed outlier: 4.358A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.194A pdb=" N LYS D 3 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.921A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP D 180 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.736A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 46 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 48 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 49 through 53 removed outlier: 6.489A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 2 through 7 removed outlier: 3.603A pdb=" N ILE E 17 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.823A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.587A pdb=" N VAL F 66 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 88 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA F 87 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 38, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.471A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN G 130 " --> pdb=" O PRO G 126 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.519A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'L' and resid 53 through 58 removed outlier: 4.918A pdb=" N ASP L 20 " --> pdb=" O TYR L 141 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'L' and resid 75 through 79 removed outlier: 7.147A pdb=" N GLY L 84 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'M' and resid 17 through 21 removed outlier: 5.996A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER M 6 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 37 through 41 removed outlier: 4.923A pdb=" N ASP M 37 " --> pdb=" O ILE M 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M' and resid 66 through 72 removed outlier: 7.480A pdb=" N SER M 67 " --> pdb=" O LYS M 78 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS M 78 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA M 69 " --> pdb=" O TYR M 76 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TYR M 76 " --> pdb=" O ALA M 69 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG M 71 " --> pdb=" O GLY M 74 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'N' and resid 73 through 77 removed outlier: 4.458A pdb=" N GLY N 108 " --> pdb=" O GLU N 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL N 77 " --> pdb=" O LYS N 110 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O' and resid 63 through 66 removed outlier: 3.704A pdb=" N ALA O 107 " --> pdb=" O LYS O 63 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS O 128 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 29 through 33 removed outlier: 6.902A pdb=" N MET P 129 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR P 113 " --> pdb=" O VAL P 135 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 72 through 76 removed outlier: 3.988A pdb=" N GLU P 72 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS P 88 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 54 through 57 removed outlier: 3.989A pdb=" N ALA Q 54 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 95 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 38 through 45 removed outlier: 3.534A pdb=" N ARG R 39 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR R 25 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R' and resid 49 through 52 removed outlier: 4.277A pdb=" N LYS R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLU R 57 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.924A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 18 through 21 removed outlier: 4.413A pdb=" N GLN T 18 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE T 20 " --> pdb=" O LEU T 95 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS T 94 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR T 59 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP T 31 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'T' and resid 64 through 68 removed outlier: 3.662A pdb=" N LYS T 64 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY T 66 " --> pdb=" O TYR T 92 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN T 90 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'U' and resid 7 through 13 removed outlier: 6.821A pdb=" N VAL U 111 " --> pdb=" O GLU U 77 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'U' and resid 78 through 84 removed outlier: 3.624A pdb=" N HIS U 107 " --> pdb=" O ASP U 82 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR U 105 " --> pdb=" O GLY U 84 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 23 through 29 removed outlier: 6.346A pdb=" N LYS V 23 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG V 76 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS V 61 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS V 74 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS V 59 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG V 76 " --> pdb=" O ASN V 57 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN V 57 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA V 78 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL V 55 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL V 80 " --> pdb=" O VAL V 53 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL V 53 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 25 through 28 removed outlier: 3.721A pdb=" N ALA W 25 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU W 34 " --> pdb=" O ALA W 25 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.612A pdb=" N ASN W 39 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Y' and resid 53 through 56 removed outlier: 7.245A pdb=" N VAL Y 89 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS Y 84 " --> pdb=" O MET Y 80 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER Y 88 " --> pdb=" O ARG Y 76 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 58 through 62 removed outlier: 7.944A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR Y 66 " --> pdb=" O GLY Y 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.639A pdb=" N SER Z 25 " --> pdb=" O LYS Z 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER Z 19 " --> pdb=" O ASN Z 23 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '2' and resid 32 through 38 removed outlier: 4.224A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '3' and resid 12 through 16 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain '5' and resid 3 through 8 Processing sheet with id= 66, first strand: chain '5' and resid 31 through 35 Processing sheet with id= 67, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain '8' and resid 14 through 19 1395 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3979 hydrogen bonds 6334 hydrogen bond angles 0 basepair planarities 1587 basepair parallelities 2358 stacking parallelities Total time for adding SS restraints: 248.42 Time building geometry restraints manager: 58.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 23402 1.33 - 1.46: 64822 1.46 - 1.58: 51618 1.58 - 1.71: 9204 1.71 - 1.83: 184 Bond restraints: 149230 Sorted by residual: bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.475 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" N1 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.635 1.329 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C5 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.155 1.376 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C13 MIA x 37 " pdb=" C14 MIA x 37 " ideal model delta sigma weight residual 1.317 1.523 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C2 4SU x 8 " pdb=" N3 4SU x 8 " ideal model delta sigma weight residual 1.499 1.338 0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 149225 not shown) Histogram of bond angle deviations from ideal: 95.80 - 104.53: 20229 104.53 - 113.25: 95517 113.25 - 121.97: 75711 121.97 - 130.69: 31878 130.69 - 139.41: 1547 Bond angle restraints: 224882 Sorted by residual: angle pdb=" N VAL i 53 " pdb=" CA VAL i 53 " pdb=" C VAL i 53 " ideal model delta sigma weight residual 112.96 107.59 5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C8 7MG x 46 " pdb=" N7 7MG x 46 " pdb=" CM7 7MG x 46 " ideal model delta sigma weight residual 126.72 111.88 14.84 3.00e+00 1.11e-01 2.45e+01 angle pdb=" N3 5MU x 54 " pdb=" C4 5MU x 54 " pdb=" O4 5MU x 54 " ideal model delta sigma weight residual 107.56 121.76 -14.20 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C6 5MU x 54 " pdb=" C5 5MU x 54 " pdb=" C5M 5MU x 54 " ideal model delta sigma weight residual 106.09 119.74 -13.65 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C1' 7MG x 46 " pdb=" N9 7MG x 46 " pdb=" C8 7MG x 46 " ideal model delta sigma weight residual 126.69 113.10 13.59 3.00e+00 1.11e-01 2.05e+01 ... (remaining 224877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84140 35.97 - 71.93: 9641 71.93 - 107.90: 1115 107.90 - 143.87: 26 143.87 - 179.83: 43 Dihedral angle restraints: 94965 sinusoidal: 79949 harmonic: 15016 Sorted by residual: dihedral pdb=" C4' C a 67 " pdb=" C3' C a 67 " pdb=" C2' C a 67 " pdb=" C1' C a 67 " ideal model delta sinusoidal sigma weight residual -35.00 31.13 -66.13 1 8.00e+00 1.56e-02 8.93e+01 dihedral pdb=" O4' C A1904 " pdb=" C1' C A1904 " pdb=" N1 C A1904 " pdb=" C2 C A1904 " ideal model delta sinusoidal sigma weight residual 200.00 31.91 168.09 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" C5' C a 67 " pdb=" C4' C a 67 " pdb=" C3' C a 67 " pdb=" O3' C a 67 " ideal model delta sinusoidal sigma weight residual 147.00 84.18 62.82 1 8.00e+00 1.56e-02 8.15e+01 ... (remaining 94962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 27394 0.078 - 0.157: 1628 0.157 - 0.235: 112 0.235 - 0.313: 12 0.313 - 0.391: 4 Chirality restraints: 29150 Sorted by residual: chirality pdb=" C3' C a 67 " pdb=" C4' C a 67 " pdb=" O3' C a 67 " pdb=" C2' C a 67 " both_signs ideal model delta sigma weight residual False -2.74 -2.35 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3' A a1208 " pdb=" C4' A a1208 " pdb=" O3' A a1208 " pdb=" C2' A a1208 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 29147 not shown) Planarity restraints: 11366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG x 46 " -0.874 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 7MG x 46 " 0.218 2.00e-02 2.50e+03 pdb=" O4' 7MG x 46 " 0.692 2.00e-02 2.50e+03 pdb=" C3' 7MG x 46 " -0.209 2.00e-02 2.50e+03 pdb=" O3' 7MG x 46 " 0.920 2.00e-02 2.50e+03 pdb=" C2' 7MG x 46 " -0.615 2.00e-02 2.50e+03 pdb=" O2' 7MG x 46 " -0.598 2.00e-02 2.50e+03 pdb=" C1' 7MG x 46 " 0.439 2.00e-02 2.50e+03 pdb=" N9 7MG x 46 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU x 54 " -0.016 2.00e-02 2.50e+03 5.20e-01 6.08e+03 pdb=" C4' 5MU x 54 " 0.422 2.00e-02 2.50e+03 pdb=" O4' 5MU x 54 " 0.609 2.00e-02 2.50e+03 pdb=" C3' 5MU x 54 " -0.574 2.00e-02 2.50e+03 pdb=" O3' 5MU x 54 " -0.448 2.00e-02 2.50e+03 pdb=" C2' 5MU x 54 " -0.260 2.00e-02 2.50e+03 pdb=" O2' 5MU x 54 " 0.797 2.00e-02 2.50e+03 pdb=" C1' 5MU x 54 " 0.239 2.00e-02 2.50e+03 pdb=" N1 5MU x 54 " -0.770 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MIA x 37 " -0.088 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C13 MIA x 37 " 0.235 2.00e-02 2.50e+03 pdb=" C14 MIA x 37 " -0.332 2.00e-02 2.50e+03 pdb=" C15 MIA x 37 " 0.140 2.00e-02 2.50e+03 pdb=" C16 MIA x 37 " 0.044 2.00e-02 2.50e+03 ... (remaining 11363 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 1002 2.55 - 3.20: 115978 3.20 - 3.84: 310488 3.84 - 4.49: 426549 4.49 - 5.14: 573638 Nonbonded interactions: 1427655 Sorted by model distance: nonbonded pdb=" OP2 U A1685 " pdb="MG MG A3048 " model vdw 1.900 2.170 nonbonded pdb=" OP2 A a 776 " pdb="MG MG a1613 " model vdw 1.900 2.170 nonbonded pdb=" OP1 C A 833 " pdb="MG MG A3026 " model vdw 1.902 2.170 nonbonded pdb=" OP2 G A2621 " pdb="MG MG A3074 " model vdw 1.911 2.170 nonbonded pdb=" OP2 U A 989 " pdb="MG MG A3033 " model vdw 1.913 2.170 ... (remaining 1427650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 30.470 Check model and map are aligned: 0.760 Set scattering table: 0.910 Process input model: 546.370 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 590.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.327 149230 Z= 0.378 Angle : 0.659 16.355 224882 Z= 0.340 Chirality : 0.040 0.391 29150 Planarity : 0.009 0.588 11366 Dihedral : 22.986 179.835 85305 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.11), residues: 5173 helix: -0.31 (0.14), residues: 1490 sheet: -0.84 (0.17), residues: 983 loop : -1.46 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP c 200 HIS 0.010 0.001 HIS l 109 PHE 0.024 0.002 PHE F 99 TYR 0.023 0.002 TYR n 49 ARG 0.021 0.001 ARG r 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 965 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 65 GLU cc_start: 0.8431 (tt0) cc_final: 0.8171 (tt0) REVERT: f 40 GLU cc_start: 0.8018 (pm20) cc_final: 0.7724 (pm20) REVERT: g 48 ASP cc_start: 0.8276 (m-30) cc_final: 0.7938 (m-30) REVERT: g 68 ASN cc_start: 0.8068 (m110) cc_final: 0.7625 (m-40) REVERT: g 138 ARG cc_start: 0.8307 (ptt90) cc_final: 0.7556 (ptt-90) REVERT: h 122 GLN cc_start: 0.8593 (mp10) cc_final: 0.8098 (mp10) REVERT: n 38 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7626 (mmtp) REVERT: q 79 GLU cc_start: 0.7952 (pp20) cc_final: 0.7705 (pp20) REVERT: C 180 GLU cc_start: 0.7893 (tt0) cc_final: 0.7657 (tt0) REVERT: D 175 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7703 (tm-30) REVERT: D 180 ASP cc_start: 0.7951 (t70) cc_final: 0.7713 (t0) REVERT: F 26 MET cc_start: 0.6070 (pmm) cc_final: 0.5805 (pmm) REVERT: F 94 GLU cc_start: 0.7995 (tp30) cc_final: 0.7560 (tp30) REVERT: F 125 ARG cc_start: 0.4893 (tmt170) cc_final: 0.4662 (tmt170) REVERT: L 20 ASP cc_start: 0.8949 (t0) cc_final: 0.8622 (t0) REVERT: L 142 GLU cc_start: 0.6842 (pm20) cc_final: 0.6491 (pm20) REVERT: P 39 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8460 (mm-30) REVERT: R 25 THR cc_start: 0.9428 (m) cc_final: 0.9001 (p) REVERT: S 102 ASP cc_start: 0.8174 (t0) cc_final: 0.7639 (t70) REVERT: U 9 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8851 (tttm) REVERT: U 64 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8250 (tm-30) REVERT: V 21 ASP cc_start: 0.8790 (t70) cc_final: 0.8582 (t70) REVERT: V 44 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8516 (tm-30) REVERT: 2 33 SER cc_start: 0.9125 (m) cc_final: 0.8914 (m) REVERT: 5 8 GLU cc_start: 0.8076 (tt0) cc_final: 0.7840 (tt0) REVERT: 5 14 ASP cc_start: 0.8187 (m-30) cc_final: 0.7878 (m-30) REVERT: 5 47 GLU cc_start: 0.7677 (pt0) cc_final: 0.7452 (pt0) outliers start: 2 outliers final: 0 residues processed: 965 average time/residue: 1.1570 time to fit residues: 1981.1921 Evaluate side-chains 871 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 870 time to evaluate : 5.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 38 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 6.9990 chunk 732 optimal weight: 5.9990 chunk 406 optimal weight: 40.0000 chunk 250 optimal weight: 8.9990 chunk 494 optimal weight: 10.0000 chunk 391 optimal weight: 20.0000 chunk 757 optimal weight: 40.0000 chunk 293 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 564 optimal weight: 10.0000 chunk 878 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 89 ASN ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS d 85 ASN ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN k 28 ASN l 5 ASN l 86 ASN p 62 ASN s 83 HIS D 32 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 9 GLN G 65 HIS ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN L 80 GLN L 97 ASN M 13 ASN N 27 ASN R 12 GLN R 41 GLN R 102 ASN S 52 GLN U 107 HIS W 67 ASN 2 17 GLN ** 3 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 75 ASN 4 23 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 149230 Z= 0.364 Angle : 0.670 13.939 224882 Z= 0.345 Chirality : 0.040 0.370 29150 Planarity : 0.005 0.119 11366 Dihedral : 23.221 179.345 77424 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.88 % Allowed : 13.33 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 5173 helix: 0.02 (0.13), residues: 1526 sheet: -0.78 (0.17), residues: 960 loop : -1.48 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP c 200 HIS 0.007 0.001 HIS l 109 PHE 0.016 0.002 PHE 7 28 TYR 0.018 0.002 TYR m 23 ARG 0.008 0.001 ARG j 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 900 time to evaluate : 5.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 65 GLU cc_start: 0.8255 (tt0) cc_final: 0.7966 (tt0) REVERT: g 48 ASP cc_start: 0.8141 (m-30) cc_final: 0.7862 (m-30) REVERT: g 68 ASN cc_start: 0.8058 (m110) cc_final: 0.7468 (m-40) REVERT: g 70 MET cc_start: 0.8275 (mmm) cc_final: 0.7896 (mmt) REVERT: g 138 ARG cc_start: 0.8252 (ptt90) cc_final: 0.7463 (ptt-90) REVERT: h 122 GLN cc_start: 0.8626 (mp10) cc_final: 0.8359 (mp10) REVERT: k 50 LEU cc_start: 0.8500 (mm) cc_final: 0.8124 (mp) REVERT: l 86 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8603 (p0) REVERT: n 19 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: o 9 ASN cc_start: 0.8722 (m110) cc_final: 0.8233 (m110) REVERT: o 10 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7523 (tm-30) REVERT: o 26 GLU cc_start: 0.8512 (pm20) cc_final: 0.7997 (pm20) REVERT: o 80 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8565 (tm-30) REVERT: r 64 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8893 (mtmm) REVERT: D 175 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7692 (tm-30) REVERT: D 180 ASP cc_start: 0.8088 (t70) cc_final: 0.7746 (t0) REVERT: F 26 MET cc_start: 0.6116 (pmm) cc_final: 0.5859 (pmm) REVERT: F 92 ARG cc_start: 0.6089 (mtt90) cc_final: 0.5282 (ttm170) REVERT: F 94 GLU cc_start: 0.8107 (tp30) cc_final: 0.7895 (mm-30) REVERT: F 152 MET cc_start: 0.7373 (ppp) cc_final: 0.6792 (ppp) REVERT: G 133 VAL cc_start: 0.9258 (t) cc_final: 0.8984 (p) REVERT: L 20 ASP cc_start: 0.8864 (t0) cc_final: 0.8552 (t0) REVERT: L 142 GLU cc_start: 0.6896 (pm20) cc_final: 0.6665 (pm20) REVERT: P 39 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8460 (mm-30) REVERT: S 89 ASP cc_start: 0.8525 (t0) cc_final: 0.8269 (t0) REVERT: S 102 ASP cc_start: 0.8170 (t0) cc_final: 0.7611 (t70) REVERT: U 20 ARG cc_start: 0.9195 (ttp-170) cc_final: 0.8501 (ttp80) REVERT: U 64 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8200 (tm-30) REVERT: V 44 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8561 (tm-30) REVERT: 2 33 SER cc_start: 0.8822 (m) cc_final: 0.8602 (m) REVERT: 4 35 GLU cc_start: 0.7890 (pm20) cc_final: 0.7606 (pm20) REVERT: 5 46 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.7145 (ttp80) outliers start: 99 outliers final: 75 residues processed: 940 average time/residue: 1.1784 time to fit residues: 1975.6677 Evaluate side-chains 940 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 863 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 16 THR Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 50.0000 chunk 272 optimal weight: 4.9990 chunk 730 optimal weight: 5.9990 chunk 597 optimal weight: 40.0000 chunk 242 optimal weight: 8.9990 chunk 879 optimal weight: 5.9990 chunk 950 optimal weight: 8.9990 chunk 783 optimal weight: 5.9990 chunk 872 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 705 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN C 153 GLN D 32 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 149230 Z= 0.256 Angle : 0.597 12.740 224882 Z= 0.311 Chirality : 0.036 0.338 29150 Planarity : 0.005 0.122 11366 Dihedral : 23.150 179.248 77420 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 3.73 % Allowed : 16.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 5173 helix: 0.33 (0.13), residues: 1541 sheet: -0.72 (0.17), residues: 981 loop : -1.39 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP c 200 HIS 0.006 0.001 HIS Q 102 PHE 0.013 0.001 PHE R 74 TYR 0.018 0.001 TYR G 157 ARG 0.005 0.000 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 910 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 56 LYS cc_start: 0.9244 (mtpt) cc_final: 0.9016 (mtpp) REVERT: d 65 GLU cc_start: 0.8166 (tt0) cc_final: 0.7815 (tt0) REVERT: d 69 LYS cc_start: 0.9299 (mmmm) cc_final: 0.9067 (mmmm) REVERT: g 48 ASP cc_start: 0.8006 (m-30) cc_final: 0.7793 (m-30) REVERT: g 68 ASN cc_start: 0.8012 (m110) cc_final: 0.7683 (m-40) REVERT: h 122 GLN cc_start: 0.8597 (mp10) cc_final: 0.8185 (mp10) REVERT: j 14 ASP cc_start: 0.8340 (t0) cc_final: 0.8104 (t0) REVERT: k 50 LEU cc_start: 0.8481 (mm) cc_final: 0.8111 (mp) REVERT: l 108 TYR cc_start: 0.8735 (m-80) cc_final: 0.8321 (m-80) REVERT: m 90 ARG cc_start: 0.9036 (mmm160) cc_final: 0.8646 (mmm-85) REVERT: n 19 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: o 9 ASN cc_start: 0.8817 (m110) cc_final: 0.8359 (m110) REVERT: o 26 GLU cc_start: 0.8457 (pm20) cc_final: 0.8134 (pm20) REVERT: t 3 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8108 (p0) REVERT: D 66 GLN cc_start: 0.8526 (mt0) cc_final: 0.8238 (mp10) REVERT: D 175 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7609 (tm-30) REVERT: D 180 ASP cc_start: 0.8079 (t70) cc_final: 0.7746 (t0) REVERT: F 26 MET cc_start: 0.5897 (pmm) cc_final: 0.5624 (pmm) REVERT: F 92 ARG cc_start: 0.6140 (mtt90) cc_final: 0.5667 (mtm-85) REVERT: F 94 GLU cc_start: 0.8110 (tp30) cc_final: 0.7875 (mm-30) REVERT: F 152 MET cc_start: 0.7354 (ppp) cc_final: 0.6741 (ppp) REVERT: L 20 ASP cc_start: 0.8882 (t0) cc_final: 0.8561 (t0) REVERT: L 44 GLN cc_start: 0.8811 (mp10) cc_final: 0.8611 (mp10) REVERT: L 142 GLU cc_start: 0.6840 (pm20) cc_final: 0.6582 (pm20) REVERT: N 146 ILE cc_start: 0.8445 (mm) cc_final: 0.8232 (mt) REVERT: Q 31 LEU cc_start: 0.9420 (tt) cc_final: 0.9085 (pt) REVERT: S 89 ASP cc_start: 0.8520 (t0) cc_final: 0.8232 (t0) REVERT: S 102 ASP cc_start: 0.8138 (t0) cc_final: 0.7658 (t70) REVERT: T 18 GLN cc_start: 0.9175 (tt0) cc_final: 0.8802 (tt0) REVERT: U 20 ARG cc_start: 0.9162 (ttp-170) cc_final: 0.8734 (ttp-170) REVERT: U 27 ASP cc_start: 0.8477 (m-30) cc_final: 0.8261 (m-30) REVERT: V 44 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8564 (tm-30) REVERT: V 49 LYS cc_start: 0.8753 (ptmm) cc_final: 0.8243 (ptmm) REVERT: V 89 ILE cc_start: 0.8085 (mt) cc_final: 0.7786 (mm) REVERT: 2 19 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: 2 33 SER cc_start: 0.8772 (m) cc_final: 0.8540 (m) REVERT: 4 35 GLU cc_start: 0.7946 (pm20) cc_final: 0.7655 (pm20) REVERT: 5 46 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.7123 (ttp80) outliers start: 128 outliers final: 98 residues processed: 962 average time/residue: 1.1632 time to fit residues: 1986.6981 Evaluate side-chains 969 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 868 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 16 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 1.9990 chunk 661 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 590 optimal weight: 50.0000 chunk 882 optimal weight: 10.0000 chunk 934 optimal weight: 0.9990 chunk 461 optimal weight: 10.0000 chunk 836 optimal weight: 0.2980 chunk 251 optimal weight: 3.9990 overall best weight: 3.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN S 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 149230 Z= 0.194 Angle : 0.555 12.831 224882 Z= 0.291 Chirality : 0.034 0.313 29150 Planarity : 0.004 0.116 11366 Dihedral : 23.086 178.428 77420 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 4.22 % Allowed : 18.89 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 5173 helix: 0.61 (0.13), residues: 1552 sheet: -0.67 (0.16), residues: 994 loop : -1.30 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP c 200 HIS 0.006 0.001 HIS Q 102 PHE 0.015 0.001 PHE F 99 TYR 0.023 0.001 TYR l 79 ARG 0.007 0.000 ARG O 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 922 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 65 GLU cc_start: 0.8051 (tt0) cc_final: 0.7666 (tt0) REVERT: g 48 ASP cc_start: 0.7972 (m-30) cc_final: 0.7755 (m-30) REVERT: g 68 ASN cc_start: 0.8004 (m110) cc_final: 0.7678 (m-40) REVERT: h 117 GLU cc_start: 0.8352 (pm20) cc_final: 0.8088 (pm20) REVERT: h 122 GLN cc_start: 0.8556 (mp10) cc_final: 0.8141 (mp10) REVERT: k 50 LEU cc_start: 0.8410 (mm) cc_final: 0.8057 (mp) REVERT: o 9 ASN cc_start: 0.8812 (m110) cc_final: 0.8331 (m110) REVERT: o 26 GLU cc_start: 0.8394 (pm20) cc_final: 0.8078 (pm20) REVERT: t 3 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8095 (p0) REVERT: D 32 GLN cc_start: 0.8544 (mt0) cc_final: 0.8257 (mt0) REVERT: D 55 ASP cc_start: 0.8160 (p0) cc_final: 0.7949 (p0) REVERT: D 66 GLN cc_start: 0.8476 (mt0) cc_final: 0.8256 (mt0) REVERT: D 175 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7510 (tm-30) REVERT: D 180 ASP cc_start: 0.7967 (t70) cc_final: 0.7662 (t0) REVERT: F 5 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7009 (pttp) REVERT: F 92 ARG cc_start: 0.6062 (mtt90) cc_final: 0.5062 (ttm110) REVERT: F 152 MET cc_start: 0.7327 (ppp) cc_final: 0.6691 (ppp) REVERT: L 20 ASP cc_start: 0.8885 (t0) cc_final: 0.8550 (t0) REVERT: L 142 GLU cc_start: 0.6815 (pm20) cc_final: 0.6579 (pm20) REVERT: P 61 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8677 (mt0) REVERT: S 89 ASP cc_start: 0.8535 (t0) cc_final: 0.8239 (t0) REVERT: S 102 ASP cc_start: 0.8037 (t0) cc_final: 0.7457 (t70) REVERT: T 18 GLN cc_start: 0.9061 (tt0) cc_final: 0.8736 (tt0) REVERT: U 20 ARG cc_start: 0.9148 (ttp-170) cc_final: 0.8715 (ttp-170) REVERT: U 27 ASP cc_start: 0.8477 (m-30) cc_final: 0.8217 (m-30) REVERT: U 68 ASP cc_start: 0.8365 (t0) cc_final: 0.8150 (t0) REVERT: V 44 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8614 (tm-30) REVERT: V 49 LYS cc_start: 0.8714 (ptmm) cc_final: 0.8271 (ptmm) REVERT: Y 80 MET cc_start: 0.8341 (mmm) cc_final: 0.8090 (mtm) REVERT: 2 19 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: 2 33 SER cc_start: 0.8731 (m) cc_final: 0.8486 (m) REVERT: 4 35 GLU cc_start: 0.7763 (pm20) cc_final: 0.7434 (pm20) REVERT: 5 46 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.7127 (ttp80) outliers start: 145 outliers final: 105 residues processed: 992 average time/residue: 1.2011 time to fit residues: 2124.3019 Evaluate side-chains 980 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 873 time to evaluate : 5.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 22 ASP Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 0.8980 chunk 530 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 695 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 797 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 838 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 overall best weight: 7.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 HIS M 13 ASN P 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 149230 Z= 0.400 Angle : 0.667 12.720 224882 Z= 0.342 Chirality : 0.040 0.383 29150 Planarity : 0.005 0.118 11366 Dihedral : 23.094 179.027 77420 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.19 % Favored : 92.73 % Rotamer: Outliers : 5.38 % Allowed : 20.17 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5173 helix: 0.44 (0.13), residues: 1536 sheet: -0.78 (0.16), residues: 996 loop : -1.41 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 200 HIS 0.008 0.001 HIS Q 102 PHE 0.014 0.002 PHE 7 28 TYR 0.020 0.002 TYR m 23 ARG 0.007 0.001 ARG O 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 873 time to evaluate : 5.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 10 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8576 (mm) REVERT: d 65 GLU cc_start: 0.8138 (tt0) cc_final: 0.7769 (tt0) REVERT: f 40 GLU cc_start: 0.8063 (pm20) cc_final: 0.7783 (pm20) REVERT: g 48 ASP cc_start: 0.7993 (m-30) cc_final: 0.7784 (m-30) REVERT: g 68 ASN cc_start: 0.8124 (m110) cc_final: 0.7793 (m-40) REVERT: h 117 GLU cc_start: 0.8400 (pm20) cc_final: 0.8077 (pm20) REVERT: j 67 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6553 (tpt) REVERT: k 50 LEU cc_start: 0.8464 (mm) cc_final: 0.8111 (mp) REVERT: n 19 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: o 9 ASN cc_start: 0.8843 (m110) cc_final: 0.8361 (m110) REVERT: o 10 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7623 (tm-30) REVERT: o 26 GLU cc_start: 0.8426 (pm20) cc_final: 0.8154 (pm20) REVERT: t 3 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8164 (p0) REVERT: D 175 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 180 ASP cc_start: 0.8085 (t70) cc_final: 0.7749 (t0) REVERT: F 92 ARG cc_start: 0.6180 (mtt90) cc_final: 0.5135 (ttm110) REVERT: F 94 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7311 (mp0) REVERT: F 152 MET cc_start: 0.7329 (ppp) cc_final: 0.6637 (ppp) REVERT: G 133 VAL cc_start: 0.9320 (t) cc_final: 0.8983 (p) REVERT: L 20 ASP cc_start: 0.8886 (t0) cc_final: 0.8562 (t0) REVERT: L 142 GLU cc_start: 0.6819 (pm20) cc_final: 0.6568 (pm20) REVERT: S 89 ASP cc_start: 0.8570 (t0) cc_final: 0.8302 (t0) REVERT: S 102 ASP cc_start: 0.8122 (t0) cc_final: 0.7472 (t70) REVERT: T 18 GLN cc_start: 0.9158 (tt0) cc_final: 0.8814 (tt0) REVERT: U 20 ARG cc_start: 0.9215 (ttp-170) cc_final: 0.8802 (ttp-170) REVERT: U 27 ASP cc_start: 0.8516 (m-30) cc_final: 0.8217 (m-30) REVERT: U 68 ASP cc_start: 0.8507 (t0) cc_final: 0.8273 (t0) REVERT: V 44 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8599 (tm-30) REVERT: V 49 LYS cc_start: 0.8809 (ptmm) cc_final: 0.8274 (ptmm) REVERT: Y 80 MET cc_start: 0.8402 (mmm) cc_final: 0.8006 (mtt) REVERT: 2 19 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: 4 35 GLU cc_start: 0.7722 (pm20) cc_final: 0.7488 (pm20) REVERT: 5 46 ARG cc_start: 0.8784 (ttm-80) cc_final: 0.6982 (tmt170) outliers start: 185 outliers final: 147 residues processed: 972 average time/residue: 1.1196 time to fit residues: 1935.6801 Evaluate side-chains 999 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 847 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 177 ASN Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 30.0000 chunk 841 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 548 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 935 optimal weight: 7.9990 chunk 776 optimal weight: 1.9990 chunk 433 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 309 optimal weight: 0.5980 chunk 491 optimal weight: 50.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS E 82 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN S 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 149230 Z= 0.243 Angle : 0.586 12.691 224882 Z= 0.306 Chirality : 0.036 0.332 29150 Planarity : 0.004 0.117 11366 Dihedral : 23.074 179.167 77420 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 5.12 % Allowed : 21.10 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 5173 helix: 0.60 (0.13), residues: 1543 sheet: -0.73 (0.16), residues: 1018 loop : -1.35 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP c 200 HIS 0.008 0.001 HIS Q 102 PHE 0.017 0.001 PHE F 99 TYR 0.013 0.001 TYR G 157 ARG 0.007 0.000 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 902 time to evaluate : 5.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 65 GLU cc_start: 0.8055 (tt0) cc_final: 0.7764 (tt0) REVERT: f 40 GLU cc_start: 0.8046 (pm20) cc_final: 0.7734 (pm20) REVERT: g 48 ASP cc_start: 0.7967 (m-30) cc_final: 0.7751 (m-30) REVERT: g 68 ASN cc_start: 0.8063 (m110) cc_final: 0.7736 (m-40) REVERT: h 117 GLU cc_start: 0.8371 (pm20) cc_final: 0.8049 (pm20) REVERT: h 122 GLN cc_start: 0.8577 (mp10) cc_final: 0.8157 (mp10) REVERT: k 50 LEU cc_start: 0.8415 (mm) cc_final: 0.8074 (mp) REVERT: l 25 ASN cc_start: 0.8924 (p0) cc_final: 0.8493 (p0) REVERT: l 108 TYR cc_start: 0.8768 (m-80) cc_final: 0.8339 (m-80) REVERT: m 92 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.7725 (ttp80) REVERT: n 19 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: n 25 GLU cc_start: 0.7918 (mp0) cc_final: 0.7568 (mp0) REVERT: o 9 ASN cc_start: 0.8866 (m110) cc_final: 0.8378 (m110) REVERT: o 26 GLU cc_start: 0.8377 (pm20) cc_final: 0.8122 (pm20) REVERT: p 5 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7994 (mt) REVERT: t 3 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8173 (p0) REVERT: D 55 ASP cc_start: 0.8234 (p0) cc_final: 0.8023 (p0) REVERT: D 66 GLN cc_start: 0.8781 (mt0) cc_final: 0.8451 (mt0) REVERT: D 175 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7576 (tm-30) REVERT: D 180 ASP cc_start: 0.8052 (t70) cc_final: 0.7727 (t0) REVERT: F 5 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7181 (pttp) REVERT: F 68 THR cc_start: 0.6784 (m) cc_final: 0.6540 (p) REVERT: F 92 ARG cc_start: 0.6182 (mtt90) cc_final: 0.5183 (ttm110) REVERT: F 94 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7303 (mp0) REVERT: F 152 MET cc_start: 0.7375 (ppp) cc_final: 0.6673 (ppp) REVERT: L 20 ASP cc_start: 0.8863 (t0) cc_final: 0.8563 (t0) REVERT: L 142 GLU cc_start: 0.6761 (pm20) cc_final: 0.6525 (pm20) REVERT: M 3 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: S 89 ASP cc_start: 0.8537 (t0) cc_final: 0.8254 (t0) REVERT: S 102 ASP cc_start: 0.7953 (t0) cc_final: 0.7337 (t70) REVERT: T 18 GLN cc_start: 0.9095 (tt0) cc_final: 0.8784 (tt0) REVERT: U 20 ARG cc_start: 0.9180 (ttp-170) cc_final: 0.8766 (ttp-170) REVERT: U 27 ASP cc_start: 0.8495 (m-30) cc_final: 0.8204 (m-30) REVERT: U 68 ASP cc_start: 0.8444 (t0) cc_final: 0.8228 (t0) REVERT: V 44 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8610 (tm-30) REVERT: V 49 LYS cc_start: 0.8764 (ptmm) cc_final: 0.8209 (ptmm) REVERT: 2 19 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: 4 35 GLU cc_start: 0.7610 (pm20) cc_final: 0.7409 (pm20) REVERT: 5 46 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.7045 (tmt170) outliers start: 176 outliers final: 145 residues processed: 990 average time/residue: 1.1333 time to fit residues: 1994.7908 Evaluate side-chains 1026 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 876 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 145 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 3 residue 15 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 11 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 683 optimal weight: 0.0030 chunk 529 optimal weight: 20.0000 chunk 787 optimal weight: 7.9990 chunk 522 optimal weight: 30.0000 chunk 932 optimal weight: 7.9990 chunk 583 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN e 89 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN 8 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 149230 Z= 0.284 Angle : 0.605 12.617 224882 Z= 0.314 Chirality : 0.037 0.346 29150 Planarity : 0.005 0.118 11366 Dihedral : 23.058 179.743 77420 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 5.85 % Allowed : 21.45 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 5173 helix: 0.60 (0.13), residues: 1544 sheet: -0.72 (0.16), residues: 1009 loop : -1.38 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 200 HIS 0.008 0.001 HIS Q 102 PHE 0.021 0.001 PHE d 72 TYR 0.015 0.002 TYR G 157 ARG 0.007 0.000 ARG 8 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 886 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 10 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8610 (mm) REVERT: d 65 GLU cc_start: 0.8052 (tt0) cc_final: 0.7785 (tt0) REVERT: f 40 GLU cc_start: 0.8075 (pm20) cc_final: 0.7652 (pm20) REVERT: g 48 ASP cc_start: 0.7979 (m-30) cc_final: 0.7756 (m-30) REVERT: g 68 ASN cc_start: 0.8097 (m110) cc_final: 0.7756 (m-40) REVERT: h 122 GLN cc_start: 0.8574 (mp10) cc_final: 0.8166 (mp10) REVERT: j 67 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6646 (tpt) REVERT: k 50 LEU cc_start: 0.8416 (mm) cc_final: 0.8062 (mp) REVERT: l 25 ASN cc_start: 0.8978 (p0) cc_final: 0.8511 (p0) REVERT: m 92 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7653 (ttp-110) REVERT: n 19 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: n 25 GLU cc_start: 0.7913 (mp0) cc_final: 0.7563 (mp0) REVERT: o 9 ASN cc_start: 0.8867 (m110) cc_final: 0.8378 (m110) REVERT: o 26 GLU cc_start: 0.8379 (pm20) cc_final: 0.8095 (pm20) REVERT: p 5 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (mt) REVERT: t 3 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8181 (p0) REVERT: C 198 GLU cc_start: 0.8636 (pm20) cc_final: 0.8431 (pm20) REVERT: D 66 GLN cc_start: 0.8769 (mt0) cc_final: 0.8413 (mt0) REVERT: D 175 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7593 (tm-30) REVERT: D 180 ASP cc_start: 0.7956 (t70) cc_final: 0.7633 (t0) REVERT: F 5 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7204 (pttp) REVERT: F 92 ARG cc_start: 0.6181 (mtt90) cc_final: 0.5184 (ttm110) REVERT: F 94 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7417 (mp0) REVERT: F 152 MET cc_start: 0.7341 (ppp) cc_final: 0.6424 (ppp) REVERT: L 20 ASP cc_start: 0.8871 (t0) cc_final: 0.8571 (t0) REVERT: L 142 GLU cc_start: 0.6794 (pm20) cc_final: 0.6561 (pm20) REVERT: M 3 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: S 89 ASP cc_start: 0.8562 (t0) cc_final: 0.8279 (t0) REVERT: S 102 ASP cc_start: 0.7951 (t0) cc_final: 0.7320 (t70) REVERT: T 18 GLN cc_start: 0.9116 (tt0) cc_final: 0.8799 (tt0) REVERT: U 20 ARG cc_start: 0.9192 (ttp-170) cc_final: 0.8767 (ttp-170) REVERT: U 27 ASP cc_start: 0.8531 (m-30) cc_final: 0.8230 (m-30) REVERT: U 68 ASP cc_start: 0.8470 (t0) cc_final: 0.8261 (t0) REVERT: V 44 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8623 (tm-30) REVERT: V 49 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8221 (ptmm) REVERT: 2 19 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: 5 46 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.7044 (tmt170) outliers start: 201 outliers final: 172 residues processed: 989 average time/residue: 1.1962 time to fit residues: 2112.9132 Evaluate side-chains 1053 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 874 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 5 ILE Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 11 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 10.0000 chunk 372 optimal weight: 50.0000 chunk 556 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 183 optimal weight: 40.0000 chunk 180 optimal weight: 4.9990 chunk 592 optimal weight: 50.0000 chunk 634 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 732 optimal weight: 0.3980 overall best weight: 5.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN S 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 149230 Z= 0.277 Angle : 0.601 12.572 224882 Z= 0.312 Chirality : 0.037 0.344 29150 Planarity : 0.005 0.118 11366 Dihedral : 23.051 179.634 77420 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 5.76 % Allowed : 21.89 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 5173 helix: 0.60 (0.14), residues: 1544 sheet: -0.70 (0.16), residues: 1009 loop : -1.38 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 200 HIS 0.009 0.001 HIS Q 102 PHE 0.018 0.001 PHE P 65 TYR 0.016 0.002 TYR f 5 ARG 0.008 0.000 ARG 8 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 886 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 10 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8620 (mm) REVERT: d 65 GLU cc_start: 0.8061 (tt0) cc_final: 0.7788 (tt0) REVERT: f 40 GLU cc_start: 0.8122 (pm20) cc_final: 0.7633 (pm20) REVERT: g 68 ASN cc_start: 0.8094 (m110) cc_final: 0.7748 (m-40) REVERT: h 122 GLN cc_start: 0.8582 (mp10) cc_final: 0.8167 (mp10) REVERT: j 67 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6659 (tpt) REVERT: k 50 LEU cc_start: 0.8405 (mm) cc_final: 0.8077 (mp) REVERT: l 25 ASN cc_start: 0.8948 (p0) cc_final: 0.8519 (p0) REVERT: m 92 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7675 (ttp-110) REVERT: n 19 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: n 25 GLU cc_start: 0.7896 (mp0) cc_final: 0.7572 (mp0) REVERT: o 9 ASN cc_start: 0.8875 (m110) cc_final: 0.8373 (m110) REVERT: o 26 GLU cc_start: 0.8407 (pm20) cc_final: 0.8141 (pm20) REVERT: p 5 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8005 (mt) REVERT: q 79 GLU cc_start: 0.8614 (pt0) cc_final: 0.8096 (pp20) REVERT: t 3 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8174 (p0) REVERT: D 55 ASP cc_start: 0.8232 (p0) cc_final: 0.7990 (p0) REVERT: D 66 GLN cc_start: 0.8768 (mt0) cc_final: 0.8431 (mt0) REVERT: D 175 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 180 ASP cc_start: 0.8056 (t70) cc_final: 0.7711 (t0) REVERT: F 5 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7203 (pttp) REVERT: F 92 ARG cc_start: 0.6210 (mtt90) cc_final: 0.5219 (ttm110) REVERT: F 94 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7436 (mp0) REVERT: F 152 MET cc_start: 0.7367 (ppp) cc_final: 0.6470 (ppp) REVERT: G 155 GLU cc_start: 0.7864 (pm20) cc_final: 0.7627 (pm20) REVERT: L 20 ASP cc_start: 0.8869 (t0) cc_final: 0.8556 (t0) REVERT: L 142 GLU cc_start: 0.6776 (pm20) cc_final: 0.6482 (pm20) REVERT: M 3 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8334 (pt0) REVERT: S 89 ASP cc_start: 0.8557 (t0) cc_final: 0.8270 (t0) REVERT: S 102 ASP cc_start: 0.7994 (t0) cc_final: 0.7365 (t70) REVERT: T 18 GLN cc_start: 0.9120 (tt0) cc_final: 0.8811 (tt0) REVERT: U 20 ARG cc_start: 0.9198 (ttp-170) cc_final: 0.8783 (ttp-170) REVERT: U 27 ASP cc_start: 0.8533 (m-30) cc_final: 0.8228 (m-30) REVERT: V 44 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8631 (tm-30) REVERT: V 49 LYS cc_start: 0.8763 (ptmm) cc_final: 0.8198 (ptmm) REVERT: 2 19 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: 5 46 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.7042 (tmt170) outliers start: 198 outliers final: 176 residues processed: 990 average time/residue: 1.1597 time to fit residues: 2045.7273 Evaluate side-chains 1058 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 875 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 132 GLN Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 74 ILE Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 27 CYS Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 51 GLU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 11 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 20.0000 chunk 892 optimal weight: 4.9990 chunk 814 optimal weight: 10.0000 chunk 868 optimal weight: 6.9990 chunk 522 optimal weight: 30.0000 chunk 378 optimal weight: 10.0000 chunk 682 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 784 optimal weight: 10.0000 chunk 821 optimal weight: 10.0000 chunk 865 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS M 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 149230 Z= 0.255 Angle : 0.589 12.506 224882 Z= 0.307 Chirality : 0.036 0.334 29150 Planarity : 0.004 0.118 11366 Dihedral : 23.037 179.285 77420 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 5.68 % Allowed : 22.35 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 5173 helix: 0.65 (0.14), residues: 1537 sheet: -0.68 (0.16), residues: 1019 loop : -1.35 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP c 200 HIS 0.010 0.001 HIS Q 102 PHE 0.012 0.001 PHE s 74 TYR 0.017 0.002 TYR G 157 ARG 0.008 0.000 ARG 8 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 889 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 10 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8591 (mm) REVERT: d 65 GLU cc_start: 0.8072 (tt0) cc_final: 0.7818 (tt0) REVERT: f 40 GLU cc_start: 0.8127 (pm20) cc_final: 0.7632 (pm20) REVERT: g 68 ASN cc_start: 0.8080 (m110) cc_final: 0.7737 (m-40) REVERT: h 117 GLU cc_start: 0.8353 (pm20) cc_final: 0.8091 (pm20) REVERT: h 122 GLN cc_start: 0.8571 (mp10) cc_final: 0.8149 (mp10) REVERT: j 67 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6637 (tpt) REVERT: k 50 LEU cc_start: 0.8346 (mm) cc_final: 0.8020 (mp) REVERT: l 25 ASN cc_start: 0.8955 (p0) cc_final: 0.8526 (p0) REVERT: n 19 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: n 25 GLU cc_start: 0.7866 (mp0) cc_final: 0.7553 (mp0) REVERT: o 9 ASN cc_start: 0.8867 (m110) cc_final: 0.8357 (m110) REVERT: o 26 GLU cc_start: 0.8384 (pm20) cc_final: 0.8133 (pm20) REVERT: p 5 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7987 (mt) REVERT: q 79 GLU cc_start: 0.8642 (pt0) cc_final: 0.8104 (pp20) REVERT: t 3 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8180 (p0) REVERT: D 55 ASP cc_start: 0.8231 (p0) cc_final: 0.8017 (p0) REVERT: D 66 GLN cc_start: 0.8763 (mt0) cc_final: 0.8364 (mt0) REVERT: D 175 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 180 ASP cc_start: 0.8053 (t70) cc_final: 0.7699 (t0) REVERT: F 5 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7206 (pttp) REVERT: F 92 ARG cc_start: 0.6218 (mtt90) cc_final: 0.5264 (ttm110) REVERT: F 94 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7460 (mp0) REVERT: F 152 MET cc_start: 0.7357 (ppp) cc_final: 0.6452 (ppp) REVERT: G 155 GLU cc_start: 0.7855 (pm20) cc_final: 0.7602 (pm20) REVERT: L 20 ASP cc_start: 0.8876 (t0) cc_final: 0.8573 (t0) REVERT: L 142 GLU cc_start: 0.6696 (pm20) cc_final: 0.6467 (pm20) REVERT: M 3 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: O 6 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7823 (ttp80) REVERT: Q 99 TYR cc_start: 0.7958 (m-10) cc_final: 0.7701 (m-10) REVERT: S 89 ASP cc_start: 0.8555 (t0) cc_final: 0.8270 (t0) REVERT: S 102 ASP cc_start: 0.7968 (t0) cc_final: 0.7330 (t70) REVERT: T 18 GLN cc_start: 0.9116 (tt0) cc_final: 0.8812 (tt0) REVERT: U 20 ARG cc_start: 0.9196 (ttp-170) cc_final: 0.8832 (ttp-170) REVERT: U 27 ASP cc_start: 0.8539 (m-30) cc_final: 0.8229 (m-30) REVERT: V 44 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8622 (tm-30) REVERT: V 49 LYS cc_start: 0.8774 (ptmm) cc_final: 0.8209 (ptmm) REVERT: 1 59 GLU cc_start: 0.8139 (pp20) cc_final: 0.7891 (tm-30) REVERT: 2 19 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: 5 46 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.7039 (tmt170) outliers start: 195 outliers final: 175 residues processed: 992 average time/residue: 1.2483 time to fit residues: 2209.6406 Evaluate side-chains 1058 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 876 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 132 GLN Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 19 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 11 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 30.0000 chunk 918 optimal weight: 9.9990 chunk 560 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 638 optimal weight: 10.0000 chunk 963 optimal weight: 5.9990 chunk 886 optimal weight: 8.9990 chunk 767 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 592 optimal weight: 50.0000 chunk 470 optimal weight: 40.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN V 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 149230 Z= 0.458 Angle : 0.724 12.968 224882 Z= 0.368 Chirality : 0.042 0.397 29150 Planarity : 0.005 0.120 11366 Dihedral : 23.104 179.588 77420 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.60 % Favored : 92.33 % Rotamer: Outliers : 5.76 % Allowed : 22.41 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 5173 helix: 0.34 (0.13), residues: 1531 sheet: -0.80 (0.16), residues: 988 loop : -1.55 (0.11), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP c 200 HIS 0.008 0.002 HIS c 33 PHE 0.021 0.002 PHE P 65 TYR 0.021 0.002 TYR m 23 ARG 0.010 0.001 ARG 8 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10346 Ramachandran restraints generated. 5173 Oldfield, 0 Emsley, 5173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 859 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 10 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8631 (mm) REVERT: d 65 GLU cc_start: 0.8170 (tt0) cc_final: 0.7934 (tt0) REVERT: f 40 GLU cc_start: 0.8230 (pm20) cc_final: 0.7441 (pm20) REVERT: g 68 ASN cc_start: 0.8143 (m110) cc_final: 0.7858 (m110) REVERT: j 67 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6765 (tpt) REVERT: k 50 LEU cc_start: 0.8445 (mm) cc_final: 0.8081 (mp) REVERT: l 25 ASN cc_start: 0.9015 (p0) cc_final: 0.8517 (p0) REVERT: n 19 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: n 25 GLU cc_start: 0.7958 (mp0) cc_final: 0.7527 (mp0) REVERT: o 9 ASN cc_start: 0.8816 (m110) cc_final: 0.8290 (m110) REVERT: o 26 GLU cc_start: 0.8402 (pm20) cc_final: 0.7986 (pm20) REVERT: p 5 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8075 (mt) REVERT: t 3 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8182 (p0) REVERT: D 66 GLN cc_start: 0.8827 (mt0) cc_final: 0.8426 (mt0) REVERT: D 175 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 180 ASP cc_start: 0.8085 (t70) cc_final: 0.7733 (t0) REVERT: F 5 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7234 (pttp) REVERT: F 92 ARG cc_start: 0.6129 (mtt90) cc_final: 0.5133 (ttm110) REVERT: F 94 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7537 (mp0) REVERT: F 152 MET cc_start: 0.7286 (ppp) cc_final: 0.6371 (ppp) REVERT: G 133 VAL cc_start: 0.9304 (t) cc_final: 0.8994 (p) REVERT: L 20 ASP cc_start: 0.8864 (t0) cc_final: 0.8577 (t0) REVERT: S 89 ASP cc_start: 0.8616 (t0) cc_final: 0.8341 (t0) REVERT: S 102 ASP cc_start: 0.8046 (t0) cc_final: 0.7406 (t70) REVERT: T 18 GLN cc_start: 0.9200 (tt0) cc_final: 0.8876 (tt0) REVERT: U 20 ARG cc_start: 0.9271 (ttp-170) cc_final: 0.8854 (ttp-170) REVERT: U 27 ASP cc_start: 0.8568 (m-30) cc_final: 0.8279 (m-30) REVERT: V 44 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8615 (tm-30) REVERT: V 49 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8278 (ptmm) REVERT: W 1 MET cc_start: 0.8078 (tpp) cc_final: 0.7765 (mtt) REVERT: 2 19 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: 5 46 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.6980 (tmt170) REVERT: 6 42 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8257 (mp) outliers start: 198 outliers final: 176 residues processed: 973 average time/residue: 1.1642 time to fit residues: 2004.9330 Evaluate side-chains 1031 residues out of total 4433 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 848 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 188 ASP Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 132 GLN Chi-restraints excluded: chain d residue 135 VAL Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 190 ASN Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 79 ASP Chi-restraints excluded: chain e residue 95 ILE Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 153 ASP Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 93 ILE Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 120 VAL Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 55 THR Chi-restraints excluded: chain i residue 58 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 88 LEU Chi-restraints excluded: chain i residue 128 SER Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 67 MET Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 20 THR Chi-restraints excluded: chain m residue 32 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 83 ILE Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 27 CYS Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain o residue 82 ILE Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 49 VAL Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 86 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 61 VAL Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain P residue 44 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 47 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 91 PHE Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 ASP Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain 1 residue 4 ASN Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 19 GLN Chi-restraints excluded: chain 2 residue 35 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 4 residue 54 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 4 THR Chi-restraints excluded: chain 6 residue 41 VAL Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 11 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 40.0000 chunk 817 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 707 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 768 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 788 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN R 41 GLN S 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076903 restraints weight = 371070.883| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.37 r_work: 0.2976 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 149230 Z= 0.146 Angle : 0.559 12.541 224882 Z= 0.293 Chirality : 0.033 0.303 29150 Planarity : 0.004 0.118 11366 Dihedral : 23.050 177.922 77420 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 3.64 % Allowed : 24.68 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.12), residues: 5173 helix: 0.76 (0.14), residues: 1532 sheet: -0.64 (0.16), residues: 1004 loop : -1.31 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP c 200 HIS 0.011 0.001 HIS Q 102 PHE 0.013 0.001 PHE i 127 TYR 0.017 0.001 TYR G 157 ARG 0.009 0.000 ARG o 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33739.51 seconds wall clock time: 587 minutes 34.82 seconds (35254.82 seconds total)