Starting phenix.real_space_refine on Sun Apr 14 12:57:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu5_42557/04_2024/8uu5_42557_updated.pdb" } resolution = 3.0 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= -0.000 sd= 1.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4627 5.49 5 Mg 490 5.21 5 S 122 5.16 5 C 69880 2.51 5 N 26003 2.21 5 O 39735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 42": "OD1" <-> "OD2" Residue "b PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ASP 192": "OD1" <-> "OD2" Residue "b ASP 204": "OD1" <-> "OD2" Residue "c ASP 160": "OD1" <-> "OD2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c ASP 180": "OD1" <-> "OD2" Residue "c ASP 189": "OD1" <-> "OD2" Residue "d TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "f TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g ASP 48": "OD1" <-> "OD2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ASP 107": "OD1" <-> "OD2" Residue "i GLU 112": "OE1" <-> "OE2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F ASP 123": "OD1" <-> "OD2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 12": "OD1" <-> "OD2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 39": "OE1" <-> "OE2" Residue "P GLU 45": "OE1" <-> "OE2" Residue "P ASP 101": "OD1" <-> "OD2" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "R ASP 6": "OD1" <-> "OD2" Residue "R PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S ASP 97": "OD1" <-> "OD2" Residue "T GLU 6": "OE1" <-> "OE2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "V TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 60": "OE1" <-> "OE2" Residue "Y GLU 78": "OE1" <-> "OE2" Residue "Z GLU 4": "OE1" <-> "OE2" Residue "1 ASP 8": "OD1" <-> "OD2" Residue "1 GLU 23": "OE1" <-> "OE2" Residue "2 GLU 5": "OE1" <-> "OE2" Residue "2 ASP 39": "OD1" <-> "OD2" Residue "5 ASP 14": "OD1" <-> "OD2" Residue "7 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 140861 Number of models: 1 Model: "" Number of chains: 88 Chain: "a" Number of atoms: 32665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32665 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 79, 'rna3p_pur': 752, 'rna3p_pyr': 580} Link IDs: {'rna2p': 191, 'rna3p': 1331} Chain breaks: 3 Chain: "b" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1765 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 213} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1547 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 200} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "d" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1562 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 191} 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, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1146 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "f" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 771 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 91} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1143 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 141} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "h" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1002 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "i" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "j" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "k" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 845 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "l" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1003 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 125} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "m" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 900 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 716 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 612 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "r" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 509 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "s" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 632 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 76} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "t" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1 Chain: "w" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 12} Chain: "A" Number of atoms: 62340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2902, 62340 Classifications: {'RNA': 2902} Modifications used: {'rna2p_pur': 311, 'rna2p_pyr': 149, 'rna3p_pur': 1392, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 460, 'rna3p': 2441} 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: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "D" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1583 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1537 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1189 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 6, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1283 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 161} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 915 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1040 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 140} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "O" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1045 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 126} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 846 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "S" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 774 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "W" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 755 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 94} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 572 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 451 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 421 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 52} 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: "3" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 555 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "4" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 49} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "5" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "6" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 370 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 520 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 266 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 32} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Unusual residues: {' MG': 219} Classifications: {'undetermined': 219} Link IDs: {None: 218} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "w" 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 248 Unusual residues: {' MG': 248} Classifications: {'undetermined': 248} Link IDs: {None: 247} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46270 SG CYS n 24 116.821 60.528 207.917 1.00 10.57 S ATOM 46296 SG CYS n 27 116.105 64.014 206.098 1.00 17.09 S ATOM 46403 SG CYS n 40 119.535 62.430 206.209 1.00 32.50 S ATOM 46428 SG CYS n 43 118.135 63.789 209.352 1.00 11.91 S ATOM A0TKW SG CYS 4 30 87.189 211.710 90.443 1.00 41.13 S ATOM A0TLG SG CYS 4 33 89.496 211.781 87.464 1.00 43.32 S ATOM A0TNR SG CYS 4 43 90.579 210.089 90.728 1.00 31.54 S ATOM A0TO9 SG CYS 4 46 90.400 213.856 90.652 1.00 38.12 S ATOM A0TRG SG CYS 5 9 136.340 65.059 90.813 1.00 41.62 S ATOM A0TS2 SG CYS 5 12 137.446 65.970 87.220 1.00 45.66 S ATOM A0TXF SG CYS 5 36 133.716 66.283 88.209 1.00 33.58 S ATOM A0URB SG CYS 8 11 46.514 118.142 145.872 1.00 42.99 S ATOM A0URR SG CYS 8 14 47.970 119.877 142.704 1.00 39.44 S ATOM A0UU5 SG CYS 8 27 45.819 121.784 145.256 1.00 42.51 S Time building chain proxies: 53.83, per 1000 atoms: 0.38 Number of scatterers: 140861 At special positions: 0 Unit cell: (224.4, 243.95, 279.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 122 16.00 P 4627 15.00 Mg 490 11.99 O 39735 8.00 N 26003 7.00 C 69880 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: 55.40 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " 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 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " Number of angles added : 15 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9716 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: 153 helices and 71 sheets defined 36.7% alpha, 19.8% beta 1582 base pairs and 2430 stacking pairs defined. Time for finding SS restraints: 71.56 Creating SS restraints... Processing helix chain 'b' and resid 7 through 12 removed outlier: 5.174A pdb=" N GLU b 11 " --> pdb=" O LYS b 7 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA b 12 " --> pdb=" O GLN b 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 7 through 12' Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.738A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.805A pdb=" N VAL b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 104 removed outlier: 3.921A pdb=" N PHE b 104 " --> pdb=" O THR b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 123 Processing helix chain 'b' and resid 131 through 149 removed outlier: 4.707A pdb=" N LYS b 138 " --> pdb=" O VAL b 134 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.570A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.013A 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: 5.114A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN b 226 " --> pdb=" O ILE b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.577A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.567A pdb=" N PHE c 31 " --> pdb=" O ASP c 27 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.928A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.545A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.621A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.287A pdb=" N VAL d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 79 removed outlier: 3.575A pdb=" N LYS d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLN d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 4.079A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.667A pdb=" N GLY d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.883A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.692A pdb=" N SER d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 4.071A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 5.300A 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: 4.204A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 3.870A pdb=" N LYS e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN e 71 " --> pdb=" O ASP e 67 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 120 Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.830A pdb=" N GLN e 147 " --> pdb=" O ASP e 143 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 159 Processing helix chain 'e' and resid 161 through 166 Processing helix chain 'f' and resid 16 through 35 removed outlier: 3.567A pdb=" N THR f 32 " --> pdb=" O ASP f 28 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN f 34 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY f 35 " --> pdb=" O LEU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 85 removed outlier: 4.336A pdb=" N ASN f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP f 85 " --> pdb=" O ALA f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.819A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.714A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.929A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.782A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.943A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.686A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.708A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 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: 4.989A pdb=" N ARG i 45 " --> pdb=" O PHE i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.954A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 94 through 102 Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.872A pdb=" N LEU j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.160A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.070A pdb=" N LYS k 57 " --> pdb=" O LYS k 53 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.832A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.161A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 21 through 26 removed outlier: 4.031A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.186A 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: 4.743A pdb=" N TYR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) removed outlier: 4.069A 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: 3.843A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.573A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.689A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LYS m 64 " --> pdb=" O LEU m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 removed outlier: 3.563A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.668A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 13 removed outlier: 4.868A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.835A pdb=" N LYS o 47 " --> pdb=" O VAL o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.545A pdb=" N TYR o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 6.200A pdb=" N THR p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 89 Processing helix chain 'r' and resid 15 through 21 removed outlier: 6.662A pdb=" N SER r 19 " --> pdb=" O CYS r 15 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 38 removed outlier: 3.584A pdb=" N LEU r 33 " --> pdb=" O ASP r 29 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS r 35 " --> pdb=" O GLU r 31 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER r 38 " --> pdb=" O LYS r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.509A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 70 removed outlier: 3.621A pdb=" N MET r 69 " --> pdb=" O ARG r 65 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA r 70 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 17 Processing helix chain 's' and resid 19 through 24 removed outlier: 4.399A pdb=" N ALA s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 19 through 24' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.740A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 64 removed outlier: 4.551A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU t 52 " --> pdb=" O ASP t 48 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA t 60 " --> pdb=" O LYS t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 4.376A pdb=" N LYS t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.111A pdb=" N HIS C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.901A pdb=" N ILE C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.933A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.421A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.645A 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: 4.186A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.986A 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 'C' and resid 197 through 202 removed outlier: 4.222A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.201A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.553A pdb=" N GLY D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 4.567A 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 'E' and resid 29 through 45 removed outlier: 3.528A pdb=" N ASP E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.659A pdb=" N LYS E 117 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.685A pdb=" N ILE E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.809A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.659A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.604A pdb=" N ASP F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS F 10 " --> pdb=" O ASP F 6 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU F 11 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix removed outlier: 3.737A pdb=" N MET F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.208A pdb=" N ASN F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.140A pdb=" N SER F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.105A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.721A 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: 3.592A pdb=" N LEU F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.928A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.554A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 71 " --> pdb=" O THR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.508A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.545A 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: 3.744A pdb=" N SER L 35 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 98 through 111 removed outlier: 3.619A pdb=" N LEU L 102 " --> pdb=" O PRO L 98 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L 108 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.609A pdb=" N PHE L 120 " --> pdb=" O GLY L 116 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.099A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.673A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.854A pdb=" N LEU N 82 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 100 Processing helix chain 'N' and resid 129 through 140 removed outlier: 3.645A pdb=" N ALA N 139 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY N 140 " --> pdb=" O ILE N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.914A pdb=" N MET O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 4.232A pdb=" N ARG O 119 " --> pdb=" O ARG O 115 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.983A 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: 3.543A pdb=" N ILE P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 54 removed outlier: 3.718A pdb=" N GLU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL P 43 " --> pdb=" O GLU P 39 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU P 45 " --> pdb=" O ARG P 41 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU P 47 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 66 removed outlier: 3.721A pdb=" N ALA P 64 " --> pdb=" O ARG P 60 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 100 Processing helix chain 'P' and resid 101 through 107 removed outlier: 3.764A pdb=" N ARG P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR P 106 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 101 through 107' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.584A pdb=" N LYS Q 13 " --> pdb=" O LYS Q 9 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER Q 20 " --> pdb=" O ALA Q 16 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS Q 21 " --> pdb=" O ARG Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 88 removed outlier: 6.234A pdb=" N ALA Q 72 " --> pdb=" O SER Q 68 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA Q 73 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER Q 74 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS Q 87 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY Q 88 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.665A pdb=" N ALA Q 109 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 11 removed outlier: 3.748A pdb=" N LYS R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER R 11 " --> pdb=" O GLU R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 104 removed outlier: 4.700A pdb=" N ASN R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 104' Processing helix chain 'S' and resid 7 through 22 removed outlier: 6.692A pdb=" N ARG S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 4.735A pdb=" N HIS S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.525A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 3.543A pdb=" N ARG S 48 " --> pdb=" O GLN S 44 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) removed outlier: 3.825A 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 101 Processing helix chain 'S' and resid 102 through 119 removed outlier: 3.628A pdb=" N THR S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS S 119 " --> pdb=" O LYS S 115 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 removed outlier: 3.944A pdb=" N ILE U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 45 removed outlier: 3.803A 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 46 through 66 Proline residue: U 50 - end of helix removed outlier: 3.506A pdb=" N GLU U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 8 removed outlier: 3.591A pdb=" N ILE V 7 " --> pdb=" O ALA V 3 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS V 8 " --> pdb=" O ARG V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 removed outlier: 3.933A pdb=" N ILE V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU V 20 " --> pdb=" O SER V 16 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'W' and resid 64 through 69 removed outlier: 4.388A pdb=" N VAL W 68 " --> pdb=" O HIS W 64 " (cutoff:3.500A) removed outlier: 5.127A 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: 3.501A pdb=" N LEU Z 54 " --> pdb=" O SER Z 50 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS Z 55 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 50 through 56' Processing helix chain '1' and resid 2 through 9 removed outlier: 5.192A pdb=" N ILE 1 6 " --> pdb=" O LYS 1 2 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU 1 9 " --> pdb=" O ASP 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 35 removed outlier: 5.820A pdb=" N ILE 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 62 removed outlier: 4.696A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE 1 56 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 Processing helix chain '2' and resid 40 through 51 Processing helix chain '3' and resid 69 through 78 removed outlier: 3.571A pdb=" N ARG 3 73 " --> pdb=" O GLY 3 69 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.824A pdb=" N ARG 4 17 " --> pdb=" O LYS 4 13 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 5.151A 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 removed outlier: 3.573A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.603A pdb=" N SER 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR 6 24 " --> pdb=" O THR 6 20 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.577A pdb=" N LYS 7 12 " --> pdb=" O ARG 7 8 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.027A pdb=" N LYS 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 5.911A 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: 3.540A pdb=" N ARG 7 45 " --> pdb=" O LYS 7 41 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 3.926A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 89 through 93 Processing sheet with id= 2, first strand: chain 'c' and resid 52 through 58 removed outlier: 3.546A pdb=" N VAL c 103 " --> pdb=" O ILE c 67 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 163 through 169 removed outlier: 3.539A pdb=" N THR c 190 " --> pdb=" O GLY c 193 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 164 through 169 removed outlier: 7.825A pdb=" N TYR d 164 " --> pdb=" O ASN d 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 13 through 17 removed outlier: 6.797A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 85 through 89 removed outlier: 3.853A pdb=" N ILE e 95 " --> pdb=" O GLY e 88 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU e 94 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA e 100 " --> pdb=" O ASP e 123 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP e 123 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL e 124 " --> pdb=" O GLY e 105 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 34 through 41 Processing sheet with id= 8, first strand: chain 'f' and resid 36 through 39 removed outlier: 4.962A pdb=" N GLU f 37 " --> pdb=" O ASN f 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN f 67 " --> pdb=" O GLU f 37 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS f 65 " --> pdb=" O ILE f 39 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS f 4 " --> pdb=" O GLU f 95 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG f 89 " --> pdb=" O ILE f 10 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 40 through 44 removed outlier: 3.839A pdb=" N GLU f 40 " --> pdb=" O LYS f 65 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR f 61 " --> pdb=" O TRP f 44 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'f' and resid 45 through 49 removed outlier: 6.958A pdb=" N ARG f 57 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 12, first strand: chain 'h' and resid 23 through 29 removed outlier: 5.851A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.836A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.429A pdb=" N LYS i 27 " --> pdb=" O TYR i 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL i 63 " --> pdb=" O LYS i 27 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.555A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'k' and resid 30 through 35 removed outlier: 6.865A pdb=" N THR k 81 " --> pdb=" O GLU k 17 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 27 through 30 Processing sheet with id= 19, first strand: chain 'l' and resid 42 through 45 removed outlier: 5.192A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'l' and resid 64 through 69 removed outlier: 4.821A 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 removed outlier: 6.449A pdb=" N ASN p 41 " --> pdb=" O PRO p 16 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU p 48 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.880A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 6.714A 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 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 's' and resid 30 through 33 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 80 through 83 removed outlier: 3.607A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 137 through 142 removed outlier: 7.310A pdb=" N VAL C 137 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLY C 166 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LYS C 170 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 91 through 96 removed outlier: 4.203A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.637A pdb=" N LYS D 3 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY D 116 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY D 165 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY D 118 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 163 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.714A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN D 184 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 31, 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: 6.526A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 106 through 109 removed outlier: 4.479A pdb=" N ASP D 106 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.699A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 35, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.294A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA F 87 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 89 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 91 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 157 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL F 155 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL F 132 " --> pdb=" O MET F 152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 16 through 19 removed outlier: 4.183A pdb=" N THR G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS G 27 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR G 25 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 24 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS G 35 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 41 through 45 removed outlier: 3.865A pdb=" N SER G 53 " --> pdb=" O THR G 42 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 82 through 89 removed outlier: 3.771A pdb=" N GLY G 135 " --> pdb=" O TYR G 83 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.747A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'L' and resid 53 through 58 removed outlier: 5.184A 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: 7.124A 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: 6.128A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER M 6 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU M 81 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG M 64 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 37 through 41 removed outlier: 4.567A pdb=" N ASP M 37 " --> pdb=" O ILE M 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M' and resid 68 through 71 removed outlier: 4.034A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'N' and resid 74 through 77 Processing sheet with id= 46, first strand: chain 'N' and resid 121 through 124 Processing sheet with id= 47, first strand: chain 'O' and resid 38 through 41 removed outlier: 6.774A pdb=" N TYR O 74 " --> pdb=" O GLU O 91 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP O 93 " --> pdb=" O LYS O 72 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS O 72 " --> pdb=" O TRP O 93 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 63 through 66 removed outlier: 4.180A pdb=" N PHE O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU O 34 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'O' and resid 31 through 37 removed outlier: 8.785A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS O 128 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'P' and resid 29 through 33 removed outlier: 4.652A pdb=" N ARG P 122 " --> pdb=" O GLY P 126 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY P 120 " --> pdb=" O PRO P 128 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL P 130 " --> pdb=" O LYS P 118 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS P 118 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE P 132 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE P 116 " --> pdb=" O ILE P 132 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU P 134 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR P 114 " --> pdb=" O LEU P 134 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 72 through 76 removed outlier: 3.590A pdb=" N GLU P 72 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS P 88 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Q' and resid 54 through 57 removed outlier: 3.874A pdb=" N ALA Q 54 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 95 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 38 through 45 removed outlier: 6.913A pdb=" N THR R 25 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 49 through 52 removed outlier: 3.862A pdb=" N LYS R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLU R 57 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.680A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL T 41 " --> pdb=" O ALA T 46 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA T 46 " --> pdb=" O VAL T 41 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY T 43 " --> pdb=" O ASP T 44 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 18 through 23 removed outlier: 4.168A pdb=" N GLN T 18 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS T 94 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR T 59 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP T 31 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 64 through 67 removed outlier: 3.610A pdb=" N GLY T 66 " --> pdb=" O TYR T 92 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 70 through 77 removed outlier: 4.226A pdb=" N TYR T 82 " --> pdb=" O LYS T 77 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'U' and resid 7 through 13 removed outlier: 6.727A pdb=" N VAL U 111 " --> pdb=" O GLU U 77 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 83 through 93 removed outlier: 5.262A pdb=" N GLU U 83 " --> pdb=" O HIS U 107 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS U 107 " --> pdb=" O GLU U 83 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR U 105 " --> pdb=" O PRO U 85 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG U 97 " --> pdb=" O ARG U 93 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'V' and resid 24 through 28 removed outlier: 5.359A pdb=" N TYR V 68 " --> pdb=" O MET V 65 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS V 61 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS V 74 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS V 59 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG V 76 " --> pdb=" O ASN V 57 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN V 57 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA V 78 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL V 55 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL V 80 " --> pdb=" O VAL V 53 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL V 53 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.373A pdb=" N ASN W 39 " --> pdb=" O ALA W 61 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU W 57 " --> pdb=" O LYS W 43 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Y' and resid 53 through 56 removed outlier: 6.343A pdb=" N VAL Y 89 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS Y 84 " --> pdb=" O MET Y 80 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Y' and resid 59 through 62 removed outlier: 4.670A pdb=" N THR Y 66 " --> pdb=" O GLY Y 62 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Z' and resid 11 through 19 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain '2' and resid 32 through 38 removed outlier: 4.154A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '3' and resid 21 through 26 removed outlier: 4.009A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP 3 16 " --> pdb=" O PHE 3 21 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '5' and resid 3 through 7 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain '5' and resid 30 through 34 removed outlier: 5.941A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain '8' and resid 1 through 4 removed outlier: 3.553A pdb=" N ARG 8 4 " --> pdb=" O LYS 8 35 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN 8 34 " --> pdb=" O VAL 8 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 36 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3971 hydrogen bonds 6326 hydrogen bond angles 0 basepair planarities 1582 basepair parallelities 2430 stacking parallelities Total time for adding SS restraints: 301.30 Time building geometry restraints manager: 60.59 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: 21151 1.33 - 1.45: 65890 1.45 - 1.58: 56028 1.58 - 1.70: 9245 1.70 - 1.82: 219 Bond restraints: 152533 Sorted by residual: bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.57e+02 bond pdb=" N1 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C5 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.155 1.387 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C13 MIA x 37 " pdb=" C14 MIA x 37 " ideal model delta sigma weight residual 1.317 1.525 -0.208 2.00e-02 2.50e+03 1.09e+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 6.46e+01 ... (remaining 152528 not shown) Histogram of bond angle deviations from ideal: 95.97 - 104.47: 20025 104.47 - 112.96: 93497 112.96 - 121.45: 77098 121.45 - 129.94: 35786 129.94 - 138.44: 2581 Bond angle restraints: 228987 Sorted by residual: angle pdb=" N VAL s 19 " pdb=" CA VAL s 19 " pdb=" C VAL s 19 " ideal model delta sigma weight residual 113.71 106.17 7.54 9.50e-01 1.11e+00 6.31e+01 angle pdb=" CB LYS b 49 " pdb=" CG LYS b 49 " pdb=" CD LYS b 49 " ideal model delta sigma weight residual 111.30 126.68 -15.38 2.30e+00 1.89e-01 4.47e+01 angle pdb=" C6 5MU x 54 " pdb=" C5 5MU x 54 " pdb=" C5M 5MU x 54 " ideal model delta sigma weight residual 106.09 120.77 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" CA LEU C 154 " pdb=" C LEU C 154 " pdb=" O LEU C 154 " ideal model delta sigma weight residual 120.80 115.81 4.99 1.05e+00 9.07e-01 2.26e+01 angle pdb=" N3 5MU x 54 " pdb=" C4 5MU x 54 " pdb=" O4 5MU x 54 " ideal model delta sigma weight residual 107.56 120.65 -13.09 3.00e+00 1.11e-01 1.90e+01 ... (remaining 228982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86412 35.98 - 71.96: 9808 71.96 - 107.95: 1142 107.95 - 143.93: 25 143.93 - 179.91: 39 Dihedral angle restraints: 97426 sinusoidal: 82317 harmonic: 15109 Sorted by residual: dihedral pdb=" O4' U A2339 " pdb=" C1' U A2339 " pdb=" N1 U A2339 " pdb=" C2 U A2339 " ideal model delta sinusoidal sigma weight residual -160.00 13.63 -173.63 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U x 33 " pdb=" C1' U x 33 " pdb=" N1 U x 33 " pdb=" C2 U x 33 " ideal model delta sinusoidal sigma weight residual 200.00 26.96 173.04 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U a 930 " pdb=" C1' U a 930 " pdb=" N1 U a 930 " pdb=" C2 U a 930 " ideal model delta sinusoidal sigma weight residual 200.00 39.77 160.23 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 97423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 28691 0.099 - 0.197: 681 0.197 - 0.296: 30 0.296 - 0.395: 0 0.395 - 0.493: 1 Chirality restraints: 29403 Sorted by residual: chirality pdb=" CB VAL R 33 " pdb=" CA VAL R 33 " pdb=" CG1 VAL R 33 " pdb=" CG2 VAL R 33 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 6.08e+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 -2.45 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1' A A1029 " pdb=" O4' A A1029 " pdb=" C2' A A1029 " pdb=" N9 A A1029 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 29400 not shown) Planarity restraints: 11764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU x 54 " 0.014 2.00e-02 2.50e+03 5.14e-01 5.93e+03 pdb=" C4' 5MU x 54 " -0.421 2.00e-02 2.50e+03 pdb=" O4' 5MU x 54 " -0.580 2.00e-02 2.50e+03 pdb=" C3' 5MU x 54 " 0.571 2.00e-02 2.50e+03 pdb=" O3' 5MU x 54 " 0.447 2.00e-02 2.50e+03 pdb=" C2' 5MU x 54 " 0.258 2.00e-02 2.50e+03 pdb=" O2' 5MU x 54 " -0.801 2.00e-02 2.50e+03 pdb=" C1' 5MU x 54 " -0.240 2.00e-02 2.50e+03 pdb=" N1 5MU x 54 " 0.754 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MIA x 37 " 0.068 2.00e-02 2.50e+03 1.88e-01 4.43e+02 pdb=" C13 MIA x 37 " -0.204 2.00e-02 2.50e+03 pdb=" C14 MIA x 37 " 0.331 2.00e-02 2.50e+03 pdb=" C15 MIA x 37 " -0.059 2.00e-02 2.50e+03 pdb=" C16 MIA x 37 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 35 " 0.025 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP i 35 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP i 35 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP i 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP i 35 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP i 35 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP i 35 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 35 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP i 35 " 0.001 2.00e-02 2.50e+03 ... (remaining 11761 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 871 2.50 - 3.10: 87652 3.10 - 3.70: 251030 3.70 - 4.30: 388523 4.30 - 4.90: 530220 Nonbonded interactions: 1258296 Sorted by model distance: nonbonded pdb=" N7 G a 950 " pdb="MG MG a3206 " model vdw 1.894 2.250 nonbonded pdb=" N7 G A2535 " pdb="MG MG A3239 " model vdw 1.895 2.250 nonbonded pdb=" N7 G a 592 " pdb="MG MG a3218 " model vdw 1.895 2.250 nonbonded pdb=" OP1 A a 973 " pdb="MG MG a3096 " model vdw 2.008 2.170 nonbonded pdb=" OP2 A A2003 " pdb="MG MG A3125 " model vdw 2.016 2.170 ... (remaining 1258291 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: 11.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.150 Extract box with map and model: 31.250 Check model and map are aligned: 1.500 Set scattering table: 0.970 Process input model: 597.780 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 658.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.003 0.321 152533 Z= 0.201 Angle : 0.547 15.383 228987 Z= 0.291 Chirality : 0.034 0.493 29403 Planarity : 0.007 0.514 11764 Dihedral : 22.715 179.911 87710 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -1.12 (0.11), residues: 5202 helix: -0.35 (0.13), residues: 1574 sheet: -0.13 (0.17), residues: 1017 loop : -1.19 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP i 35 HIS 0.007 0.001 HIS c 33 PHE 0.029 0.001 PHE b 54 TYR 0.015 0.001 TYR L 141 ARG 0.012 0.001 ARG o 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 855 time to evaluate : 5.650 Fit side-chains REVERT: P 23 ASP cc_start: 0.8339 (m-30) cc_final: 0.7997 (m-30) REVERT: Q 39 ASN cc_start: 0.7566 (m-40) cc_final: 0.7278 (m-40) outliers start: 1 outliers final: 0 residues processed: 855 average time/residue: 2.2376 time to fit residues: 2669.7198 Evaluate side-chains 701 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 821 optimal weight: 7.9990 chunk 737 optimal weight: 5.9990 chunk 409 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 762 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 463 optimal weight: 8.9990 chunk 567 optimal weight: 20.0000 chunk 883 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 77 GLN ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN c 122 GLN c 135 GLN d 36 HIS d 50 GLN d 85 ASN d 112 GLN d 118 HIS e 150 ASN f 62 HIS f 67 ASN f 75 ASN g 68 ASN g 129 ASN h 16 ASN i 68 HIS i 75 GLN l 6 GLN l 59 ASN l 109 HIS m 76 ASN n 52 GLN o 18 HIS o 37 ASN o 42 HIS o 46 HIS o 65 ASN p 72 ASN p 85 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN t 21 ASN C 263 ASN C 264 ASN D 33 ASN D 152 ASN D 201 GLN E 9 GLN E 46 GLN G 48 ASN G 147 ASN M 13 ASN M 82 ASN M 109 ASN N 27 ASN Q 15 HIS Q 43 GLN R 2 ASN S 37 GLN T 81 ASN U 73 ASN W 58 ASN Y 20 ASN Z 23 ASN Z 34 GLN 1 36 GLN 2 40 ASN 3 6 HIS 4 48 GLN 5 26 ASN 7 35 ASN 7 40 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 152533 Z= 0.445 Angle : 0.686 14.568 228987 Z= 0.356 Chirality : 0.044 0.407 29403 Planarity : 0.006 0.125 11764 Dihedral : 23.025 179.702 77744 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.89 % Rotamer: Outliers : 3.11 % Allowed : 13.71 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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 (0.11), residues: 5202 helix: 0.13 (0.13), residues: 1620 sheet: -0.21 (0.16), residues: 1046 loop : -1.33 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP i 35 HIS 0.014 0.002 HIS n 31 PHE 0.021 0.002 PHE b 54 TYR 0.019 0.002 TYR 5 35 ARG 0.010 0.001 ARG i 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 714 time to evaluate : 5.657 Fit side-chains revert: symmetry clash REVERT: b 59 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: c 40 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7189 (t0) REVERT: d 51 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: d 191 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: g 143 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7623 (mttt) REVERT: m 14 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6567 (mtt180) REVERT: n 61 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.7725 (t60) REVERT: o 14 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: C 272 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8238 (ptp90) REVERT: D 98 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7978 (mtpp) REVERT: V 15 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: 1 29 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8662 (mtt90) REVERT: 3 76 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7556 (tttp) outliers start: 130 outliers final: 62 residues processed: 757 average time/residue: 2.2328 time to fit residues: 2362.9647 Evaluate side-chains 749 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 675 time to evaluate : 5.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 109 LYS Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 140 ASP Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 96 ARG Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 14 ARG Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 76 LYS Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 49 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 491 optimal weight: 50.0000 chunk 274 optimal weight: 1.9990 chunk 735 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 885 optimal weight: 8.9990 chunk 956 optimal weight: 7.9990 chunk 788 optimal weight: 0.8980 chunk 877 optimal weight: 0.9980 chunk 301 optimal weight: 30.0000 chunk 710 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN d 50 GLN d 70 ASN d 112 GLN d 118 HIS f 67 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN p 72 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN M 45 GLN N 17 ASN P 96 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN 8 34 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 152533 Z= 0.142 Angle : 0.518 13.098 228987 Z= 0.275 Chirality : 0.033 0.284 29403 Planarity : 0.004 0.116 11764 Dihedral : 22.917 179.376 77744 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.33 % Rotamer: Outliers : 2.73 % Allowed : 16.87 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: -0.59 (0.11), residues: 5202 helix: 0.72 (0.13), residues: 1612 sheet: -0.02 (0.16), residues: 1038 loop : -1.27 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP i 35 HIS 0.008 0.001 HIS d 118 PHE 0.013 0.001 PHE b 54 TYR 0.023 0.001 TYR l 65 ARG 0.010 0.000 ARG f 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 733 time to evaluate : 5.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 148 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8630 (tp) REVERT: g 143 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7540 (mttm) REVERT: g 144 MET cc_start: 0.7244 (mpm) cc_final: 0.6926 (mmt) REVERT: n 15 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7910 (tttt) REVERT: n 25 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: o 14 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: o 40 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8461 (t0) REVERT: D 29 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: D 98 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7920 (mtpp) REVERT: P 23 ASP cc_start: 0.8100 (m-30) cc_final: 0.7797 (m-30) REVERT: R 91 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8228 (tttp) REVERT: U 95 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8699 (mt0) REVERT: V 15 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: W 32 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8115 (mtt180) REVERT: 1 29 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8569 (mtt90) REVERT: 8 28 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7669 (pt0) outliers start: 114 outliers final: 37 residues processed: 787 average time/residue: 2.2220 time to fit residues: 2455.5445 Evaluate side-chains 733 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 684 time to evaluate : 5.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain n residue 15 LYS Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 65 MET Chi-restraints excluded: chain 8 residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 874 optimal weight: 6.9990 chunk 665 optimal weight: 10.0000 chunk 459 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 422 optimal weight: 8.9990 chunk 594 optimal weight: 50.0000 chunk 888 optimal weight: 0.9990 chunk 940 optimal weight: 1.9990 chunk 464 optimal weight: 8.9990 chunk 841 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 141 GLN c 61 ASN c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN m 105 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN p 62 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN S 37 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN 8 34 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 152533 Z= 0.330 Angle : 0.604 13.255 228987 Z= 0.316 Chirality : 0.039 0.369 29403 Planarity : 0.005 0.115 11764 Dihedral : 22.885 179.941 77744 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 3.95 % Allowed : 18.04 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.58 (0.11), residues: 5202 helix: 0.76 (0.13), residues: 1615 sheet: -0.09 (0.16), residues: 1074 loop : -1.28 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP i 35 HIS 0.007 0.001 HIS c 33 PHE 0.021 0.002 PHE b 54 TYR 0.017 0.002 TYR 5 35 ARG 0.007 0.001 ARG 6 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 703 time to evaluate : 5.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 40 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7172 (t0) REVERT: c 148 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8693 (tp) REVERT: d 51 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: d 191 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6695 (pp20) REVERT: g 143 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7634 (mttt) REVERT: g 144 MET cc_start: 0.7349 (mpm) cc_final: 0.7057 (mmt) REVERT: l 26 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7280 (ptpt) REVERT: m 105 ASN cc_start: 0.8354 (t0) cc_final: 0.8127 (t0) REVERT: n 25 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: n 61 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7944 (t60) REVERT: o 14 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: D 29 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: D 98 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8050 (mtpp) REVERT: P 23 ASP cc_start: 0.8208 (m-30) cc_final: 0.7909 (m-30) REVERT: Q 21 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (mtmt) REVERT: R 89 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7373 (mtt90) REVERT: R 91 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (tttp) REVERT: S 37 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8825 (mt0) REVERT: V 15 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: 1 29 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8609 (mtt90) outliers start: 165 outliers final: 83 residues processed: 782 average time/residue: 2.2636 time to fit residues: 2501.0472 Evaluate side-chains 783 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 684 time to evaluate : 5.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 83 HIS Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 49 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 783 optimal weight: 6.9990 chunk 533 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 700 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 802 optimal weight: 0.6980 chunk 650 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 844 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN S 37 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 152533 Z= 0.248 Angle : 0.567 13.307 228987 Z= 0.299 Chirality : 0.037 0.345 29403 Planarity : 0.005 0.115 11764 Dihedral : 22.887 179.906 77744 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.56 % Rotamer: Outliers : 4.26 % Allowed : 19.33 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.52 (0.11), residues: 5202 helix: 0.86 (0.13), residues: 1612 sheet: -0.02 (0.16), residues: 1051 loop : -1.29 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP i 35 HIS 0.008 0.001 HIS c 33 PHE 0.016 0.001 PHE b 54 TYR 0.014 0.001 TYR 5 35 ARG 0.006 0.000 ARG m 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 690 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 40 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7169 (t0) REVERT: c 148 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8672 (tp) REVERT: d 51 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: d 157 VAL cc_start: 0.5707 (OUTLIER) cc_final: 0.5488 (t) REVERT: g 143 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7607 (mttt) REVERT: g 144 MET cc_start: 0.7438 (mpm) cc_final: 0.7150 (mmt) REVERT: m 66 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: n 25 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: n 61 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.7905 (t60) REVERT: o 14 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: C 267 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: D 29 GLU cc_start: 0.7270 (tt0) cc_final: 0.7060 (tt0) REVERT: D 98 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8001 (mtpp) REVERT: M 34 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7356 (t0) REVERT: P 23 ASP cc_start: 0.8156 (m-30) cc_final: 0.7853 (m-30) REVERT: R 38 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6660 (mt-10) REVERT: R 89 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7403 (mtt90) REVERT: R 91 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8303 (tttp) REVERT: U 95 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8710 (mt0) REVERT: V 15 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: V 49 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7699 (tmtm) REVERT: 1 29 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8595 (mtt90) outliers start: 178 outliers final: 98 residues processed: 786 average time/residue: 2.1971 time to fit residues: 2439.4547 Evaluate side-chains 799 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 683 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 142 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 24 GLN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 49 LYS Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 49 MET Chi-restraints excluded: chain 7 residue 65 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 316 optimal weight: 1.9990 chunk 846 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 552 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 941 optimal weight: 0.2980 chunk 781 optimal weight: 0.2980 chunk 435 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 494 optimal weight: 50.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN S 37 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN 8 34 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 152533 Z= 0.139 Angle : 0.524 13.356 228987 Z= 0.278 Chirality : 0.034 0.301 29403 Planarity : 0.004 0.115 11764 Dihedral : 22.902 179.878 77744 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 3.49 % Allowed : 20.48 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.39 (0.12), residues: 5202 helix: 1.02 (0.13), residues: 1614 sheet: 0.06 (0.16), residues: 1032 loop : -1.24 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP i 35 HIS 0.006 0.001 HIS i 68 PHE 0.016 0.001 PHE b 54 TYR 0.013 0.001 TYR C 83 ARG 0.007 0.000 ARG d 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 692 time to evaluate : 5.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 148 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8601 (tp) REVERT: d 191 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: g 143 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7607 (mttm) REVERT: l 26 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7242 (ptpt) REVERT: l 101 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7939 (ttpt) REVERT: n 25 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: n 61 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7834 (t60) REVERT: o 14 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: o 40 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8540 (t0) REVERT: t 65 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8336 (pt) REVERT: C 267 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: D 29 GLU cc_start: 0.7243 (tt0) cc_final: 0.7023 (tt0) REVERT: D 98 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7978 (mtpp) REVERT: M 34 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7335 (t0) REVERT: P 23 ASP cc_start: 0.8089 (m-30) cc_final: 0.7787 (m-30) REVERT: P 110 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: R 38 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6611 (mt-10) REVERT: R 89 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7355 (mtt90) REVERT: R 91 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8291 (tttp) REVERT: U 95 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8693 (mt0) REVERT: V 15 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: 1 29 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8568 (mtt90) outliers start: 146 outliers final: 73 residues processed: 771 average time/residue: 2.1940 time to fit residues: 2391.6741 Evaluate side-chains 766 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 674 time to evaluate : 5.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 81 LYS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 19 ASN Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain l residue 26 LYS Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 65 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 907 optimal weight: 0.0970 chunk 106 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 687 optimal weight: 7.9990 chunk 532 optimal weight: 10.0000 chunk 792 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 chunk 937 optimal weight: 1.9990 chunk 586 optimal weight: 8.9990 chunk 571 optimal weight: 20.0000 chunk 432 optimal weight: 10.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN S 37 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 152533 Z= 0.359 Angle : 0.623 13.435 228987 Z= 0.325 Chirality : 0.040 0.383 29403 Planarity : 0.005 0.115 11764 Dihedral : 22.871 179.879 77744 Min Nonbonded Distance : 0.998 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.02 % Favored : 93.89 % Rotamer: Outliers : 4.26 % Allowed : 20.60 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.53 (0.11), residues: 5202 helix: 0.88 (0.13), residues: 1619 sheet: -0.06 (0.16), residues: 1050 loop : -1.31 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP i 35 HIS 0.007 0.001 HIS E 49 PHE 0.018 0.002 PHE b 54 TYR 0.017 0.002 TYR i 116 ARG 0.011 0.001 ARG d 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 679 time to evaluate : 5.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.8081 (mmt) cc_final: 0.7820 (mmt) REVERT: c 40 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7176 (t0) REVERT: c 148 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8706 (tp) REVERT: d 51 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: d 191 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6747 (pp20) REVERT: g 63 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7220 (mt-10) REVERT: g 74 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5774 (tt0) REVERT: g 143 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7664 (mttt) REVERT: g 144 MET cc_start: 0.7207 (mpm) cc_final: 0.6980 (mmt) REVERT: n 25 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: n 61 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7994 (t60) REVERT: o 14 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: o 40 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8572 (t0) REVERT: t 65 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (pt) REVERT: C 247 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: C 267 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: D 29 GLU cc_start: 0.7300 (tt0) cc_final: 0.7080 (tt0) REVERT: D 98 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: M 34 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7361 (t0) REVERT: P 23 ASP cc_start: 0.8127 (m-30) cc_final: 0.7832 (m-30) REVERT: P 110 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: R 38 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: R 89 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7408 (mtt90) REVERT: R 91 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8311 (tttp) REVERT: S 37 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8998 (mt0) REVERT: U 95 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: V 15 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: Y 80 MET cc_start: 0.8118 (mtm) cc_final: 0.7867 (mtm) REVERT: 1 29 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8638 (mtt90) REVERT: 3 70 ARG cc_start: 0.7627 (mpp-170) cc_final: 0.7387 (mpp-170) outliers start: 178 outliers final: 103 residues processed: 773 average time/residue: 2.2102 time to fit residues: 2427.5604 Evaluate side-chains 789 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 664 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 145 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 113 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 16 MET Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 37 GLN Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 65 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 580 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 560 optimal weight: 6.9990 chunk 282 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 596 optimal weight: 50.0000 chunk 638 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 737 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN S 37 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 152533 Z= 0.304 Angle : 0.600 13.460 228987 Z= 0.315 Chirality : 0.039 0.366 29403 Planarity : 0.005 0.115 11764 Dihedral : 22.875 179.843 77744 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 3.88 % Allowed : 21.51 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.54 (0.11), residues: 5202 helix: 0.88 (0.13), residues: 1620 sheet: -0.05 (0.16), residues: 1057 loop : -1.32 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 200 HIS 0.007 0.001 HIS c 33 PHE 0.018 0.001 PHE b 54 TYR 0.015 0.002 TYR 5 35 ARG 0.012 0.001 ARG d 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 677 time to evaluate : 5.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.8133 (mmt) cc_final: 0.7870 (mmt) REVERT: c 40 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7156 (t0) REVERT: c 148 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8708 (tp) REVERT: d 24 LYS cc_start: 0.6829 (pptt) cc_final: 0.6603 (pptt) REVERT: d 51 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: d 191 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: g 74 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: g 143 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7646 (mttt) REVERT: g 144 MET cc_start: 0.7263 (mpm) cc_final: 0.7031 (mmt) REVERT: l 101 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: n 25 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: n 61 TRP cc_start: 0.8613 (OUTLIER) cc_final: 0.7960 (t60) REVERT: o 14 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: o 40 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8584 (t0) REVERT: t 65 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8371 (pt) REVERT: C 216 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8648 (mttm) REVERT: C 247 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: C 267 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: D 29 GLU cc_start: 0.7285 (tt0) cc_final: 0.7067 (tt0) REVERT: D 98 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8092 (mtpp) REVERT: G 148 ILE cc_start: 0.8755 (mp) cc_final: 0.8464 (mp) REVERT: M 34 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7350 (t0) REVERT: P 23 ASP cc_start: 0.8116 (m-30) cc_final: 0.7817 (m-30) REVERT: P 110 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: R 38 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: R 89 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7385 (mtt90) REVERT: R 91 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8336 (tttp) REVERT: U 95 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8722 (mt0) REVERT: V 15 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: Y 80 MET cc_start: 0.8084 (mtm) cc_final: 0.7816 (mtm) REVERT: 1 29 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (mtt90) REVERT: 2 44 ARG cc_start: 0.8353 (mmt90) cc_final: 0.8089 (mmt180) outliers start: 162 outliers final: 107 residues processed: 765 average time/residue: 2.2090 time to fit residues: 2395.1874 Evaluate side-chains 801 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 672 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 168 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 113 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 157 VAL Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 17 ARG Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 1 residue 53 MET Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 49 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 853 optimal weight: 9.9990 chunk 898 optimal weight: 3.9990 chunk 819 optimal weight: 5.9990 chunk 873 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 686 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 chunk 789 optimal weight: 4.9990 chunk 826 optimal weight: 0.9980 chunk 870 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 152533 Z= 0.186 Angle : 0.564 13.475 228987 Z= 0.297 Chirality : 0.035 0.333 29403 Planarity : 0.005 0.115 11764 Dihedral : 22.898 179.746 77744 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.40 % Favored : 94.50 % Rotamer: Outliers : 3.45 % Allowed : 21.99 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.44 (0.12), residues: 5202 helix: 1.00 (0.13), residues: 1619 sheet: -0.01 (0.16), residues: 1042 loop : -1.28 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.008 0.001 HIS c 33 PHE 0.017 0.001 PHE b 54 TYR 0.026 0.001 TYR i 7 ARG 0.011 0.000 ARG f 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 683 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.8124 (mmt) cc_final: 0.7852 (mmt) REVERT: c 40 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7161 (t0) REVERT: c 148 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8654 (tp) REVERT: d 51 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: d 191 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: g 143 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7682 (mptt) REVERT: g 144 MET cc_start: 0.7254 (mpm) cc_final: 0.7028 (mmt) REVERT: h 13 ARG cc_start: 0.8926 (mtt-85) cc_final: 0.8718 (mtp85) REVERT: l 101 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8062 (ttpt) REVERT: n 61 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7974 (t60) REVERT: o 14 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: s 55 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7769 (ttm170) REVERT: t 65 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8362 (pt) REVERT: C 216 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8638 (mttm) REVERT: C 247 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: C 267 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: D 29 GLU cc_start: 0.7264 (tt0) cc_final: 0.7047 (tt0) REVERT: D 98 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: F 19 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (ttpt) REVERT: G 148 ILE cc_start: 0.8778 (mp) cc_final: 0.8480 (mp) REVERT: M 34 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7331 (t0) REVERT: P 23 ASP cc_start: 0.8084 (m-30) cc_final: 0.7791 (m-30) REVERT: P 110 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: R 38 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: R 89 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7374 (mtt90) REVERT: R 91 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8320 (tttp) REVERT: U 95 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8730 (mt0) REVERT: V 15 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: Y 80 MET cc_start: 0.8078 (mtm) cc_final: 0.7812 (mtm) REVERT: 1 29 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8588 (mtt90) REVERT: 2 44 ARG cc_start: 0.8321 (mmt90) cc_final: 0.8067 (mmt180) outliers start: 144 outliers final: 97 residues processed: 760 average time/residue: 2.2118 time to fit residues: 2383.8905 Evaluate side-chains 791 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 673 time to evaluate : 5.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain d residue 113 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 99 GLU Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 83 HIS Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 53 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 95 GLN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 7 residue 49 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 573 optimal weight: 10.0000 chunk 924 optimal weight: 9.9990 chunk 564 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 642 optimal weight: 8.9990 chunk 969 optimal weight: 2.9990 chunk 892 optimal weight: 0.0870 chunk 771 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 596 optimal weight: 50.0000 chunk 473 optimal weight: 50.0000 overall best weight: 6.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN g 142 HIS j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN G 61 HIS ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 152533 Z= 0.434 Angle : 0.680 13.496 228987 Z= 0.352 Chirality : 0.044 0.407 29403 Planarity : 0.006 0.114 11764 Dihedral : 22.906 179.918 77744 Min Nonbonded Distance : 0.970 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 3.69 % Allowed : 21.85 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.67 (0.11), residues: 5202 helix: 0.75 (0.13), residues: 1620 sheet: -0.12 (0.16), residues: 1062 loop : -1.39 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP i 35 HIS 0.008 0.002 HIS c 6 PHE 0.020 0.002 PHE b 54 TYR 0.021 0.002 TYR i 7 ARG 0.009 0.001 ARG 6 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 688 time to evaluate : 5.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 40 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7172 (t0) REVERT: c 148 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8727 (tp) REVERT: d 24 LYS cc_start: 0.6899 (pptt) cc_final: 0.6634 (pptt) REVERT: d 51 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: d 191 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6812 (pp20) REVERT: g 143 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7707 (mptt) REVERT: g 144 MET cc_start: 0.7142 (mpm) cc_final: 0.6897 (mmt) REVERT: h 13 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8758 (mtp85) REVERT: n 61 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.8069 (t60) REVERT: o 14 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: s 83 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.5368 (t-90) REVERT: t 65 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8395 (pt) REVERT: C 247 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8144 (mtm) REVERT: D 29 GLU cc_start: 0.7287 (tt0) cc_final: 0.7064 (tt0) REVERT: D 98 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8150 (mtpp) REVERT: F 19 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (ttpt) REVERT: G 86 LYS cc_start: 0.7367 (mmmt) cc_final: 0.7116 (mmmm) REVERT: G 148 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8425 (mp) REVERT: M 34 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7333 (t0) REVERT: P 23 ASP cc_start: 0.8157 (m-30) cc_final: 0.7882 (m-30) REVERT: P 110 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6723 (mp10) REVERT: R 38 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6695 (mt-10) REVERT: R 91 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8346 (tttp) REVERT: V 15 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: W 30 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8634 (mtpp) REVERT: Y 80 MET cc_start: 0.8139 (mtm) cc_final: 0.7895 (mtm) REVERT: 1 29 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8649 (mtt90) REVERT: 2 44 ARG cc_start: 0.8372 (mmt90) cc_final: 0.8089 (mmt180) outliers start: 154 outliers final: 106 residues processed: 769 average time/residue: 2.2018 time to fit residues: 2393.9705 Evaluate side-chains 806 residues out of total 4457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 682 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 194 ASP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 51 GLN Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 77 LYS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 145 SER Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 15 ILE Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain l residue 76 VAL Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 133 LYS Chi-restraints excluded: chain m residue 12 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 14 GLU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 38 SER Chi-restraints excluded: chain r residue 49 THR Chi-restraints excluded: chain s residue 19 VAL Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 83 HIS Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 45 ASN Chi-restraints excluded: chain t residue 65 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 110 GLN Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 38 GLU Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 91 LYS Chi-restraints excluded: chain S residue 10 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 14 VAL Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 2 residue 5 GLU Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 7 residue 19 SER Chi-restraints excluded: chain 7 residue 49 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 613 optimal weight: 10.0000 chunk 822 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 711 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 773 optimal weight: 9.9990 chunk 323 optimal weight: 0.9980 chunk 793 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 135 GLN d 50 GLN ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 67 ASN g 68 ASN g 129 ASN j 78 ASN ** n 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.154579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110741 restraints weight = 175578.269| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.18 r_work: 0.2902 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 152533 Z= 0.140 Angle : 0.556 13.516 228987 Z= 0.295 Chirality : 0.035 0.319 29403 Planarity : 0.004 0.114 11764 Dihedral : 22.954 179.559 77744 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 2.56 % Allowed : 23.19 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.46 (0.12), residues: 5202 helix: 0.96 (0.13), residues: 1610 sheet: -0.04 (0.16), residues: 1054 loop : -1.25 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 200 HIS 0.008 0.001 HIS i 68 PHE 0.018 0.001 PHE d 197 TYR 0.021 0.001 TYR i 6 ARG 0.008 0.000 ARG d 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36548.97 seconds wall clock time: 636 minutes 41.55 seconds (38201.55 seconds total)