Starting phenix.real_space_refine on Thu Mar 21 04:31:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xza_10656/03_2024/6xza_10656_updated.pdb" } resolution = 2.66 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= -0.015 sd= 0.734 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: 5 Type Number sf(0) Gaussians P 4618 5.49 5 S 150 5.16 5 C 72322 2.51 5 N 26818 2.21 5 O 40075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B1 GLU 52": "OE1" <-> "OE2" Residue "B1 GLU 78": "OE1" <-> "OE2" Residue "B1 GLU 140": "OE1" <-> "OE2" Residue "B1 GLU 142": "OE1" <-> "OE2" Residue "B1 GLU 145": "OE1" <-> "OE2" Residue "B1 ARG 225": "NH1" <-> "NH2" Residue "C1 GLU 82": "OE1" <-> "OE2" Residue "C1 GLU 110": "OE1" <-> "OE2" Residue "C1 GLU 125": "OE1" <-> "OE2" Residue "C1 ARG 131": "NH1" <-> "NH2" Residue "C1 GLU 161": "OE1" <-> "OE2" Residue "C1 GLU 166": "OE1" <-> "OE2" Residue "D1 GLU 147": "OE1" <-> "OE2" Residue "D1 GLU 163": "OE1" <-> "OE2" Residue "E1 GLU 55": "OE1" <-> "OE2" Residue "E1 GLU 65": "OE1" <-> "OE2" Residue "E1 GLU 162": "OE1" <-> "OE2" Residue "E1 GLU 163": "OE1" <-> "OE2" Residue "F1 ARG 2": "NH1" <-> "NH2" Residue "F1 GLU 69": "OE1" <-> "OE2" Residue "F1 GLU 75": "OE1" <-> "OE2" Residue "F1 GLU 98": "OE1" <-> "OE2" Residue "G1 GLU 21": "OE1" <-> "OE2" Residue "G1 GLU 40": "OE1" <-> "OE2" Residue "G1 GLU 60": "OE1" <-> "OE2" Residue "G1 GLU 67": "OE1" <-> "OE2" Residue "G1 GLU 123": "OE1" <-> "OE2" Residue "G1 GLU 129": "OE1" <-> "OE2" Residue "G1 GLU 146": "OE1" <-> "OE2" Residue "H1 GLU 42": "OE1" <-> "OE2" Residue "H1 GLU 43": "OE1" <-> "OE2" Residue "H1 GLU 47": "OE1" <-> "OE2" Residue "H1 GLU 52": "OE1" <-> "OE2" Residue "H1 GLU 58": "OE1" <-> "OE2" Residue "I1 ARG 119": "NH1" <-> "NH2" Residue "I1 ARG 124": "NH1" <-> "NH2" Residue "J1 GLU 24": "OE1" <-> "OE2" Residue "J1 GLU 27": "OE1" <-> "OE2" Residue "J1 GLU 78": "OE1" <-> "OE2" Residue "J1 GLU 81": "OE1" <-> "OE2" Residue "K1 GLU 94": "OE1" <-> "OE2" Residue "L1 GLU 25": "OE1" <-> "OE2" Residue "L1 ARG 56": "NH1" <-> "NH2" Residue "L1 GLU 76": "OE1" <-> "OE2" Residue "M1 GLU 47": "OE1" <-> "OE2" Residue "M1 GLU 50": "OE1" <-> "OE2" Residue "M1 GLU 72": "OE1" <-> "OE2" Residue "N1 GLU 26": "OE1" <-> "OE2" Residue "N1 GLU 39": "OE1" <-> "OE2" Residue "N1 ARG 65": "NH1" <-> "NH2" Residue "O1 GLU 6": "OE1" <-> "OE2" Residue "O1 GLU 14": "OE1" <-> "OE2" Residue "O1 GLU 26": "OE1" <-> "OE2" Residue "O1 GLU 83": "OE1" <-> "OE2" Residue "O1 ARG 89": "NH1" <-> "NH2" Residue "P1 ARG 28": "NH1" <-> "NH2" Residue "P1 GLU 47": "OE1" <-> "OE2" Residue "P1 GLU 77": "OE1" <-> "OE2" Residue "Q1 GLU 49": "OE1" <-> "OE2" Residue "Q1 GLU 80": "OE1" <-> "OE2" Residue "R1 GLU 20": "OE1" <-> "OE2" Residue "S1 GLU 24": "OE1" <-> "OE2" Residue "T1 GLU 53": "OE1" <-> "OE2" Residue "U1 GLU 36": "OE1" <-> "OE2" Residue "U1 GLU 39": "OE1" <-> "OE2" Residue "C2 ARG 52": "NH1" <-> "NH2" Residue "C2 ARG 63": "NH1" <-> "NH2" Residue "C2 ARG 80": "NH1" <-> "NH2" Residue "C2 GLU 82": "OE1" <-> "OE2" Residue "C2 GLU 100": "OE1" <-> "OE2" Residue "C2 ARG 133": "NH1" <-> "NH2" Residue "C2 ARG 167": "NH1" <-> "NH2" Residue "C2 ARG 177": "NH1" <-> "NH2" Residue "C2 ARG 182": "NH1" <-> "NH2" Residue "C2 GLU 185": "OE1" <-> "OE2" Residue "C2 ARG 189": "NH1" <-> "NH2" Residue "C2 ARG 203": "NH1" <-> "NH2" Residue "C2 ARG 212": "NH1" <-> "NH2" Residue "C2 GLU 236": "OE1" <-> "OE2" Residue "D2 ARG 13": "NH1" <-> "NH2" Residue "D2 GLU 28": "OE1" <-> "OE2" Residue "D2 ARG 33": "NH1" <-> "NH2" Residue "D2 ARG 59": "NH1" <-> "NH2" Residue "D2 GLU 64": "OE1" <-> "OE2" Residue "D2 GLU 74": "OE1" <-> "OE2" Residue "D2 ARG 77": "NH1" <-> "NH2" Residue "D2 GLU 81": "OE1" <-> "OE2" Residue "D2 ARG 83": "NH1" <-> "NH2" Residue "D2 GLU 86": "OE1" <-> "OE2" Residue "D2 GLU 88": "OE1" <-> "OE2" Residue "D2 ARG 169": "NH1" <-> "NH2" Residue "D2 ARG 184": "NH1" <-> "NH2" Residue "E2 GLU 2": "OE1" <-> "OE2" Residue "E2 ARG 21": "NH1" <-> "NH2" Residue "E2 ARG 44": "NH1" <-> "NH2" Residue "E2 ARG 49": "NH1" <-> "NH2" Residue "E2 ARG 61": "NH1" <-> "NH2" Residue "E2 ARG 88": "NH1" <-> "NH2" Residue "E2 ARG 102": "NH1" <-> "NH2" Residue "E2 GLU 111": "OE1" <-> "OE2" Residue "E2 GLU 122": "OE1" <-> "OE2" Residue "E2 GLU 127": "OE1" <-> "OE2" Residue "E2 GLU 144": "OE1" <-> "OE2" Residue "E2 GLU 152": "OE1" <-> "OE2" Residue "E2 GLU 155": "OE1" <-> "OE2" Residue "E2 ARG 162": "NH1" <-> "NH2" Residue "E2 ARG 170": "NH1" <-> "NH2" Residue "F2 GLU 11": "OE1" <-> "OE2" Residue "F2 GLU 32": "OE1" <-> "OE2" Residue "F2 GLU 42": "OE1" <-> "OE2" Residue "F2 ARG 71": "NH1" <-> "NH2" Residue "F2 ARG 92": "NH1" <-> "NH2" Residue "F2 GLU 94": "OE1" <-> "OE2" Residue "F2 ARG 102": "NH1" <-> "NH2" Residue "F2 ARG 110": "NH1" <-> "NH2" Residue "F2 ARG 115": "NH1" <-> "NH2" Residue "F2 ARG 133": "NH1" <-> "NH2" Residue "F2 GLU 164": "OE1" <-> "OE2" Residue "F2 GLU 165": "OE1" <-> "OE2" Residue "G2 ARG 3": "NH1" <-> "NH2" Residue "G2 GLU 42": "OE1" <-> "OE2" Residue "G2 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 ARG 153": "NH1" <-> "NH2" Residue "G2 GLU 155": "OE1" <-> "OE2" Residue "G2 ARG 163": "NH1" <-> "NH2" Residue "G2 ARG 170": "NH1" <-> "NH2" Residue "G2 GLU 173": "OE1" <-> "OE2" Residue "H2 GLU 87": "OE1" <-> "OE2" Residue "H2 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 GLU 114": "OE1" <-> "OE2" Residue "H2 GLU 133": "OE1" <-> "OE2" Residue "J2 GLU 9": "OE1" <-> "OE2" Residue "J2 ARG 13": "NH1" <-> "NH2" Residue "J2 ARG 37": "NH1" <-> "NH2" Residue "J2 GLU 90": "OE1" <-> "OE2" Residue "J2 GLU 91": "OE1" <-> "OE2" Residue "J2 ARG 96": "NH1" <-> "NH2" Residue "J2 GLU 102": "OE1" <-> "OE2" Residue "J2 ARG 120": "NH1" <-> "NH2" Residue "K2 GLU 4": "OE1" <-> "OE2" Residue "K2 GLU 106": "OE1" <-> "OE2" Residue "K2 GLU 110": "OE1" <-> "OE2" Residue "L2 GLU 10": "OE1" <-> "OE2" Residue "L2 ARG 21": "NH1" <-> "NH2" Residue "L2 ARG 33": "NH1" <-> "NH2" Residue "L2 ARG 41": "NH1" <-> "NH2" Residue "L2 ARG 47": "NH1" <-> "NH2" Residue "L2 ARG 60": "NH1" <-> "NH2" Residue "L2 GLU 76": "OE1" <-> "OE2" Residue "L2 ARG 78": "NH1" <-> "NH2" Residue "L2 GLU 106": "OE1" <-> "OE2" Residue "L2 ARG 126": "NH1" <-> "NH2" Residue "M2 ARG 10": "NH1" <-> "NH2" Residue "M2 ARG 18": "NH1" <-> "NH2" Residue "M2 ARG 40": "NH1" <-> "NH2" Residue "M2 ARG 44": "NH1" <-> "NH2" Residue "M2 GLU 47": "OE1" <-> "OE2" Residue "M2 ARG 50": "NH1" <-> "NH2" Residue "M2 ARG 59": "NH1" <-> "NH2" Residue "M2 GLU 90": "OE1" <-> "OE2" Residue "M2 GLU 104": "OE1" <-> "OE2" Residue "M2 ARG 114": "NH1" <-> "NH2" Residue "N2 ARG 8": "NH1" <-> "NH2" Residue "N2 ARG 12": "NH1" <-> "NH2" Residue "N2 ARG 17": "NH1" <-> "NH2" Residue "N2 ARG 22": "NH1" <-> "NH2" Residue "N2 GLU 32": "OE1" <-> "OE2" Residue "N2 GLU 43": "OE1" <-> "OE2" Residue "N2 ARG 46": "NH1" <-> "NH2" Residue "N2 GLU 49": "OE1" <-> "OE2" Residue "N2 ARG 63": "NH1" <-> "NH2" Residue "N2 ARG 64": "NH1" <-> "NH2" Residue "N2 ARG 69": "NH1" <-> "NH2" Residue "N2 ARG 71": "NH1" <-> "NH2" Residue "N2 GLU 82": "OE1" <-> "OE2" Residue "N2 ARG 96": "NH1" <-> "NH2" Residue "N2 ARG 118": "NH1" <-> "NH2" Residue "N2 GLU 120": "OE1" <-> "OE2" Residue "O2 ARG 10": "NH1" <-> "NH2" Residue "O2 ARG 16": "NH1" <-> "NH2" Residue "O2 ARG 25": "NH1" <-> "NH2" Residue "O2 GLU 55": "OE1" <-> "OE2" Residue "O2 GLU 60": "OE1" <-> "OE2" Residue "O2 GLU 80": "OE1" <-> "OE2" Residue "O2 ARG 81": "NH1" <-> "NH2" Residue "O2 ARG 94": "NH1" <-> "NH2" Residue "O2 ARG 102": "NH1" <-> "NH2" Residue "O2 ARG 111": "NH1" <-> "NH2" Residue "O2 GLU 112": "OE1" <-> "OE2" Residue "P2 ARG 21": "NH1" <-> "NH2" Residue "P2 ARG 39": "NH1" <-> "NH2" Residue "P2 ARG 62": "NH1" <-> "NH2" Residue "P2 ARG 89": "NH1" <-> "NH2" Residue "P2 ARG 101": "NH1" <-> "NH2" Residue "P2 ARG 109": "NH1" <-> "NH2" Residue "Q2 ARG 3": "NH1" <-> "NH2" Residue "Q2 ARG 6": "NH1" <-> "NH2" Residue "Q2 ARG 13": "NH1" <-> "NH2" Residue "Q2 ARG 33": "NH1" <-> "NH2" Residue "Q2 ARG 48": "NH1" <-> "NH2" Residue "Q2 ARG 70": "NH1" <-> "NH2" Residue "Q2 GLU 89": "OE1" <-> "OE2" Residue "Q2 GLU 111": "OE1" <-> "OE2" Residue "R2 ARG 21": "NH1" <-> "NH2" Residue "R2 GLU 23": "OE1" <-> "OE2" Residue "R2 GLU 31": "OE1" <-> "OE2" Residue "R2 GLU 37": "OE1" <-> "OE2" Residue "R2 ARG 68": "NH1" <-> "NH2" Residue "R2 GLU 70": "OE1" <-> "OE2" Residue "R2 ARG 78": "NH1" <-> "NH2" Residue "R2 ARG 79": "NH1" <-> "NH2" Residue "R2 ARG 84": "NH1" <-> "NH2" Residue "S2 ARG 84": "NH1" <-> "NH2" Residue "S2 ARG 88": "NH1" <-> "NH2" Residue "S2 ARG 95": "NH1" <-> "NH2" Residue "S2 ARG 110": "NH1" <-> "NH2" Residue "T2 GLU 56": "OE1" <-> "OE2" Residue "T2 ARG 73": "NH1" <-> "NH2" Residue "U2 ARG 6": "NH1" <-> "NH2" Residue "U2 ARG 7": "NH1" <-> "NH2" Residue "U2 GLU 10": "OE1" <-> "OE2" Residue "U2 GLU 62": "OE1" <-> "OE2" Residue "U2 ARG 82": "NH1" <-> "NH2" Residue "U2 ARG 86": "NH1" <-> "NH2" Residue "U2 ARG 94": "NH1" <-> "NH2" Residue "W2 GLU 29": "OE1" <-> "OE2" Residue "W2 GLU 70": "OE1" <-> "OE2" Residue "W2 GLU 83": "OE1" <-> "OE2" Residue "W2 GLU 85": "OE1" <-> "OE2" Residue "X2 ARG 3": "NH1" <-> "NH2" Residue "X2 ARG 11": "NH1" <-> "NH2" Residue "X2 ARG 18": "NH1" <-> "NH2" Residue "X2 ARG 37": "NH1" <-> "NH2" Residue "X2 GLU 41": "OE1" <-> "OE2" Residue "X2 ARG 50": "NH1" <-> "NH2" Residue "X2 ARG 57": "NH1" <-> "NH2" Residue "X2 ARG 74": "NH1" <-> "NH2" Residue "X2 TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y2 GLU 5": "OE1" <-> "OE2" Residue "Y2 GLU 24": "OE1" <-> "OE2" Residue "Y2 ARG 29": "NH1" <-> "NH2" Residue "Y2 ARG 47": "NH1" <-> "NH2" Residue "Y2 ARG 52": "NH1" <-> "NH2" Residue "Y2 GLU 59": "OE1" <-> "OE2" Residue "Z2 ARG 11": "NH1" <-> "NH2" Residue "Z2 ARG 30": "NH1" <-> "NH2" Residue "Z2 ARG 45": "NH1" <-> "NH2" Residue "Z2 GLU 58": "OE1" <-> "OE2" Residue "a2 ARG 10": "NH1" <-> "NH2" Residue "a2 ARG 16": "NH1" <-> "NH2" Residue "a2 ARG 52": "NH1" <-> "NH2" Residue "b2 ARG 44": "NH1" <-> "NH2" Residue "b2 GLU 51": "OE1" <-> "OE2" Residue "c2 ARG 3": "NH1" <-> "NH2" Residue "c2 ARG 12": "NH1" <-> "NH2" Residue "c2 ARG 14": "NH1" <-> "NH2" Residue "c2 ARG 19": "NH1" <-> "NH2" Residue "c2 ARG 21": "NH1" <-> "NH2" Residue "c2 ARG 33": "NH1" <-> "NH2" Residue "c2 ARG 41": "NH1" <-> "NH2" Residue "d2 ARG 13": "NH1" <-> "NH2" Residue "d2 ARG 30": "NH1" <-> "NH2" Residue "d2 ARG 40": "NH1" <-> "NH2" Residue "d2 ARG 42": "NH1" <-> "NH2" Residue "e2 ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143983 Number of models: 1 Model: "" Number of chains: 54 Chain: "A1" Number of atoms: 32681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32681 Classifications: {'RNA': 1523} Modifications used: {'rna2p_pur': 117, 'rna2p_pyr': 86, 'rna3p_pur': 752, 'rna3p_pyr': 568} Link IDs: {'rna2p': 203, 'rna3p': 1319} Chain breaks: 9 Chain: "B1" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C1" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D1" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E1" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "F1" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G1" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H1" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I1" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J1" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 796 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "K1" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L1" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain breaks: 1 Chain: "M1" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N1" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O1" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P1" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q1" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R1" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S1" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U1" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "A2" Number of atoms: 62252 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 429, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Conformer: "B" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 429, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 bond proxies already assigned to first conformer: 69623 Chain: "B2" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C2" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D2" Number of atoms: 1566 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E2" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F2" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G2" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H2" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 128} Chain: "I2" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "J2" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K2" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L2" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M2" Number of atoms: 1075 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N2" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "O2" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "P2" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q2" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R2" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S2" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T2" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U2" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V2" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W2" Number of atoms: 580 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X2" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y2" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z2" Number of atoms: 449 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a2" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "b2" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "d2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e2" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "f2" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "A2" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'DI0': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" P A CA22888 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B CA22888 " occ=0.47 residue: pdb=" N AMEQD2 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2AMEQD2 150 " occ=0.49 residue: pdb=" N AARGW2 41 " occ=0.51 ... (9 atoms not shown) pdb=" NH2AARGW2 41 " occ=0.51 residue: pdb=" N AALAZ2 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALAZ2 2 " occ=0.50 residue: pdb=" N ALYSZ2 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYSZ2 3 " occ=0.50 Time building chain proxies: 75.50, per 1000 atoms: 0.52 Number of scatterers: 143983 At special positions: 0 Unit cell: (251.12, 255.42, 271.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 4618 15.00 O 40075 8.00 N 26818 7.00 C 72322 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 Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23094 O5' AA11080 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.62 Conformation dependent library (CDL) restraints added in 6.4 seconds 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10534 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: 180 helices and 67 sheets defined 39.9% alpha, 18.8% beta 1540 base pairs and 2493 stacking pairs defined. Time for finding SS restraints: 76.88 Creating SS restraints... Processing helix chain 'B1' and resid 5 through 13 Processing helix chain 'B1' and resid 24 through 32 removed outlier: 4.095A pdb=" N LYSB1 28 " --> pdb=" O ASNB1 24 " (cutoff:3.500A) Proline residue: B1 29 - end of helix removed outlier: 5.762A pdb=" N PHEB1 32 " --> pdb=" O LYSB1 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 24 through 32' Processing helix chain 'B1' and resid 42 through 64 Proline residue: B1 48 - end of helix removed outlier: 3.790A pdb=" N LYSB1 64 " --> pdb=" O ILEB1 60 " (cutoff:3.500A) Processing helix chain 'B1' and resid 76 through 88 removed outlier: 3.794A pdb=" N CYSB1 87 " --> pdb=" O ALAB1 83 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASPB1 88 " --> pdb=" O ALAB1 84 " (cutoff:3.500A) Processing helix chain 'B1' and resid 103 through 123 removed outlier: 4.559A pdb=" N GLNB1 109 " --> pdb=" O LYSB1 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SERB1 110 " --> pdb=" O THRB1 106 " (cutoff:3.500A) Processing helix chain 'B1' and resid 130 through 148 removed outlier: 5.985A pdb=" N ALAB1 134 " --> pdb=" O THRB1 130 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEUB1 135 " --> pdb=" O LYSB1 131 " (cutoff:3.500A) Processing helix chain 'B1' and resid 165 through 170 removed outlier: 3.610A pdb=" N HISB1 170 " --> pdb=" O ALAB1 166 " (cutoff:3.500A) Processing helix chain 'B1' and resid 171 through 180 Processing helix chain 'B1' and resid 206 through 227 Processing helix chain 'C1' and resid 6 through 12 removed outlier: 3.885A pdb=" N ARGC1 11 " --> pdb=" O PROC1 7 " (cutoff:3.500A) Processing helix chain 'C1' and resid 28 through 48 removed outlier: 3.617A pdb=" N ALAC1 48 " --> pdb=" O THRC1 44 " (cutoff:3.500A) Processing helix chain 'C1' and resid 72 through 78 Processing helix chain 'C1' and resid 81 through 96 removed outlier: 3.730A pdb=" N ASPC1 93 " --> pdb=" O LYSC1 89 " (cutoff:3.500A) Processing helix chain 'C1' and resid 108 through 113 removed outlier: 3.947A pdb=" N ASPC1 112 " --> pdb=" O LYSC1 108 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALAC1 113 " --> pdb=" O PROC1 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 108 through 113' Processing helix chain 'C1' and resid 114 through 127 Processing helix chain 'C1' and resid 129 through 145 removed outlier: 3.807A pdb=" N GLYC1 145 " --> pdb=" O ALAC1 141 " (cutoff:3.500A) Processing helix chain 'D1' and resid 7 through 16 removed outlier: 4.575A pdb=" N LEUD1 11 " --> pdb=" O PROD1 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SERD1 12 " --> pdb=" O LYSD1 8 " (cutoff:3.500A) Processing helix chain 'D1' and resid 27 through 32 removed outlier: 3.655A pdb=" N LYSD1 31 " --> pdb=" O ALAD1 27 " (cutoff:3.500A) Processing helix chain 'D1' and resid 49 through 66 Processing helix chain 'D1' and resid 68 through 83 removed outlier: 5.103A pdb=" N LYSD1 83 " --> pdb=" O ALAD1 79 " (cutoff:3.500A) Processing helix chain 'D1' and resid 85 through 97 removed outlier: 4.041A pdb=" N ARGD1 97 " --> pdb=" O LEUD1 93 " (cutoff:3.500A) Processing helix chain 'D1' and resid 98 through 106 Processing helix chain 'D1' and resid 110 through 121 removed outlier: 3.873A pdb=" N LYSD1 121 " --> pdb=" O LEUD1 117 " (cutoff:3.500A) Processing helix chain 'D1' and resid 146 through 151 removed outlier: 4.790A pdb=" N LYSD1 151 " --> pdb=" O GLUD1 147 " (cutoff:3.500A) Processing helix chain 'D1' and resid 152 through 166 removed outlier: 3.716A pdb=" N LYSD1 156 " --> pdb=" O GLND1 152 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLUD1 166 " --> pdb=" O ALAD1 162 " (cutoff:3.500A) Processing helix chain 'D1' and resid 187 through 192 removed outlier: 3.866A pdb=" N LEUD1 191 " --> pdb=" O GLUD1 187 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SERD1 192 " --> pdb=" O ARGD1 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D1' and resid 187 through 192' Processing helix chain 'D1' and resid 196 through 206 removed outlier: 3.784A pdb=" N ILED1 200 " --> pdb=" O ASND1 196 " (cutoff:3.500A) Processing helix chain 'E1' and resid 55 through 71 removed outlier: 4.301A pdb=" N ASNE1 70 " --> pdb=" O LYSE1 66 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N METE1 71 " --> pdb=" O ALAE1 67 " (cutoff:3.500A) Processing helix chain 'E1' and resid 108 through 119 removed outlier: 3.623A pdb=" N GLYE1 119 " --> pdb=" O LEUE1 115 " (cutoff:3.500A) Processing helix chain 'E1' and resid 132 through 148 removed outlier: 5.801A pdb=" N ASNE1 148 " --> pdb=" O LEUE1 144 " (cutoff:3.500A) Processing helix chain 'E1' and resid 149 through 158 Processing helix chain 'F1' and resid 15 through 33 Proline residue: F1 19 - end of helix removed outlier: 3.750A pdb=" N ALAF1 32 " --> pdb=" O ALAF1 28 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUF1 33 " --> pdb=" O ILEF1 29 " (cutoff:3.500A) Processing helix chain 'F1' and resid 67 through 81 removed outlier: 3.530A pdb=" N ILEF1 71 " --> pdb=" O PROF1 67 " (cutoff:3.500A) Processing helix chain 'F1' and resid 100 through 105 Processing helix chain 'G1' and resid 20 through 31 Processing helix chain 'G1' and resid 35 through 55 removed outlier: 3.557A pdb=" N GLNG1 52 " --> pdb=" O GLUG1 48 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARGG1 53 " --> pdb=" O THRG1 49 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SERG1 54 " --> pdb=" O LEUG1 50 " (cutoff:3.500A) Processing helix chain 'G1' and resid 57 through 70 removed outlier: 4.814A pdb=" N ALAG1 61 " --> pdb=" O SERG1 57 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASNG1 68 " --> pdb=" O VALG1 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALG1 69 " --> pdb=" O ALAG1 65 " (cutoff:3.500A) Processing helix chain 'G1' and resid 92 through 112 removed outlier: 3.965A pdb=" N ARGG1 111 " --> pdb=" O ALAG1 107 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLYG1 112 " --> pdb=" O ALAG1 108 " (cutoff:3.500A) Processing helix chain 'G1' and resid 115 through 130 Processing helix chain 'G1' and resid 132 through 149 Processing helix chain 'H1' and resid 5 through 21 Processing helix chain 'H1' and resid 30 through 44 Processing helix chain 'H1' and resid 112 through 120 Processing helix chain 'I1' and resid 34 through 40 removed outlier: 4.145A pdb=" N GLYI1 40 " --> pdb=" O GLUI1 36 " (cutoff:3.500A) Processing helix chain 'I1' and resid 41 through 56 Proline residue: I1 51 - end of helix removed outlier: 3.927A pdb=" N LEUI1 54 " --> pdb=" O GLNI1 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VALI1 55 " --> pdb=" O PROI1 51 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASPI1 56 " --> pdb=" O LEUI1 52 " (cutoff:3.500A) Processing helix chain 'I1' and resid 71 through 92 Processing helix chain 'I1' and resid 94 through 102 Processing helix chain 'J1' and resid 14 through 33 Processing helix chain 'J1' and resid 80 through 90 removed outlier: 3.988A pdb=" N ARGJ1 89 " --> pdb=" O ASPJ1 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUJ1 90 " --> pdb=" O ALAJ1 86 " (cutoff:3.500A) Processing helix chain 'K1' and resid 46 through 51 removed outlier: 4.196A pdb=" N GLYK1 51 " --> pdb=" O ALAK1 47 " (cutoff:3.500A) Processing helix chain 'K1' and resid 54 through 59 removed outlier: 4.169A pdb=" N SERK1 58 " --> pdb=" O GLYK1 54 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THRK1 59 " --> pdb=" O SERK1 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K1' and resid 54 through 59' Processing helix chain 'K1' and resid 60 through 76 removed outlier: 3.620A pdb=" N VALK1 74 " --> pdb=" O CYSK1 70 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYSK1 75 " --> pdb=" O ALAK1 71 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLUK1 76 " --> pdb=" O ASPK1 72 " (cutoff:3.500A) Processing helix chain 'K1' and resid 92 through 104 removed outlier: 3.561A pdb=" N THRK1 96 " --> pdb=" O GLYK1 92 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILEK1 97 " --> pdb=" O ARGK1 93 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLYK1 104 " --> pdb=" O LEUK1 100 " (cutoff:3.500A) Processing helix chain 'L1' and resid 3 through 11 Proline residue: L1 11 - end of helix Processing helix chain 'L1' and resid 113 through 118 removed outlier: 3.934A pdb=" N TYRL1 117 " --> pdb=" O ALAL1 113 " (cutoff:3.500A) Processing helix chain 'M1' and resid 14 through 22 removed outlier: 4.096A pdb=" N THRM1 20 " --> pdb=" O VALM1 16 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SERM1 21 " --> pdb=" O ILEM1 17 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILEM1 22 " --> pdb=" O ALAM1 18 " (cutoff:3.500A) Processing helix chain 'M1' and resid 26 through 38 Processing helix chain 'M1' and resid 49 through 64 removed outlier: 4.288A pdb=" N LYSM1 62 " --> pdb=" O ASPM1 58 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHEM1 63 " --> pdb=" O GLUM1 59 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VALM1 64 " --> pdb=" O VALM1 60 " (cutoff:3.500A) Processing helix chain 'M1' and resid 66 through 84 removed outlier: 3.934A pdb=" N ARGM1 70 " --> pdb=" O GLUM1 66 " (cutoff:3.500A) Processing helix chain 'M1' and resid 85 through 94 Processing helix chain 'M1' and resid 106 through 111 Processing helix chain 'N1' and resid 3 through 24 removed outlier: 4.171A pdb=" N ALAN1 22 " --> pdb=" O ASPN1 18 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYSN1 23 " --> pdb=" O LYSN1 19 " (cutoff:3.500A) Processing helix chain 'N1' and resid 25 through 34 Processing helix chain 'N1' and resid 43 through 51 removed outlier: 3.720A pdb=" N GLNN1 49 " --> pdb=" O VALN1 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRN1 50 " --> pdb=" O LEUN1 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUN1 51 " --> pdb=" O LYSN1 47 " (cutoff:3.500A) Processing helix chain 'N1' and resid 80 through 91 Processing helix chain 'N1' and resid 52 through 57 Proline residue: N1 57 - end of helix Processing helix chain 'O1' and resid 4 through 16 Processing helix chain 'O1' and resid 24 through 44 removed outlier: 4.018A pdb=" N GLYO1 41 " --> pdb=" O ASNO1 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HISO1 42 " --> pdb=" O HISO1 38 " (cutoff:3.500A) Processing helix chain 'O1' and resid 49 through 74 removed outlier: 3.886A pdb=" N GLYO1 55 " --> pdb=" O HISO1 51 " (cutoff:3.500A) Processing helix chain 'O1' and resid 75 through 86 Processing helix chain 'P1' and resid 53 through 64 removed outlier: 3.526A pdb=" N ILEP1 57 " --> pdb=" O ASPP1 53 " (cutoff:3.500A) Processing helix chain 'P1' and resid 68 through 82 Processing helix chain 'R1' and resid 25 through 34 removed outlier: 4.201A pdb=" N ASNR1 31 " --> pdb=" O ALAR1 27 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYRR1 32 " --> pdb=" O THRR1 28 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILER1 33 " --> pdb=" O LEUR1 29 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THRR1 34 " --> pdb=" O LYSR1 30 " (cutoff:3.500A) Processing helix chain 'R1' and resid 41 through 46 Processing helix chain 'R1' and resid 48 through 66 Processing helix chain 'S1' and resid 12 through 26 removed outlier: 3.507A pdb=" N GLYS1 26 " --> pdb=" O ALAS1 22 " (cutoff:3.500A) Processing helix chain 'S1' and resid 70 through 76 removed outlier: 4.537A pdb=" N PHES1 74 " --> pdb=" O LYSS1 70 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALAS1 75 " --> pdb=" O LEUS1 71 " (cutoff:3.500A) Proline residue: S1 76 - end of helix No H-bonds generated for 'chain 'S1' and resid 70 through 76' Processing helix chain 'T1' and resid 4 through 41 removed outlier: 3.715A pdb=" N VALT1 35 " --> pdb=" O PHET1 31 " (cutoff:3.500A) Processing helix chain 'T1' and resid 44 through 65 Proline residue: T1 56 - end of helix Processing helix chain 'T1' and resid 68 through 87 removed outlier: 4.087A pdb=" N LEUT1 86 " --> pdb=" O GLNT1 82 " (cutoff:3.500A) Processing helix chain 'U1' and resid 11 through 27 removed outlier: 3.515A pdb=" N ALAU1 15 " --> pdb=" O PROU1 11 " (cutoff:3.500A) Processing helix chain 'U1' and resid 28 through 37 removed outlier: 3.800A pdb=" N GLUU1 36 " --> pdb=" O VALU1 32 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHEU1 37 " --> pdb=" O ARGU1 33 " (cutoff:3.500A) Processing helix chain 'U1' and resid 40 through 56 removed outlier: 4.449A pdb=" N HISU1 56 " --> pdb=" O ALAU1 52 " (cutoff:3.500A) Processing helix chain 'C2' and resid 10 through 15 removed outlier: 5.027A pdb=" N HISC2 15 " --> pdb=" O PROC2 11 " (cutoff:3.500A) Processing helix chain 'C2' and resid 30 through 35 removed outlier: 3.953A pdb=" N LEUC2 34 " --> pdb=" O PHEC2 30 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLUC2 35 " --> pdb=" O ALAC2 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 30 through 35' Processing helix chain 'C2' and resid 131 through 136 removed outlier: 3.683A pdb=" N ILEC2 135 " --> pdb=" O PROC2 131 " (cutoff:3.500A) Proline residue: C2 136 - end of helix No H-bonds generated for 'chain 'C2' and resid 131 through 136' Processing helix chain 'C2' and resid 207 through 215 removed outlier: 3.898A pdb=" N ALAC2 211 " --> pdb=" O LYSC2 207 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARGC2 214 " --> pdb=" O ALAC2 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLYC2 215 " --> pdb=" O ALAC2 211 " (cutoff:3.500A) Processing helix chain 'C2' and resid 221 through 226 removed outlier: 3.912A pdb=" N METC2 225 " --> pdb=" O ARGC2 221 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASNC2 226 " --> pdb=" O GLYC2 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 221 through 226' Processing helix chain 'C2' and resid 260 through 268 removed outlier: 3.698A pdb=" N ASPC2 264 " --> pdb=" O ASNC2 260 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYSC2 265 " --> pdb=" O LYSC2 261 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHEC2 266 " --> pdb=" O ARGC2 262 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILEC2 267 " --> pdb=" O THRC2 263 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VALC2 268 " --> pdb=" O ASPC2 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 260 through 268' Processing helix chain 'C2' and resid 197 through 202 removed outlier: 3.920A pdb=" N METC2 201 " --> pdb=" O ALAC2 198 " (cutoff:3.500A) Processing helix chain 'D2' and resid 56 through 61 removed outlier: 3.552A pdb=" N VALD2 60 " --> pdb=" O LYSD2 56 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THRD2 61 " --> pdb=" O ALAD2 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 56 through 61' Processing helix chain 'D2' and resid 62 through 72 removed outlier: 3.525A pdb=" N ALAD2 71 " --> pdb=" O HISD2 67 " (cutoff:3.500A) Processing helix chain 'D2' and resid 98 through 103 removed outlier: 4.507A pdb=" N ALAD2 102 " --> pdb=" O VALD2 98 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASPD2 103 " --> pdb=" O GLUD2 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 98 through 103' Processing helix chain 'D2' and resid 120 through 125 Processing helix chain 'D2' and resid 39 through 44 Processing helix chain 'E2' and resid 15 through 20 Processing helix chain 'E2' and resid 24 through 41 removed outlier: 3.562A pdb=" N ARGE2 40 " --> pdb=" O ALAE2 36 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLNE2 41 " --> pdb=" O ALAE2 37 " (cutoff:3.500A) Processing helix chain 'E2' and resid 48 through 53 removed outlier: 6.717A pdb=" N THRE2 53 " --> pdb=" O ARGE2 49 " (cutoff:3.500A) Processing helix chain 'E2' and resid 97 through 116 Processing helix chain 'E2' and resid 130 through 142 removed outlier: 3.527A pdb=" N LEUE2 134 " --> pdb=" O LYSE2 130 " (cutoff:3.500A) Processing helix chain 'E2' and resid 154 through 163 removed outlier: 4.562A pdb=" N ASNE2 163 " --> pdb=" O LEUE2 159 " (cutoff:3.500A) Processing helix chain 'E2' and resid 176 through 183 removed outlier: 3.575A pdb=" N ILEE2 181 " --> pdb=" O PROE2 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHEE2 183 " --> pdb=" O SERE2 179 " (cutoff:3.500A) Processing helix chain 'E2' and resid 189 through 201 Processing helix chain 'F2' and resid 2 through 11 removed outlier: 3.550A pdb=" N ASPF2 10 " --> pdb=" O ASPF2 6 " (cutoff:3.500A) Processing helix chain 'F2' and resid 12 through 21 removed outlier: 3.576A pdb=" N THRF2 18 " --> pdb=" O LYSF2 14 " (cutoff:3.500A) Processing helix chain 'F2' and resid 42 through 47 removed outlier: 4.104A pdb=" N ASPF2 46 " --> pdb=" O GLUF2 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYSF2 47 " --> pdb=" O ALAF2 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F2' and resid 42 through 47' Processing helix chain 'F2' and resid 48 through 62 removed outlier: 3.874A pdb=" N ASNF2 52 " --> pdb=" O LYSF2 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SERF2 61 " --> pdb=" O LEUF2 57 " (cutoff:3.500A) Processing helix chain 'F2' and resid 93 through 111 removed outlier: 3.708A pdb=" N ARGF2 102 " --> pdb=" O GLUF2 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILEF2 104 " --> pdb=" O PHEF2 100 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VALF2 108 " --> pdb=" O ILEF2 104 " (cutoff:3.500A) Proline residue: F2 109 - end of helix Processing helix chain 'F2' and resid 162 through 174 Processing helix chain 'G2' and resid 2 through 8 removed outlier: 4.034A pdb=" N ALAG2 7 " --> pdb=" O ARGG2 3 " (cutoff:3.500A) Proline residue: G2 8 - end of helix Processing helix chain 'G2' and resid 60 through 81 removed outlier: 3.663A pdb=" N THRG2 67 " --> pdb=" O ALAG2 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THRG2 80 " --> pdb=" O VALG2 76 " (cutoff:3.500A) Processing helix chain 'G2' and resid 137 through 153 removed outlier: 4.277A pdb=" N ARGG2 152 " --> pdb=" O LEUG2 148 " (cutoff:3.500A) Processing helix chain 'H2' and resid 4 through 22 removed outlier: 3.571A pdb=" N GLYH2 21 " --> pdb=" O GLUH2 17 " (cutoff:3.500A) Processing helix chain 'H2' and resid 34 through 49 Processing helix chain 'H2' and resid 56 through 68 removed outlier: 3.553A pdb=" N ARGH2 62 " --> pdb=" O THRH2 58 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLYH2 66 " --> pdb=" O ARGH2 62 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THRH2 67 " --> pdb=" O ALAH2 63 " (cutoff:3.500A) Proline residue: H2 68 - end of helix Processing helix chain 'H2' and resid 69 through 77 removed outlier: 4.013A pdb=" N LYSH2 73 " --> pdb=" O PHEH2 69 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASPH2 74 " --> pdb=" O GLUH2 70 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALAH2 75 " --> pdb=" O CYSH2 71 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHEH2 76 " --> pdb=" O LEUH2 72 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VALH2 77 " --> pdb=" O LYSH2 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 69 through 77' Processing helix chain 'H2' and resid 90 through 104 removed outlier: 5.845A pdb=" N ARGH2 94 " --> pdb=" O GLYH2 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSH2 97 " --> pdb=" O ALAH2 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLUH2 98 " --> pdb=" O ARGH2 94 " (cutoff:3.500A) Processing helix chain 'H2' and resid 123 through 129 Processing helix chain 'I2' and resid 24 through 32 removed outlier: 3.580A pdb=" N LEUI2 28 " --> pdb=" O VALI2 24 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLNI2 31 " --> pdb=" O ALAI2 27 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLYI2 32 " --> pdb=" O LEUI2 28 " (cutoff:3.500A) Processing helix chain 'I2' and resid 34 through 47 Processing helix chain 'I2' and resid 75 through 85 Processing helix chain 'I2' and resid 102 through 115 Processing helix chain 'I2' and resid 121 through 137 Processing helix chain 'J2' and resid 24 through 38 removed outlier: 4.034A pdb=" N GLUJ2 31 " --> pdb=" O ARGJ2 27 " (cutoff:3.500A) Processing helix chain 'J2' and resid 88 through 96 Processing helix chain 'J2' and resid 97 through 110 removed outlier: 4.234A pdb=" N ILEJ2 101 " --> pdb=" O PROJ2 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N METJ2 108 " --> pdb=" O ALAJ2 104 " (cutoff:3.500A) Proline residue: J2 110 - end of helix Processing helix chain 'J2' and resid 112 through 122 removed outlier: 3.917A pdb=" N LYSJ2 121 " --> pdb=" O ALAJ2 117 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEUJ2 122 " --> pdb=" O METJ2 118 " (cutoff:3.500A) Processing helix chain 'K2' and resid 104 through 109 removed outlier: 4.814A pdb=" N ARGK2 108 " --> pdb=" O THRK2 104 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SERK2 109 " --> pdb=" O ARGK2 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K2' and resid 104 through 109' Processing helix chain 'K2' and resid 112 through 119 Processing helix chain 'L2' and resid 37 through 42 removed outlier: 3.740A pdb=" N ARGL2 41 " --> pdb=" O GLYL2 37 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SERL2 42 " --> pdb=" O GLNL2 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 37 through 42' Processing helix chain 'L2' and resid 56 through 62 removed outlier: 3.510A pdb=" N LEUL2 61 " --> pdb=" O LEUL2 57 " (cutoff:3.500A) Proline residue: L2 62 - end of helix Processing helix chain 'L2' and resid 68 through 75 removed outlier: 4.126A pdb=" N ALAL2 72 " --> pdb=" O SERL2 68 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEL2 73 " --> pdb=" O ARGL2 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRL2 74 " --> pdb=" O LYSL2 70 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALAL2 75 " --> pdb=" O ALAL2 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 68 through 75' Processing helix chain 'L2' and resid 78 through 85 removed outlier: 3.811A pdb=" N LEUL2 82 " --> pdb=" O ARGL2 78 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALAL2 83 " --> pdb=" O LEUL2 79 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYSL2 84 " --> pdb=" O SERL2 80 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALL2 85 " --> pdb=" O ASPL2 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 78 through 85' Processing helix chain 'L2' and resid 91 through 99 Processing helix chain 'L2' and resid 128 through 139 removed outlier: 3.647A pdb=" N GLYL2 139 " --> pdb=" O ILEL2 135 " (cutoff:3.500A) Processing helix chain 'M2' and resid 42 through 58 removed outlier: 3.508A pdb=" N LYSM2 58 " --> pdb=" O THRM2 54 " (cutoff:3.500A) Processing helix chain 'M2' and resid 109 through 125 removed outlier: 3.603A pdb=" N GLUM2 115 " --> pdb=" O GLUM2 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYSM2 123 " --> pdb=" O LEUM2 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEUM2 124 " --> pdb=" O ALAM2 120 " (cutoff:3.500A) Proline residue: M2 125 - end of helix Processing helix chain 'N2' and resid 13 through 32 Processing helix chain 'N2' and resid 38 through 57 removed outlier: 4.270A pdb=" N ARGN2 46 " --> pdb=" O LYSN2 42 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VALN2 47 " --> pdb=" O GLUN2 43 " (cutoff:3.500A) Proline residue: N2 50 - end of helix removed outlier: 4.653A pdb=" N THRN2 57 " --> pdb=" O THRN2 53 " (cutoff:3.500A) Processing helix chain 'N2' and resid 59 through 71 Processing helix chain 'N2' and resid 72 through 88 removed outlier: 4.831A pdb=" N GLYN2 84 " --> pdb=" O PHEN2 80 " (cutoff:3.500A) Proline residue: N2 85 - end of helix Processing helix chain 'N2' and resid 119 through 124 removed outlier: 4.281A pdb=" N GLUN2 123 " --> pdb=" O GLUN2 120 " (cutoff:3.500A) Processing helix chain 'O2' and resid 2 through 22 removed outlier: 3.537A pdb=" N ARGO2 10 " --> pdb=" O ALAO2 6 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARGO2 13 " --> pdb=" O ARGO2 9 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALAO2 14 " --> pdb=" O ARGO2 10 " (cutoff:3.500A) Processing helix chain 'O2' and resid 55 through 63 removed outlier: 5.846A pdb=" N GLNO2 61 " --> pdb=" O ALAO2 57 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEUO2 62 " --> pdb=" O ILEO2 58 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYSO2 63 " --> pdb=" O ALAO2 59 " (cutoff:3.500A) Processing helix chain 'O2' and resid 67 through 86 removed outlier: 3.569A pdb=" N GLUO2 84 " --> pdb=" O GLUO2 80 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSO2 85 " --> pdb=" O ARGO2 81 " (cutoff:3.500A) Processing helix chain 'O2' and resid 101 through 114 Processing helix chain 'P2' and resid 2 through 14 removed outlier: 3.748A pdb=" N GLUP2 11 " --> pdb=" O GLNP2 7 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLNP2 12 " --> pdb=" O LEUP2 8 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYSP2 14 " --> pdb=" O GLNP2 10 " (cutoff:3.500A) Processing helix chain 'P2' and resid 97 through 104 removed outlier: 4.680A pdb=" N ARGP2 101 " --> pdb=" O LEUP2 97 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLUP2 102 " --> pdb=" O TYRP2 98 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARGP2 103 " --> pdb=" O TYRP2 99 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THRP2 104 " --> pdb=" O LEUP2 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P2' and resid 97 through 104' Processing helix chain 'Q2' and resid 6 through 22 removed outlier: 3.568A pdb=" N GLNQ2 20 " --> pdb=" O LYSQ2 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYSQ2 22 " --> pdb=" O LEUQ2 18 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 26 through 31 removed outlier: 3.806A pdb=" N ARGQ2 30 " --> pdb=" O GLYQ2 26 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 32 through 37 removed outlier: 3.651A pdb=" N GLNQ2 37 " --> pdb=" O ARGQ2 33 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 39 through 73 removed outlier: 3.856A pdb=" N ARGQ2 51 " --> pdb=" O TYRQ2 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSQ2 54 " --> pdb=" O ARGQ2 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARGQ2 55 " --> pdb=" O ARGQ2 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARGQ2 58 " --> pdb=" O LYSQ2 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASNQ2 72 " --> pdb=" O ALAQ2 68 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 75 through 87 Processing helix chain 'Q2' and resid 91 through 102 Processing helix chain 'Q2' and resid 103 through 118 Processing helix chain 'S2' and resid 13 through 25 removed outlier: 3.762A pdb=" N LEUS2 19 " --> pdb=" O GLNS2 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VALS2 20 " --> pdb=" O LYSS2 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEUS2 23 " --> pdb=" O LEUS2 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILES2 24 " --> pdb=" O VALS2 20 " (cutoff:3.500A) Processing helix chain 'S2' and resid 28 through 39 removed outlier: 3.574A pdb=" N ASPS2 34 " --> pdb=" O SERS2 30 " (cutoff:3.500A) Processing helix chain 'S2' and resid 41 through 61 removed outlier: 3.752A pdb=" N VALS2 45 " --> pdb=" O LYSS2 41 " (cutoff:3.500A) Processing helix chain 'T2' and resid 3 through 11 removed outlier: 3.980A pdb=" N LYST2 9 " --> pdb=" O GLUT2 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALT2 10 " --> pdb=" O ARGT2 6 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEUT2 11 " --> pdb=" O LEUT2 7 " (cutoff:3.500A) Processing helix chain 'T2' and resid 17 through 27 Processing helix chain 'T2' and resid 39 through 51 Processing helix chain 'U2' and resid 66 through 71 removed outlier: 3.887A pdb=" N VALU2 70 " --> pdb=" O GLNU2 66 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALAU2 71 " --> pdb=" O VALU2 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U2' and resid 66 through 71' Processing helix chain 'V2' and resid 13 through 24 Processing helix chain 'V2' and resid 43 through 53 removed outlier: 3.533A pdb=" N METV2 50 " --> pdb=" O LYSV2 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAV2 52 " --> pdb=" O METV2 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYSV2 53 " --> pdb=" O ASNV2 49 " (cutoff:3.500A) Processing helix chain 'V2' and resid 54 through 59 removed outlier: 4.117A pdb=" N SERV2 58 " --> pdb=" O ALAV2 54 " (cutoff:3.500A) Processing helix chain 'X2' and resid 52 through 63 Processing helix chain 'X2' and resid 64 through 75 Processing helix chain 'Y2' and resid 2 through 10 removed outlier: 6.030A pdb=" N LEUY2 6 " --> pdb=" O LYSY2 2 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARGY2 7 " --> pdb=" O ALAY2 3 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLUY2 8 " --> pdb=" O LYSY2 4 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYSY2 9 " --> pdb=" O GLUY2 5 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SERY2 10 " --> pdb=" O LEUY2 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y2' and resid 2 through 10' Processing helix chain 'Y2' and resid 11 through 35 Processing helix chain 'Y2' and resid 39 through 63 removed outlier: 4.661A pdb=" N LEUY2 43 " --> pdb=" O GLNY2 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSY2 44 " --> pdb=" O SERY2 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLYY2 62 " --> pdb=" O ASNY2 58 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 17 through 28 Processing helix chain 'Z2' and resid 41 through 52 Processing helix chain 'a2' and resid 9 through 19 removed outlier: 4.811A pdb=" N HISa2 19 " --> pdb=" O METa2 15 " (cutoff:3.500A) Processing helix chain 'c2' and resid 8 through 16 Processing helix chain 'c2' and resid 17 through 24 removed outlier: 4.311A pdb=" N THRc2 24 " --> pdb=" O ALAc2 20 " (cutoff:3.500A) Processing helix chain 'c2' and resid 25 through 38 Processing helix chain 'd2' and resid 7 through 14 removed outlier: 3.885A pdb=" N ARGd2 13 " --> pdb=" O GLYd2 9 " (cutoff:3.500A) Processing helix chain 'd2' and resid 32 through 37 removed outlier: 5.124A pdb=" N LYSd2 36 " --> pdb=" O ILEd2 32 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALAd2 37 " --> pdb=" O LEUd2 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd2' and resid 32 through 37' Processing helix chain 'd2' and resid 38 through 46 Proline residue: d2 46 - end of helix Processing helix chain 'd2' and resid 51 through 63 removed outlier: 4.838A pdb=" N GLYd2 56 " --> pdb=" O LYSd2 52 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEUd2 57 " --> pdb=" O GLYd2 53 " (cutoff:3.500A) Proline residue: d2 63 - end of helix Processing sheet with id= 1, first strand: chain 'B1' and resid 90 through 93 removed outlier: 3.584A pdb=" N PHEB1 90 " --> pdb=" O ILEB1 67 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C1' and resid 53 through 59 Processing sheet with id= 3, first strand: chain 'C1' and resid 164 through 169 removed outlier: 5.716A pdb=" N ARGC1 164 " --> pdb=" O GLYC1 155 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYC1 194 " --> pdb=" O THRC1 191 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASPC1 181 " --> pdb=" O LYSC1 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D1' and resid 141 through 145 removed outlier: 3.643A pdb=" N ASPD1 141 " --> pdb=" O PHED1 182 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N METD1 178 " --> pdb=" O ILED1 145 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E1' and resid 12 through 16 removed outlier: 6.706A pdb=" N LEUE1 36 " --> pdb=" O ILEE1 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E1' and resid 84 through 88 removed outlier: 3.661A pdb=" N ALAE1 99 " --> pdb=" O ASNE1 122 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASNE1 122 " --> pdb=" O ALAE1 99 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E1' and resid 33 through 40 Processing sheet with id= 8, first strand: chain 'F1' and resid 38 through 42 removed outlier: 5.792A pdb=" N TYRF1 59 " --> pdb=" O TRPF1 42 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HISF1 3 " --> pdb=" O THRF1 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARGF1 86 " --> pdb=" O METF1 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F1' and resid 43 through 47 removed outlier: 5.920A pdb=" N LEUF1 47 " --> pdb=" O HISF1 55 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HISF1 55 " --> pdb=" O LEUF1 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G1' and resid 73 through 79 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'H1' and resid 23 through 29 removed outlier: 6.558A pdb=" N ALAH1 23 " --> pdb=" O LEUH1 63 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASPH1 48 " --> pdb=" O THRH1 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H1' and resid 74 through 77 removed outlier: 6.621A pdb=" N VALH1 103 " --> pdb=" O ILEH1 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I1' and resid 5 through 11 Processing sheet with id= 14, first strand: chain 'J1' and resid 42 through 52 removed outlier: 4.882A pdb=" N LEUJ1 71 " --> pdb=" O PROJ1 43 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K1' and resid 42 through 45 removed outlier: 3.730A pdb=" N ASNK1 29 " --> pdb=" O SERK1 26 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L1' and resid 29 through 32 removed outlier: 5.208A pdb=" N LEUL1 81 " --> pdb=" O VALL1 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLYL1 85 " --> pdb=" O ARGL1 94 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARGL1 94 " --> pdb=" O GLYL1 85 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L1' and resid 36 through 41 removed outlier: 5.263A pdb=" N LYSL1 51 " --> pdb=" O ILEL1 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'P1' and resid 4 through 10 removed outlier: 3.831A pdb=" N PHEP1 38 " --> pdb=" O ARGP1 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARGP1 51 " --> pdb=" O PHEP1 38 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLYP1 49 " --> pdb=" O ASNP1 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Q1' and resid 7 through 11 removed outlier: 6.870A pdb=" N GLUQ1 60 " --> pdb=" O VALQ1 76 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q1' and resid 19 through 30 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'S1' and resid 30 through 33 removed outlier: 4.746A pdb=" N LEUS1 47 " --> pdb=" O VALS1 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C2' and resid 2 through 6 removed outlier: 5.541A pdb=" N VALC2 16 " --> pdb=" O CYSC2 6 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C2' and resid 80 through 83 removed outlier: 3.641A pdb=" N ARGC2 80 " --> pdb=" O LEUC2 93 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEUC2 93 " --> pdb=" O GLUC2 79 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILEC2 74 " --> pdb=" O SERC2 118 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SERC2 118 " --> pdb=" O ILEC2 74 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASPC2 114 " --> pdb=" O VALC2 78 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLYC2 127 " --> pdb=" O GLNC2 115 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLNC2 117 " --> pdb=" O GLYC2 127 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C2' and resid 162 through 165 removed outlier: 3.734A pdb=" N GLNC2 163 " --> pdb=" O ARGC2 175 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THRC2 173 " --> pdb=" O VALC2 165 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLUC2 180 " --> pdb=" O LEUC2 176 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C2' and resid 90 through 96 removed outlier: 5.378A pdb=" N ASNC2 90 " --> pdb=" O ALAC2 106 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLUC2 100 " --> pdb=" O TYRC2 96 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D2' and resid 3 through 6 removed outlier: 3.993A pdb=" N GLUD2 168 " --> pdb=" O SERD2 113 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D2' and resid 10 through 16 removed outlier: 3.603A pdb=" N GLYD2 10 " --> pdb=" O VALD2 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALD2 20 " --> pdb=" O THRD2 16 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D2' and resid 79 through 84 removed outlier: 5.775A pdb=" N ARGD2 46 " --> pdb=" O LEUD2 84 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLND2 49 " --> pdb=" O THRD2 35 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLND2 94 " --> pdb=" O VALD2 34 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D2' and resid 105 through 108 removed outlier: 6.599A pdb=" N LYSD2 105 " --> pdb=" O VALD2 177 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E2' and resid 1 through 6 removed outlier: 4.695A pdb=" N SERE2 10 " --> pdb=" O LEUE2 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E2' and resid 117 through 120 removed outlier: 5.515A pdb=" N ARGE2 117 " --> pdb=" O ASPE2 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASPE2 168 " --> pdb=" O VALE2 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F2' and resid 65 through 69 removed outlier: 3.855A pdb=" N LYSF2 33 " --> pdb=" O THRF2 157 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THRF2 35 " --> pdb=" O THRF2 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRF2 155 " --> pdb=" O THRF2 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLYF2 39 " --> pdb=" O GLYF2 151 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLYF2 151 " --> pdb=" O GLYF2 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G2' and resid 16 through 19 Processing sheet with id= 34, first strand: chain 'G2' and resid 82 through 89 removed outlier: 5.804A pdb=" N THRG2 129 " --> pdb=" O LEUG2 89 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G2' and resid 94 through 98 removed outlier: 3.615A pdb=" N ARGG2 95 " --> pdb=" O SERG2 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALG2 113 " --> pdb=" O LEUG2 105 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H2' and resid 50 through 54 removed outlier: 3.907A pdb=" N SERH2 24 " --> pdb=" O VALH2 85 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VALH2 27 " --> pdb=" O LYSH2 109 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASPH2 29 " --> pdb=" O GLUH2 107 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLUH2 107 " --> pdb=" O ASPH2 29 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'I2' and resid 8 through 13 removed outlier: 3.876A pdb=" N SERI2 66 " --> pdb=" O TYRI2 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'J2' and resid 52 through 57 removed outlier: 5.268A pdb=" N ASPJ2 19 " --> pdb=" O LEUJ2 140 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J2' and resid 74 through 78 removed outlier: 7.296A pdb=" N GLYJ2 83 " --> pdb=" O THRJ2 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'K2' and resid 18 through 21 removed outlier: 4.119A pdb=" N THRK2 6 " --> pdb=" O CYSK2 21 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASNK2 82 " --> pdb=" O METK2 7 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K2' and resid 38 through 41 Processing sheet with id= 42, first strand: chain 'M2' and resid 37 through 40 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'M2' and resid 62 through 65 removed outlier: 3.698A pdb=" N TYRM2 103 " --> pdb=" O LEUM2 33 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEUM2 33 " --> pdb=" O LEUM2 102 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYSM2 100 " --> pdb=" O ALAM2 35 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M2' and resid 30 through 36 removed outlier: 7.538A pdb=" N SERM2 30 " --> pdb=" O LYSM2 133 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYSM2 127 " --> pdb=" O VALM2 36 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'N2' and resid 33 through 37 removed outlier: 4.610A pdb=" N METN2 110 " --> pdb=" O CYSN2 100 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYRN2 94 " --> pdb=" O VALN2 116 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O2' and resid 49 through 53 removed outlier: 3.788A pdb=" N VALO2 49 " --> pdb=" O VALO2 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILEO2 35 " --> pdb=" O THRO2 53 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P2' and resid 38 through 45 removed outlier: 6.800A pdb=" N THRP2 25 " --> pdb=" O LYSP2 87 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P2' and resid 49 through 52 removed outlier: 3.714A pdb=" N ALAP2 49 " --> pdb=" O THRP2 60 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R2' and resid 11 through 15 removed outlier: 6.633A pdb=" N LEUR2 39 " --> pdb=" O GLYR2 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R2' and resid 18 through 23 removed outlier: 4.034A pdb=" N GLNR2 18 " --> pdb=" O ILER2 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASPR2 95 " --> pdb=" O VALR2 64 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYSR2 60 " --> pdb=" O THRR2 99 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLUR2 31 " --> pdb=" O VALR2 63 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R2' and resid 57 through 60 Processing sheet with id= 52, first strand: chain 'R2' and resid 65 through 68 Processing sheet with id= 53, first strand: chain 'R2' and resid 71 through 78 removed outlier: 4.149A pdb=" N TYRR2 83 " --> pdb=" O ARGR2 78 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S2' and resid 2 through 8 removed outlier: 6.927A pdb=" N VALS2 106 " --> pdb=" O THRS2 72 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S2' and resid 81 through 88 removed outlier: 3.829A pdb=" N ARGS2 92 " --> pdb=" O ARGS2 88 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T2' and resid 28 through 33 removed outlier: 6.483A pdb=" N ASNT2 28 " --> pdb=" O LEUT2 87 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYST2 66 " --> pdb=" O ARGT2 77 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASPT2 79 " --> pdb=" O LYST2 64 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYST2 64 " --> pdb=" O ASPT2 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYST2 81 " --> pdb=" O VALT2 62 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VALT2 62 " --> pdb=" O LYST2 81 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALAT2 83 " --> pdb=" O THRT2 60 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THRT2 60 " --> pdb=" O ALAT2 83 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VALT2 85 " --> pdb=" O VALT2 58 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VALT2 58 " --> pdb=" O VALT2 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'U2' and resid 82 through 86 removed outlier: 6.985A pdb=" N ARGU2 82 " --> pdb=" O LYSU2 97 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARGU2 94 " --> pdb=" O ILEU2 103 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLUU2 101 " --> pdb=" O PHEU2 96 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'V2' and resid 69 through 72 removed outlier: 6.591A pdb=" N ALAV2 39 " --> pdb=" O ARGV2 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEV2 89 " --> pdb=" O PROV2 27 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W2' and resid 51 through 54 removed outlier: 6.439A pdb=" N GLYW2 52 " --> pdb=" O LEUW2 59 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEUW2 59 " --> pdb=" O GLYW2 52 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLYW2 54 " --> pdb=" O HISW2 57 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W2' and resid 65 through 72 Processing sheet with id= 61, first strand: chain 'X2' and resid 12 through 19 removed outlier: 4.490A pdb=" N ASNX2 23 " --> pdb=" O SERX2 19 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X2' and resid 35 through 41 Processing sheet with id= 63, first strand: chain 'Z2' and resid 33 through 39 removed outlier: 4.423A pdb=" N HISZ2 34 " --> pdb=" O GLNZ2 9 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N METZ2 54 " --> pdb=" O THRZ2 10 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a2' and resid 28 through 31 removed outlier: 6.472A pdb=" N SERa2 29 " --> pdb=" O LYSa2 37 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSa2 37 " --> pdb=" O SERa2 29 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASPa2 31 " --> pdb=" O GLYa2 35 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'b2' and resid 20 through 25 removed outlier: 7.283A pdb=" N ILEb2 48 " --> pdb=" O SERb2 14 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEUb2 34 " --> pdb=" O GLUb2 51 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'd2' and resid 22 through 25 removed outlier: 5.657A pdb=" N PHEd2 22 " --> pdb=" O VALd2 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e2' and resid 1 through 5 removed outlier: 6.503A pdb=" N HISe2 33 " --> pdb=" O CYSe2 27 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N CYSe2 27 " --> pdb=" O HISe2 33 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILEe2 23 " --> pdb=" O GLNe2 37 " (cutoff:3.500A) 1933 hydrogen bonds defined for protein. 5688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3869 hydrogen bonds 6002 hydrogen bond angles 0 basepair planarities 1540 basepair parallelities 2495 stacking parallelities Total time for adding SS restraints: 232.90 Time building geometry restraints manager: 64.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11674 1.28 - 1.41: 55192 1.41 - 1.55: 80046 1.55 - 1.68: 9295 1.68 - 1.81: 272 Bond restraints: 156479 Sorted by residual: bond pdb=" C4 5MUf2 54 " pdb=" C5 5MUf2 54 " ideal model delta sigma weight residual 1.802 1.400 0.402 2.00e-02 2.50e+03 4.05e+02 bond pdb=" C4 5MUA21939 " pdb=" C5 5MUA21939 " ideal model delta sigma weight residual 1.802 1.422 0.380 2.00e-02 2.50e+03 3.60e+02 bond pdb=" C4 5MUA2 747 " pdb=" C5 5MUA2 747 " ideal model delta sigma weight residual 1.802 1.424 0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" N1 5MUf2 54 " pdb=" C6 5MUf2 54 " ideal model delta sigma weight residual 1.635 1.286 0.349 2.00e-02 2.50e+03 3.05e+02 bond pdb=" N1 5MUA21939 " pdb=" C6 5MUA21939 " ideal model delta sigma weight residual 1.635 1.297 0.338 2.00e-02 2.50e+03 2.86e+02 ... (remaining 156474 not shown) Histogram of bond angle deviations from ideal: 76.38 - 88.43: 12 88.43 - 100.48: 102 100.48 - 112.53: 113285 112.53 - 124.58: 101216 124.58 - 136.63: 19530 Bond angle restraints: 234145 Sorted by residual: angle pdb=" O2' Gf2 5 " pdb=" C2' Gf2 5 " pdb=" C1' Gf2 5 " ideal model delta sigma weight residual 108.40 76.38 32.02 1.50e+00 4.44e-01 4.56e+02 angle pdb=" O2' GA22255 " pdb=" C2' GA22255 " pdb=" C1' GA22255 " ideal model delta sigma weight residual 108.40 78.33 30.07 1.50e+00 4.44e-01 4.02e+02 angle pdb=" O2' Af2 73 " pdb=" C2' Af2 73 " pdb=" C1' Af2 73 " ideal model delta sigma weight residual 108.40 79.72 28.68 1.50e+00 4.44e-01 3.66e+02 angle pdb=" O2' Af2 57 " pdb=" C2' Af2 57 " pdb=" C1' Af2 57 " ideal model delta sigma weight residual 108.40 80.13 28.27 1.50e+00 4.44e-01 3.55e+02 angle pdb=" O2' Cf2 74 " pdb=" C2' Cf2 74 " pdb=" C1' Cf2 74 " ideal model delta sigma weight residual 108.40 81.45 26.95 1.50e+00 4.44e-01 3.23e+02 ... (remaining 234140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 88013 35.85 - 71.71: 10945 71.71 - 107.56: 1281 107.56 - 143.41: 24 143.41 - 179.26: 16 Dihedral angle restraints: 100279 sinusoidal: 83951 harmonic: 16328 Sorted by residual: dihedral pdb=" C4' AA1 532 " pdb=" C3' AA1 532 " pdb=" C2' AA1 532 " pdb=" C1' AA1 532 " ideal model delta sinusoidal sigma weight residual -35.00 34.79 -69.79 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" CA HISd2 31 " pdb=" C HISd2 31 " pdb=" N ILEd2 32 " pdb=" CA ILEd2 32 " ideal model delta harmonic sigma weight residual -180.00 -131.12 -48.88 0 5.00e+00 4.00e-02 9.56e+01 dihedral pdb=" CA VALR2 51 " pdb=" C VALR2 51 " pdb=" N PROR2 52 " pdb=" CA PROR2 52 " ideal model delta harmonic sigma weight residual -180.00 -131.49 -48.51 0 5.00e+00 4.00e-02 9.41e+01 ... (remaining 100276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 29849 0.381 - 0.762: 23 0.762 - 1.143: 2 1.143 - 1.524: 0 1.524 - 1.904: 1 Chirality restraints: 29875 Sorted by residual: chirality pdb=" C2' Af2 58 " pdb=" C3' Af2 58 " pdb=" O2' Af2 58 " pdb=" C1' Af2 58 " both_signs ideal model delta sigma weight residual False -2.52 -0.61 -1.90 2.00e-01 2.50e+01 9.07e+01 chirality pdb=" C2' 4SUf2 8 " pdb=" C3' 4SUf2 8 " pdb=" O2' 4SUf2 8 " pdb=" C1' 4SUf2 8 " both_signs ideal model delta sigma weight residual False -2.75 -1.98 -0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" C3' Gf2 70 " pdb=" C4' Gf2 70 " pdb=" O3' Gf2 70 " pdb=" C2' Gf2 70 " both_signs ideal model delta sigma weight residual False -2.48 -1.71 -0.76 2.00e-01 2.50e+01 1.46e+01 ... (remaining 29872 not shown) Planarity restraints: 12503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MGA22445 " -0.038 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' 2MGA22445 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 2MGA22445 " -0.694 2.00e-02 2.50e+03 pdb=" C3' 2MGA22445 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MGA22445 " 0.589 2.00e-02 2.50e+03 pdb=" C2' 2MGA22445 " 0.212 2.00e-02 2.50e+03 pdb=" O2' 2MGA22445 " -0.919 2.00e-02 2.50e+03 pdb=" C1' 2MGA22445 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MGA22445 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCA22498 " 0.055 2.00e-02 2.50e+03 5.85e-01 7.70e+03 pdb=" C4' OMCA22498 " 0.435 2.00e-02 2.50e+03 pdb=" O4' OMCA22498 " 0.609 2.00e-02 2.50e+03 pdb=" C3' OMCA22498 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMCA22498 " -0.617 2.00e-02 2.50e+03 pdb=" C2' OMCA22498 " -0.185 2.00e-02 2.50e+03 pdb=" O2' OMCA22498 " 0.954 2.00e-02 2.50e+03 pdb=" C1' OMCA22498 " 0.231 2.00e-02 2.50e+03 pdb=" N1 OMCA22498 " -0.885 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGA22251 " 0.030 2.00e-02 2.50e+03 5.79e-01 7.55e+03 pdb=" C4' OMGA22251 " 0.442 2.00e-02 2.50e+03 pdb=" O4' OMGA22251 " 0.665 2.00e-02 2.50e+03 pdb=" C3' OMGA22251 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMGA22251 " -0.573 2.00e-02 2.50e+03 pdb=" C2' OMGA22251 " -0.216 2.00e-02 2.50e+03 pdb=" O2' OMGA22251 " 0.908 2.00e-02 2.50e+03 pdb=" C1' OMGA22251 " 0.219 2.00e-02 2.50e+03 pdb=" N9 OMGA22251 " -0.885 2.00e-02 2.50e+03 ... (remaining 12500 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 25 1.26 - 2.17: 64 2.17 - 3.08: 91510 3.08 - 3.99: 474455 3.99 - 4.90: 786009 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1352063 Sorted by model distance: nonbonded pdb=" OP1 AA11080 " pdb=" CE LYSE1 52 " model vdw 0.349 3.440 nonbonded pdb=" NH1 ARGI1 130 " pdb=" C4 Uf2 33 " model vdw 0.529 3.340 nonbonded pdb=" P AA11080 " pdb=" NZ LYSE1 52 " model vdw 0.656 3.480 nonbonded pdb=" C4 AA21050 " pdb=" N2 GA22751 " model vdw 0.668 3.340 nonbonded pdb=" P AA11081 " pdb=" CE LYSE1 23 " model vdw 0.718 3.800 ... (remaining 1352058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 31.060 Check model and map are aligned: 1.430 Set scattering table: 0.920 Process input model: 547.270 Find NCS groups from input model: 3.180 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: 0.020 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 600.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 : 0.007 0.402 156479 Z= 0.441 Angle : 0.675 32.019 234145 Z= 0.397 Chirality : 0.042 1.904 29875 Planarity : 0.017 0.592 12503 Dihedral : 23.016 179.265 89745 Min Nonbonded Distance : 0.349 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.13 % Favored : 96.45 % Rotamer: Outliers : 2.91 % Allowed : 15.60 % Favored : 81.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.04 % 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: -1.96 (0.10), residues: 5626 helix: -1.28 (0.10), residues: 1901 sheet: -1.19 (0.14), residues: 1097 loop : -1.22 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPC2 248 HIS 0.005 0.001 HISC2 230 PHE 0.026 0.001 PHEH2 106 TYR 0.015 0.001 TYRH2 132 ARG 0.007 0.001 ARGG2 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2290 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 2154 time to evaluate : 5.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 138 THR cc_start: 0.8223 (p) cc_final: 0.7913 (p) REVERT: G1 97 ASN cc_start: 0.6314 (m-40) cc_final: 0.4934 (m110) REVERT: C2 21 ASN cc_start: 0.8445 (t0) cc_final: 0.8141 (t160) REVERT: C2 96 TYR cc_start: 0.9037 (m-80) cc_final: 0.8817 (m-80) REVERT: C2 114 ASP cc_start: 0.7543 (m-30) cc_final: 0.6606 (m-30) REVERT: C2 173 THR cc_start: 0.8956 (m) cc_final: 0.8727 (p) REVERT: D2 137 SER cc_start: 0.8803 (m) cc_final: 0.8525 (p) REVERT: E2 10 SER cc_start: 0.8243 (m) cc_final: 0.7913 (t) REVERT: F2 3 LYS cc_start: 0.9277 (tppt) cc_final: 0.8897 (tppp) REVERT: F2 24 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8784 (t) REVERT: F2 113 ASP cc_start: 0.7527 (m-30) cc_final: 0.6581 (m-30) REVERT: G2 8 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8494 (Cg_endo) REVERT: G2 25 THR cc_start: 0.7659 (t) cc_final: 0.7388 (m) REVERT: G2 88 GLN cc_start: 0.8186 (pt0) cc_final: 0.7853 (tm-30) REVERT: G2 95 ARG cc_start: 0.7881 (ptm-80) cc_final: 0.7589 (pmt-80) REVERT: G2 164 TYR cc_start: 0.8609 (m-80) cc_final: 0.8337 (m-80) REVERT: K2 88 ASN cc_start: 0.8702 (t0) cc_final: 0.8402 (t0) REVERT: K2 92 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: N2 57 THR cc_start: 0.8616 (m) cc_final: 0.8050 (p) REVERT: O2 17 LYS cc_start: 0.9165 (tppt) cc_final: 0.8815 (tptt) REVERT: O2 99 TYR cc_start: 0.8913 (t80) cc_final: 0.8250 (t80) REVERT: O2 111 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.7928 (mtm-85) REVERT: P2 72 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7936 (ttt-90) REVERT: Q2 87 SER cc_start: 0.8972 (m) cc_final: 0.8746 (p) REVERT: R2 2 TYR cc_start: 0.8953 (p90) cc_final: 0.8747 (p90) REVERT: R2 27 ILE cc_start: 0.8847 (mm) cc_final: 0.8510 (mp) REVERT: T2 39 THR cc_start: 0.9220 (p) cc_final: 0.8987 (p) REVERT: U2 48 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8066 (Cg_exo) REVERT: U2 74 ASN cc_start: 0.8651 (t0) cc_final: 0.8333 (t0) REVERT: U2 96 PHE cc_start: 0.8999 (m-80) cc_final: 0.8533 (m-80) REVERT: V2 2 PHE cc_start: 0.7279 (m-80) cc_final: 0.7078 (m-80) REVERT: V2 46 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8779 (ttmm) REVERT: W2 81 SER cc_start: 0.8619 (p) cc_final: 0.8294 (m) REVERT: a2 36 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6216 (mt-10) REVERT: e2 9 LYS cc_start: 0.8515 (mtpm) cc_final: 0.8177 (mtpm) outliers start: 136 outliers final: 35 residues processed: 2231 average time/residue: 2.2569 time to fit residues: 7064.6190 Evaluate side-chains 1661 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1624 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 57 LEU Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain G1 residue 3 ARG Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain I1 residue 41 ARG Chi-restraints excluded: chain J1 residue 35 GLN Chi-restraints excluded: chain J1 residue 75 ASP Chi-restraints excluded: chain M1 residue 9 ILE Chi-restraints excluded: chain P1 residue 52 LEU Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain F2 residue 24 SER Chi-restraints excluded: chain F2 residue 35 THR Chi-restraints excluded: chain F2 residue 51 ASP Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 155 THR Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 87 LEU Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 131 ILE Chi-restraints excluded: chain H2 residue 86 THR Chi-restraints excluded: chain J2 residue 142 ILE Chi-restraints excluded: chain K2 residue 92 GLU Chi-restraints excluded: chain K2 residue 109 SER Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 47 GLU Chi-restraints excluded: chain M2 residue 59 ARG Chi-restraints excluded: chain N2 residue 29 VAL Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain S2 residue 55 ILE Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 68 SER Chi-restraints excluded: chain V2 residue 59 GLU Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain b2 residue 17 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 852 optimal weight: 3.9990 chunk 765 optimal weight: 7.9990 chunk 424 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 516 optimal weight: 6.9990 chunk 408 optimal weight: 20.0000 chunk 791 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 481 optimal weight: 8.9990 chunk 589 optimal weight: 20.0000 chunk 917 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 24 ASN B1 168 HIS B1 227 GLN C1 100 GLN C1 139 GLN C1 140 ASN D1 36 GLN D1 54 GLN D1 85 ASN D1 164 GLN E1 70 ASN E1 83 HIS E1 122 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 146 ASN ** F1 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 17 GLN F1 68 GLN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 56 HIS J1 58 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 6 GLN L1 73 ASN L1 112 GLN ** N1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1 62 GLN ** P1 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1 9 GLN ** S1 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1 20 HIS C2 134 ASN C2 153 GLN C2 197 ASN D2 130 GLN D2 136 ASN E2 9 GLN E2 41 GLN E2 94 GLN E2 163 ASN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 111 HIS G2 115 HIS G2 143 GLN J2 67 ASN J2 136 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 93 GLN ** L2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN M2 3 GLN N2 107 ASN O2 19 GLN ** P2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P2 41 GLN Q2 20 GLN R2 18 GLN ** R2 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 9 HIS S2 61 ASN T2 48 GLN U2 54 GLN U2 69 ASN ** U2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 49 ASN V2 75 GLN W2 76 ASN X2 6 GLN b2 19 HIS c2 29 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 156479 Z= 0.350 Angle : 0.713 15.278 234145 Z= 0.374 Chirality : 0.040 0.427 29875 Planarity : 0.006 0.131 12503 Dihedral : 23.220 179.990 78541 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 8.09 % Allowed : 29.08 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5626 helix: 0.22 (0.11), residues: 1928 sheet: -0.61 (0.15), residues: 1063 loop : -0.82 (0.11), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPB1 23 HIS 0.009 0.001 HISO2 29 PHE 0.032 0.002 PHEU2 95 TYR 0.019 0.002 TYRG2 151 ARG 0.012 0.001 ARGB1 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2124 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1746 time to evaluate : 5.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 77 SER cc_start: 0.6345 (OUTLIER) cc_final: 0.6111 (t) REVERT: B1 113 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7551 (tpt-90) REVERT: B1 115 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7988 (mptt) REVERT: B1 135 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7353 (tp) REVERT: B1 186 ILE cc_start: 0.8352 (mp) cc_final: 0.8056 (mt) REVERT: G1 97 ASN cc_start: 0.6468 (m-40) cc_final: 0.5033 (m110) REVERT: L1 83 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5751 (ptp90) REVERT: L1 103 ASP cc_start: 0.2715 (OUTLIER) cc_final: 0.1967 (m-30) REVERT: O1 46 HIS cc_start: 0.7193 (m90) cc_final: 0.6883 (m-70) REVERT: T1 39 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6043 (mm) REVERT: C2 21 ASN cc_start: 0.8592 (t0) cc_final: 0.8374 (t160) REVERT: C2 79 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C2 98 ASP cc_start: 0.7740 (p0) cc_final: 0.7500 (p0) REVERT: C2 108 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8715 (tppp) REVERT: C2 150 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8844 (tttm) REVERT: C2 153 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: C2 197 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8742 (t0) REVERT: C2 271 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.6866 (ptp90) REVERT: E2 24 ASN cc_start: 0.8789 (t0) cc_final: 0.8573 (t0) REVERT: E2 111 GLU cc_start: 0.8541 (tp30) cc_final: 0.7971 (tp30) REVERT: E2 115 GLN cc_start: 0.8770 (mt0) cc_final: 0.8268 (mt0) REVERT: E2 145 ASP cc_start: 0.6630 (t0) cc_final: 0.6342 (t70) REVERT: E2 179 SER cc_start: 0.9256 (m) cc_final: 0.8992 (m) REVERT: F2 14 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9059 (pptt) REVERT: F2 19 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8597 (tm-30) REVERT: F2 26 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8221 (mpt) REVERT: F2 38 MET cc_start: 0.7967 (ttp) cc_final: 0.7708 (ttp) REVERT: F2 42 GLU cc_start: 0.8350 (pp20) cc_final: 0.7622 (pp20) REVERT: F2 94 GLU cc_start: 0.8799 (pm20) cc_final: 0.8563 (pp20) REVERT: F2 98 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: F2 99 PHE cc_start: 0.8988 (t80) cc_final: 0.8783 (t80) REVERT: F2 125 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.8611 (mmm-85) REVERT: F2 136 ILE cc_start: 0.9122 (pp) cc_final: 0.8724 (pp) REVERT: F2 154 ILE cc_start: 0.9561 (mt) cc_final: 0.9358 (mm) REVERT: F2 163 ASP cc_start: 0.8431 (m-30) cc_final: 0.7898 (t70) REVERT: F2 175 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: G2 38 ASN cc_start: 0.8264 (p0) cc_final: 0.7856 (p0) REVERT: G2 88 GLN cc_start: 0.8245 (pt0) cc_final: 0.7824 (pt0) REVERT: G2 95 ARG cc_start: 0.7853 (ptm-80) cc_final: 0.7352 (pmt-80) REVERT: G2 130 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: G2 164 TYR cc_start: 0.8590 (m-80) cc_final: 0.8390 (m-80) REVERT: J2 31 GLU cc_start: 0.7621 (tp30) cc_final: 0.7392 (tp30) REVERT: J2 34 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7576 (ttp80) REVERT: K2 92 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: M2 17 ASN cc_start: 0.8575 (t0) cc_final: 0.8337 (t0) REVERT: N2 57 THR cc_start: 0.8702 (m) cc_final: 0.8086 (p) REVERT: O2 4 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: O2 84 GLU cc_start: 0.9143 (pm20) cc_final: 0.8740 (pm20) REVERT: O2 99 TYR cc_start: 0.8966 (t80) cc_final: 0.8114 (t80) REVERT: R2 27 ILE cc_start: 0.8743 (mm) cc_final: 0.8512 (mp) REVERT: R2 34 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7879 (mm-30) REVERT: R2 60 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8154 (ttmm) REVERT: R2 79 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8068 (ptt90) REVERT: T2 3 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8525 (mtp85) REVERT: T2 50 LEU cc_start: 0.9249 (mm) cc_final: 0.8963 (mt) REVERT: U2 47 LYS cc_start: 0.8763 (pptt) cc_final: 0.8400 (tmmt) REVERT: U2 66 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8374 (mm-40) REVERT: V2 25 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8215 (mmmm) REVERT: V2 55 GLU cc_start: 0.8872 (pm20) cc_final: 0.8439 (pm20) REVERT: X2 11 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8170 (ptp-110) REVERT: Y2 20 ASN cc_start: 0.8970 (m110) cc_final: 0.8759 (m110) REVERT: Y2 23 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8155 (ttm170) REVERT: Y2 31 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8189 (tp-100) REVERT: b2 38 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8507 (mttp) REVERT: b2 49 TYR cc_start: 0.8991 (m-80) cc_final: 0.8090 (m-80) outliers start: 378 outliers final: 153 residues processed: 1908 average time/residue: 2.0645 time to fit residues: 5642.1331 Evaluate side-chains 1754 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1578 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 4 VAL Chi-restraints excluded: chain B1 residue 31 ILE Chi-restraints excluded: chain B1 residue 77 SER Chi-restraints excluded: chain B1 residue 102 THR Chi-restraints excluded: chain B1 residue 107 VAL Chi-restraints excluded: chain B1 residue 115 LYS Chi-restraints excluded: chain B1 residue 135 LEU Chi-restraints excluded: chain B1 residue 207 ILE Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 26 THR Chi-restraints excluded: chain C1 residue 90 VAL Chi-restraints excluded: chain C1 residue 114 LYS Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 128 VAL Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 191 THR Chi-restraints excluded: chain C1 residue 195 VAL Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain C1 residue 200 VAL Chi-restraints excluded: chain E1 residue 18 VAL Chi-restraints excluded: chain E1 residue 21 VAL Chi-restraints excluded: chain E1 residue 22 SER Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 15 SER Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain G1 residue 32 VAL Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 54 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 123 GLU Chi-restraints excluded: chain G1 residue 129 GLU Chi-restraints excluded: chain H1 residue 34 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain J1 residue 35 GLN Chi-restraints excluded: chain K1 residue 26 SER Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain K1 residue 97 ILE Chi-restraints excluded: chain K1 residue 121 CYS Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 40 THR Chi-restraints excluded: chain L1 residue 52 VAL Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain L1 residue 103 ASP Chi-restraints excluded: chain M1 residue 49 SER Chi-restraints excluded: chain M1 residue 68 ASP Chi-restraints excluded: chain O1 residue 14 GLU Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain O1 residue 40 GLN Chi-restraints excluded: chain O1 residue 60 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 44 ILE Chi-restraints excluded: chain T1 residue 30 THR Chi-restraints excluded: chain T1 residue 39 ILE Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 7 LYS Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 108 LYS Chi-restraints excluded: chain C2 residue 150 LYS Chi-restraints excluded: chain C2 residue 153 GLN Chi-restraints excluded: chain C2 residue 178 SER Chi-restraints excluded: chain C2 residue 197 ASN Chi-restraints excluded: chain C2 residue 205 LEU Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 176 ASP Chi-restraints excluded: chain E2 residue 65 THR Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 96 VAL Chi-restraints excluded: chain E2 residue 166 LYS Chi-restraints excluded: chain E2 residue 175 ILE Chi-restraints excluded: chain F2 residue 12 VAL Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 26 MET Chi-restraints excluded: chain F2 residue 35 THR Chi-restraints excluded: chain F2 residue 44 ILE Chi-restraints excluded: chain F2 residue 66 LEU Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 88 LYS Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 155 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 23 VAL Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 92 VAL Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 131 ILE Chi-restraints excluded: chain H2 residue 7 ASP Chi-restraints excluded: chain J2 residue 34 ARG Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain K2 residue 6 THR Chi-restraints excluded: chain K2 residue 61 VAL Chi-restraints excluded: chain K2 residue 92 GLU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 40 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 46 VAL Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 54 THR Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain N2 residue 15 SER Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 53 THR Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 97 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 4 LYS Chi-restraints excluded: chain P2 residue 26 VAL Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain P2 residue 85 SER Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain S2 residue 4 ILE Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain S2 residue 85 ILE Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 27 SER Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 60 THR Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 68 SER Chi-restraints excluded: chain U2 residue 77 THR Chi-restraints excluded: chain U2 residue 100 SER Chi-restraints excluded: chain V2 residue 9 ARG Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 34 LYS Chi-restraints excluded: chain V2 residue 77 VAL Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 43 THR Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 11 VAL Chi-restraints excluded: chain Y2 residue 23 ARG Chi-restraints excluded: chain Z2 residue 4 THR Chi-restraints excluded: chain Z2 residue 52 SER Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain a2 residue 29 SER Chi-restraints excluded: chain a2 residue 54 VAL Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 17 THR Chi-restraints excluded: chain b2 residue 38 LYS Chi-restraints excluded: chain b2 residue 47 VAL Chi-restraints excluded: chain b2 residue 51 GLU Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 509 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 763 optimal weight: 9.9990 chunk 624 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 918 optimal weight: 0.8980 chunk 992 optimal weight: 1.9990 chunk 818 optimal weight: 0.9980 chunk 911 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 737 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 8 ASN C1 140 ASN ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 85 ASN E1 78 ASN E1 132 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 126 GLN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 6 GLN L1 73 ASN ** N1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 57 HIS T1 3 ASN D2 130 GLN D2 136 ASN E2 41 GLN E2 62 GLN E2 94 GLN E2 163 ASN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2 52 ASN F2 127 ASN G2 143 GLN J2 58 ASN J2 67 ASN J2 128 ASN J2 136 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 89 ASN ** L2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN P2 12 GLN ** Q2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R2 18 GLN R2 43 ASN R2 87 GLN S2 9 HIS S2 57 ASN S2 61 ASN T2 48 GLN T2 59 ASN U2 74 ASN V2 49 ASN ** V2 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W2 76 ASN X2 6 GLN Y2 25 GLN a2 4 GLN c2 13 ASN d2 28 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 156479 Z= 0.173 Angle : 0.599 14.239 234145 Z= 0.322 Chirality : 0.034 0.398 29875 Planarity : 0.006 0.126 12503 Dihedral : 23.158 179.278 78499 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 6.78 % Allowed : 33.42 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5626 helix: 0.69 (0.12), residues: 1908 sheet: -0.38 (0.15), residues: 1077 loop : -0.58 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRPB1 23 HIS 0.007 0.001 HISE2 165 PHE 0.047 0.002 PHEG1 18 TYR 0.024 0.002 TYRO1 78 ARG 0.016 0.001 ARGL1 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1962 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1645 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 168 HIS cc_start: 0.8130 (t70) cc_final: 0.7849 (t70) REVERT: G1 95 ARG cc_start: 0.5810 (OUTLIER) cc_final: 0.5538 (ttt-90) REVERT: I1 122 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.5912 (mmt-90) REVERT: K1 101 ASN cc_start: 0.7231 (t0) cc_final: 0.7031 (t0) REVERT: L1 83 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5764 (ptp90) REVERT: O1 48 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7248 (mmmm) REVERT: C2 98 ASP cc_start: 0.8004 (p0) cc_final: 0.7692 (p0) REVERT: C2 111 LYS cc_start: 0.8687 (pmtt) cc_final: 0.8468 (pmtt) REVERT: C2 115 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7866 (tp40) REVERT: C2 132 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: C2 153 GLN cc_start: 0.7967 (mt0) cc_final: 0.7435 (mt0) REVERT: C2 271 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6752 (ptp90) REVERT: D2 61 THR cc_start: 0.8945 (p) cc_final: 0.8594 (t) REVERT: E2 24 ASN cc_start: 0.8673 (t0) cc_final: 0.8439 (t0) REVERT: E2 47 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: E2 111 GLU cc_start: 0.8352 (tp30) cc_final: 0.7815 (tp30) REVERT: E2 115 GLN cc_start: 0.8770 (mt0) cc_final: 0.8200 (mt0) REVERT: E2 141 MET cc_start: 0.8095 (mtm) cc_final: 0.7851 (mtm) REVERT: E2 145 ASP cc_start: 0.6634 (t0) cc_final: 0.6352 (t70) REVERT: F2 19 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F2 26 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8172 (mpt) REVERT: F2 42 GLU cc_start: 0.8374 (pp20) cc_final: 0.7679 (pp20) REVERT: F2 85 ILE cc_start: 0.8337 (tt) cc_final: 0.7848 (pp) REVERT: F2 98 GLU cc_start: 0.8088 (pp20) cc_final: 0.7362 (pp20) REVERT: F2 125 ARG cc_start: 0.9172 (mmm-85) cc_final: 0.8602 (mmm-85) REVERT: F2 137 ILE cc_start: 0.8516 (mt) cc_final: 0.8247 (mp) REVERT: F2 163 ASP cc_start: 0.8397 (m-30) cc_final: 0.7644 (t0) REVERT: F2 175 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: G2 88 GLN cc_start: 0.8214 (pt0) cc_final: 0.7838 (pt0) REVERT: G2 95 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7279 (pmt-80) REVERT: G2 117 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9011 (mm) REVERT: G2 130 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: J2 31 GLU cc_start: 0.7501 (tp30) cc_final: 0.7280 (tp30) REVERT: K2 1 MET cc_start: 0.7890 (tpp) cc_final: 0.7642 (mtp) REVERT: K2 118 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8801 (mt) REVERT: M2 17 ASN cc_start: 0.8551 (t0) cc_final: 0.8219 (t0) REVERT: O2 84 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8779 (pm20) REVERT: O2 99 TYR cc_start: 0.8976 (t80) cc_final: 0.8157 (t80) REVERT: O2 104 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8206 (tm-30) REVERT: Q2 5 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8831 (mtmm) REVERT: R2 27 ILE cc_start: 0.8723 (mm) cc_final: 0.8511 (mp) REVERT: R2 79 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8021 (ptt90) REVERT: R2 90 ARG cc_start: 0.9054 (mtp85) cc_final: 0.8766 (mtp180) REVERT: R2 97 LYS cc_start: 0.9291 (ttpt) cc_final: 0.8845 (ttpt) REVERT: U2 66 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8334 (mm-40) REVERT: U2 74 ASN cc_start: 0.7974 (t0) cc_final: 0.7717 (t0) REVERT: V2 2 PHE cc_start: 0.7908 (m-80) cc_final: 0.7517 (m-80) REVERT: V2 25 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8376 (mtpp) REVERT: X2 11 ARG cc_start: 0.8399 (ptp90) cc_final: 0.8184 (ptp-110) REVERT: Y2 20 ASN cc_start: 0.8927 (m110) cc_final: 0.8648 (m110) REVERT: Y2 31 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8454 (mm-40) REVERT: Y2 59 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8368 (tm-30) REVERT: b2 49 TYR cc_start: 0.8917 (m-80) cc_final: 0.8124 (m-80) REVERT: c2 6 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7977 (mp10) outliers start: 317 outliers final: 135 residues processed: 1783 average time/residue: 2.0378 time to fit residues: 5268.2545 Evaluate side-chains 1727 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1574 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 4 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 107 VAL Chi-restraints excluded: chain B1 residue 117 LEU Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 187 VAL Chi-restraints excluded: chain B1 residue 194 ASP Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 162 ILE Chi-restraints excluded: chain C1 residue 186 THR Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain E1 residue 12 GLN Chi-restraints excluded: chain E1 residue 22 SER Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 3 ARG Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain I1 residue 122 ARG Chi-restraints excluded: chain J1 residue 35 GLN Chi-restraints excluded: chain K1 residue 40 ASN Chi-restraints excluded: chain K1 residue 97 ILE Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 7 LEU Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 40 THR Chi-restraints excluded: chain L1 residue 52 VAL Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain M1 residue 17 ILE Chi-restraints excluded: chain M1 residue 45 ILE Chi-restraints excluded: chain N1 residue 56 SER Chi-restraints excluded: chain O1 residue 14 GLU Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 48 LYS Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain T1 residue 3 ASN Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 115 GLN Chi-restraints excluded: chain C2 residue 120 VAL Chi-restraints excluded: chain C2 residue 132 MET Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 176 ASP Chi-restraints excluded: chain E2 residue 47 LYS Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 96 VAL Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 166 LYS Chi-restraints excluded: chain E2 residue 189 THR Chi-restraints excluded: chain F2 residue 26 MET Chi-restraints excluded: chain F2 residue 66 LEU Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 155 THR Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 159 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 23 VAL Chi-restraints excluded: chain G2 residue 37 LEU Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 117 LEU Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 167 GLU Chi-restraints excluded: chain H2 residue 64 VAL Chi-restraints excluded: chain I2 residue 13 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 17 VAL Chi-restraints excluded: chain J2 residue 45 THR Chi-restraints excluded: chain J2 residue 93 ILE Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain J2 residue 142 ILE Chi-restraints excluded: chain K2 residue 43 ILE Chi-restraints excluded: chain K2 residue 118 LEU Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 60 ARG Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 97 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 8 LEU Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 90 ILE Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain S2 residue 67 ASP Chi-restraints excluded: chain S2 residue 69 LEU Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 27 SER Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 41 LEU Chi-restraints excluded: chain U2 residue 58 ILE Chi-restraints excluded: chain U2 residue 68 SER Chi-restraints excluded: chain U2 residue 100 SER Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 3 THR Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 34 LYS Chi-restraints excluded: chain V2 residue 86 LEU Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 43 THR Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 22 LEU Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 11 VAL Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 29 SER Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 17 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain c2 residue 6 GLN Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 907 optimal weight: 2.9990 chunk 690 optimal weight: 5.9990 chunk 476 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 chunk 438 optimal weight: 6.9990 chunk 616 optimal weight: 10.0000 chunk 922 optimal weight: 10.0000 chunk 976 optimal weight: 1.9990 chunk 481 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 178 ASN C1 8 ASN C1 140 ASN ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 54 GLN ** D1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 73 ASN E1 97 GLN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 97 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 32 GLN K1 22 HIS ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 73 ASN ** N1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 57 HIS ** C2 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 153 GLN C2 197 ASN D2 130 GLN D2 167 ASN E2 41 GLN E2 94 GLN E2 163 ASN E2 195 GLN ** G2 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN J2 67 ASN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N2 3 HIS P2 12 GLN ** Q2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 81 ASN R2 43 ASN R2 87 GLN S2 9 HIS S2 61 ASN T2 48 GLN V2 49 ASN V2 75 GLN W2 57 HIS X2 6 GLN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e2 35 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 156479 Z= 0.387 Angle : 0.713 15.874 234145 Z= 0.373 Chirality : 0.039 0.423 29875 Planarity : 0.007 0.134 12503 Dihedral : 23.059 179.810 78492 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % Rotamer: Outliers : 8.77 % Allowed : 33.40 % Favored : 57.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.26 (0.11), residues: 5626 helix: 0.67 (0.12), residues: 1911 sheet: -0.48 (0.15), residues: 1103 loop : -0.57 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPB1 23 HIS 0.007 0.001 HISS2 9 PHE 0.031 0.002 PHEH1 49 TYR 0.034 0.002 TYRO1 78 ARG 0.014 0.001 ARGc2 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2064 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 1654 time to evaluate : 5.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 168 HIS cc_start: 0.8238 (t70) cc_final: 0.7979 (t70) REVERT: G1 33 ASP cc_start: 0.6873 (m-30) cc_final: 0.6656 (m-30) REVERT: G1 97 ASN cc_start: 0.6873 (m-40) cc_final: 0.5431 (m110) REVERT: H1 41 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7441 (tmmm) REVERT: I1 122 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6095 (mmt-90) REVERT: K1 101 ASN cc_start: 0.7339 (t0) cc_final: 0.7128 (t0) REVERT: L1 83 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6157 (ptp90) REVERT: L1 103 ASP cc_start: 0.4249 (OUTLIER) cc_final: 0.3833 (m-30) REVERT: O1 48 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7401 (mmmm) REVERT: T1 39 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6377 (mm) REVERT: C2 98 ASP cc_start: 0.8148 (p0) cc_final: 0.7797 (p0) REVERT: C2 108 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8772 (tppp) REVERT: C2 111 LYS cc_start: 0.8669 (pmtt) cc_final: 0.8443 (pmtt) REVERT: C2 132 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8364 (mtm) REVERT: C2 197 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8762 (t0) REVERT: C2 271 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7075 (ptp90) REVERT: E2 24 ASN cc_start: 0.8725 (t0) cc_final: 0.8492 (t0) REVERT: E2 111 GLU cc_start: 0.8436 (tp30) cc_final: 0.7972 (tp30) REVERT: E2 115 GLN cc_start: 0.8857 (mt0) cc_final: 0.8320 (mt0) REVERT: E2 145 ASP cc_start: 0.6745 (t0) cc_final: 0.6494 (t70) REVERT: E2 195 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: F2 14 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9116 (pptt) REVERT: F2 27 GLN cc_start: 0.9371 (mt0) cc_final: 0.9149 (mm110) REVERT: F2 42 GLU cc_start: 0.8373 (pp20) cc_final: 0.7968 (pp20) REVERT: F2 85 ILE cc_start: 0.8533 (tt) cc_final: 0.8183 (pp) REVERT: F2 98 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7646 (pp20) REVERT: F2 165 GLU cc_start: 0.8634 (mp0) cc_final: 0.8308 (mp0) REVERT: G2 25 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7195 (p) REVERT: G2 69 ARG cc_start: 0.8371 (tpt-90) cc_final: 0.8156 (tpt90) REVERT: G2 88 GLN cc_start: 0.8274 (pt0) cc_final: 0.7960 (pt0) REVERT: G2 95 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7160 (pmt-80) REVERT: G2 130 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: G2 149 ARG cc_start: 0.9107 (ptm-80) cc_final: 0.8859 (ttt-90) REVERT: G2 163 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7596 (ptp90) REVERT: M2 17 ASN cc_start: 0.8636 (t0) cc_final: 0.8227 (t0) REVERT: M2 45 GLN cc_start: 0.8850 (mt0) cc_final: 0.8440 (mt0) REVERT: N2 57 THR cc_start: 0.8839 (m) cc_final: 0.8338 (p) REVERT: N2 60 VAL cc_start: 0.9027 (m) cc_final: 0.8822 (p) REVERT: O2 84 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8893 (pm20) REVERT: O2 99 TYR cc_start: 0.9038 (t80) cc_final: 0.8349 (t80) REVERT: O2 104 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8383 (tm-30) REVERT: Q2 5 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8919 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8529 (t80) cc_final: 0.8144 (t80) REVERT: Q2 51 ARG cc_start: 0.8605 (mpt90) cc_final: 0.7657 (mpt90) REVERT: R2 31 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7623 (tm-30) REVERT: R2 79 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8028 (ptt90) REVERT: S2 70 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8151 (mtpp) REVERT: S2 88 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: T2 66 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8504 (mtpp) REVERT: U2 74 ASN cc_start: 0.8061 (t0) cc_final: 0.7827 (t0) REVERT: V2 2 PHE cc_start: 0.7960 (m-80) cc_final: 0.7714 (m-80) REVERT: V2 25 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8600 (mmmm) REVERT: V2 51 GLN cc_start: 0.8922 (pp30) cc_final: 0.8319 (tm-30) REVERT: W2 75 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8990 (mmtp) REVERT: X2 32 ASN cc_start: 0.8856 (t0) cc_final: 0.8421 (t0) REVERT: X2 77 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8380 (mmpt) REVERT: Y2 20 ASN cc_start: 0.8975 (m110) cc_final: 0.8671 (m110) REVERT: Y2 23 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8316 (ttm170) REVERT: Y2 31 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8442 (mm-40) REVERT: d2 16 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8587 (tppp) outliers start: 410 outliers final: 209 residues processed: 1841 average time/residue: 2.0215 time to fit residues: 5404.9066 Evaluate side-chains 1818 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1584 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 66 LYS Chi-restraints excluded: chain B1 residue 106 THR Chi-restraints excluded: chain B1 residue 107 VAL Chi-restraints excluded: chain B1 residue 111 ILE Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain B1 residue 207 ILE Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 26 THR Chi-restraints excluded: chain C1 residue 33 LEU Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 90 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 186 THR Chi-restraints excluded: chain C1 residue 195 VAL Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain C1 residue 200 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 74 ASN Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain D1 residue 161 LEU Chi-restraints excluded: chain D1 residue 165 ARG Chi-restraints excluded: chain E1 residue 21 VAL Chi-restraints excluded: chain E1 residue 34 THR Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain F1 residue 36 ILE Chi-restraints excluded: chain F1 residue 61 LEU Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 31 MET Chi-restraints excluded: chain G1 residue 54 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain G1 residue 129 GLU Chi-restraints excluded: chain H1 residue 11 LEU Chi-restraints excluded: chain H1 residue 34 VAL Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 95 VAL Chi-restraints excluded: chain H1 residue 106 THR Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 66 THR Chi-restraints excluded: chain I1 residue 122 ARG Chi-restraints excluded: chain K1 residue 26 SER Chi-restraints excluded: chain K1 residue 40 ASN Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain K1 residue 97 ILE Chi-restraints excluded: chain K1 residue 114 THR Chi-restraints excluded: chain K1 residue 121 CYS Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 52 VAL Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain L1 residue 103 ASP Chi-restraints excluded: chain M1 residue 12 HIS Chi-restraints excluded: chain M1 residue 46 SER Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain M1 residue 49 SER Chi-restraints excluded: chain N1 residue 35 ASN Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain N1 residue 49 GLN Chi-restraints excluded: chain N1 residue 56 SER Chi-restraints excluded: chain N1 residue 64 CYS Chi-restraints excluded: chain O1 residue 3 LEU Chi-restraints excluded: chain O1 residue 14 GLU Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 24 SER Chi-restraints excluded: chain O1 residue 40 GLN Chi-restraints excluded: chain O1 residue 48 LYS Chi-restraints excluded: chain O1 residue 60 VAL Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 65 LEU Chi-restraints excluded: chain T1 residue 39 ILE Chi-restraints excluded: chain U1 residue 42 THR Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 108 LYS Chi-restraints excluded: chain C2 residue 120 VAL Chi-restraints excluded: chain C2 residue 132 MET Chi-restraints excluded: chain C2 residue 157 SER Chi-restraints excluded: chain C2 residue 191 THR Chi-restraints excluded: chain C2 residue 197 ASN Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 50 VAL Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain E2 residue 10 SER Chi-restraints excluded: chain E2 residue 65 THR Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 164 LEU Chi-restraints excluded: chain E2 residue 166 LYS Chi-restraints excluded: chain E2 residue 175 ILE Chi-restraints excluded: chain E2 residue 178 VAL Chi-restraints excluded: chain E2 residue 189 THR Chi-restraints excluded: chain E2 residue 195 GLN Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 44 ILE Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 144 ASP Chi-restraints excluded: chain F2 residue 159 THR Chi-restraints excluded: chain F2 residue 162 SER Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 23 VAL Chi-restraints excluded: chain G2 residue 25 THR Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 92 VAL Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain I2 residue 13 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain J2 residue 140 LEU Chi-restraints excluded: chain K2 residue 6 THR Chi-restraints excluded: chain K2 residue 43 ILE Chi-restraints excluded: chain K2 residue 61 VAL Chi-restraints excluded: chain K2 residue 118 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 40 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 46 VAL Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 54 THR Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 15 SER Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 70 THR Chi-restraints excluded: chain N2 residue 97 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 12 THR Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 8 LEU Chi-restraints excluded: chain P2 residue 26 VAL Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 78 SER Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain P2 residue 85 SER Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain R2 residue 43 ASN Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain S2 residue 57 ASN Chi-restraints excluded: chain S2 residue 70 LYS Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 27 SER Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 54 GLU Chi-restraints excluded: chain T2 residue 55 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 60 THR Chi-restraints excluded: chain T2 residue 66 LYS Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 68 SER Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 3 THR Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 34 LYS Chi-restraints excluded: chain V2 residue 79 ARG Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 38 VAL Chi-restraints excluded: chain W2 residue 43 THR Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain W2 residue 75 LYS Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 11 VAL Chi-restraints excluded: chain Y2 residue 12 GLU Chi-restraints excluded: chain Y2 residue 23 ARG Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 4 THR Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 9 THR Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain a2 residue 29 SER Chi-restraints excluded: chain a2 residue 46 ASP Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 17 THR Chi-restraints excluded: chain b2 residue 47 VAL Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain c2 residue 11 LYS Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 16 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain d2 residue 38 THR Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 813 optimal weight: 6.9990 chunk 554 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 726 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 833 optimal weight: 5.9990 chunk 674 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 498 optimal weight: 5.9990 chunk 876 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 24 ASN B1 168 HIS C1 8 ASN C1 140 ASN ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 54 GLN D1 59 GLN E1 12 GLN E1 132 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 75 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN ** N1 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 57 HIS T1 3 ASN T1 78 ASN C2 21 ASN C2 153 GLN D2 130 GLN ** D2 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2 41 GLN E2 94 GLN E2 163 ASN E2 195 GLN F2 63 GLN G2 143 GLN H2 88 HIS J2 67 ASN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 89 ASN ** L2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P2 7 GLN ** P2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 81 ASN R2 18 GLN R2 87 GLN S2 61 ASN T2 48 GLN X2 6 GLN c2 13 ASN c2 26 ASN e2 35 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 156479 Z= 0.442 Angle : 0.740 15.836 234145 Z= 0.385 Chirality : 0.041 0.405 29875 Planarity : 0.007 0.134 12503 Dihedral : 23.104 179.426 78488 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 9.33 % Allowed : 34.45 % Favored : 56.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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 (0.11), residues: 5626 helix: 0.60 (0.12), residues: 1901 sheet: -0.53 (0.15), residues: 1091 loop : -0.69 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPB1 23 HIS 0.010 0.001 HISG2 115 PHE 0.032 0.002 PHEH1 49 TYR 0.033 0.002 TYRL1 66 ARG 0.024 0.001 ARGJ2 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2115 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1679 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 132 LYS cc_start: 0.6541 (tppt) cc_final: 0.6227 (tttt) REVERT: G1 4 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5756 (tmm-80) REVERT: G1 97 ASN cc_start: 0.6811 (m-40) cc_final: 0.5842 (m110) REVERT: H1 41 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7419 (tmmm) REVERT: I1 122 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6176 (mmt-90) REVERT: L1 83 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6494 (ptp90) REVERT: L1 103 ASP cc_start: 0.5291 (OUTLIER) cc_final: 0.4990 (m-30) REVERT: O1 10 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7009 (mppt) REVERT: O1 26 GLU cc_start: 0.6414 (mp0) cc_final: 0.6163 (mp0) REVERT: O1 48 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7389 (mmmm) REVERT: R1 61 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7235 (mtt180) REVERT: C2 25 HIS cc_start: 0.8432 (t70) cc_final: 0.8193 (t70) REVERT: C2 68 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8827 (mtpm) REVERT: C2 98 ASP cc_start: 0.8395 (p0) cc_final: 0.7978 (p0) REVERT: C2 108 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8694 (tppp) REVERT: C2 111 LYS cc_start: 0.8677 (pmtt) cc_final: 0.8420 (pmtt) REVERT: C2 271 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7303 (ptp90) REVERT: D2 88 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: E2 24 ASN cc_start: 0.8808 (t0) cc_final: 0.8592 (t0) REVERT: E2 111 GLU cc_start: 0.8562 (tp30) cc_final: 0.7947 (tp30) REVERT: E2 115 GLN cc_start: 0.8877 (mt0) cc_final: 0.8293 (mt0) REVERT: E2 145 ASP cc_start: 0.6827 (t0) cc_final: 0.6530 (t70) REVERT: F2 19 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8606 (tm-30) REVERT: F2 42 GLU cc_start: 0.8397 (pp20) cc_final: 0.7819 (pp20) REVERT: F2 85 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8003 (pp) REVERT: F2 98 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7685 (pp20) REVERT: F2 125 ARG cc_start: 0.9366 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: F2 163 ASP cc_start: 0.8485 (m-30) cc_final: 0.8231 (t0) REVERT: G2 2 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7607 (p) REVERT: G2 95 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.6921 (pmt-80) REVERT: G2 130 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: G2 163 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.7271 (ptp90) REVERT: I2 117 MET cc_start: -0.0643 (mmp) cc_final: -0.1561 (ttp) REVERT: L2 142 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8806 (pp) REVERT: M2 17 ASN cc_start: 0.8584 (t0) cc_final: 0.8270 (t0) REVERT: M2 45 GLN cc_start: 0.8874 (mt0) cc_final: 0.8496 (mt0) REVERT: N2 57 THR cc_start: 0.8917 (m) cc_final: 0.8531 (p) REVERT: O2 84 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: O2 99 TYR cc_start: 0.9095 (t80) cc_final: 0.8528 (t80) REVERT: O2 104 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8402 (tm-30) REVERT: P2 7 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: P2 29 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8594 (mtpm) REVERT: P2 75 GLN cc_start: 0.8122 (mp10) cc_final: 0.7873 (mp10) REVERT: Q2 5 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8911 (mtmm) REVERT: Q2 22 LYS cc_start: 0.8564 (mttp) cc_final: 0.8361 (mttm) REVERT: R2 21 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8475 (ttm-80) REVERT: R2 31 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7429 (tm-30) REVERT: R2 79 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8065 (ptt90) REVERT: R2 97 LYS cc_start: 0.9299 (ttpt) cc_final: 0.8858 (ttpt) REVERT: S2 95 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7547 (ttm110) REVERT: T2 66 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8392 (mtpp) REVERT: T2 69 ARG cc_start: 0.8452 (tpp-160) cc_final: 0.8249 (ttm110) REVERT: U2 22 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8157 (ttp-170) REVERT: U2 26 LYS cc_start: 0.8750 (mmtp) cc_final: 0.7998 (mptp) REVERT: U2 37 GLU cc_start: 0.8403 (pm20) cc_final: 0.7763 (pm20) REVERT: U2 96 PHE cc_start: 0.8827 (m-80) cc_final: 0.8623 (m-10) REVERT: V2 2 PHE cc_start: 0.8041 (m-80) cc_final: 0.7717 (m-80) REVERT: V2 25 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8409 (mmmm) REVERT: V2 53 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8185 (mtmm) REVERT: W2 75 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9005 (mmtp) REVERT: X2 32 ASN cc_start: 0.8836 (t0) cc_final: 0.8369 (t0) REVERT: Y2 20 ASN cc_start: 0.8979 (m110) cc_final: 0.8659 (m110) REVERT: Y2 31 GLN cc_start: 0.8735 (mm-40) cc_final: 0.7990 (tp-100) REVERT: b2 35 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: d2 16 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8609 (tppp) REVERT: d2 42 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8189 (ttm-80) outliers start: 436 outliers final: 227 residues processed: 1855 average time/residue: 2.0995 time to fit residues: 5670.5719 Evaluate side-chains 1844 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1587 time to evaluate : 5.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 106 THR Chi-restraints excluded: chain B1 residue 107 VAL Chi-restraints excluded: chain B1 residue 142 GLU Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain B1 residue 199 VAL Chi-restraints excluded: chain B1 residue 207 ILE Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 128 VAL Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 162 ILE Chi-restraints excluded: chain C1 residue 186 THR Chi-restraints excluded: chain C1 residue 191 THR Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain C1 residue 200 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 53 VAL Chi-restraints excluded: chain D1 residue 142 VAL Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain D1 residue 144 SER Chi-restraints excluded: chain D1 residue 165 ARG Chi-restraints excluded: chain D1 residue 202 GLU Chi-restraints excluded: chain E1 residue 21 VAL Chi-restraints excluded: chain E1 residue 34 THR Chi-restraints excluded: chain E1 residue 56 VAL Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain G1 residue 4 ARG Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 31 MET Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain G1 residue 129 GLU Chi-restraints excluded: chain H1 residue 11 LEU Chi-restraints excluded: chain H1 residue 34 VAL Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 71 VAL Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 95 VAL Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 104 VAL Chi-restraints excluded: chain I1 residue 122 ARG Chi-restraints excluded: chain K1 residue 26 SER Chi-restraints excluded: chain K1 residue 36 ASP Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain K1 residue 119 ASN Chi-restraints excluded: chain K1 residue 121 CYS Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 52 VAL Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain L1 residue 103 ASP Chi-restraints excluded: chain M1 residue 9 ILE Chi-restraints excluded: chain M1 residue 76 SER Chi-restraints excluded: chain M1 residue 108 THR Chi-restraints excluded: chain N1 residue 35 ASN Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain N1 residue 64 CYS Chi-restraints excluded: chain O1 residue 3 LEU Chi-restraints excluded: chain O1 residue 10 LYS Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 24 SER Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain O1 residue 48 LYS Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 34 THR Chi-restraints excluded: chain R1 residue 45 THR Chi-restraints excluded: chain R1 residue 61 ARG Chi-restraints excluded: chain R1 residue 65 LEU Chi-restraints excluded: chain S1 residue 63 THR Chi-restraints excluded: chain S1 residue 66 MET Chi-restraints excluded: chain T1 residue 27 MET Chi-restraints excluded: chain U1 residue 42 THR Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 53 HIS Chi-restraints excluded: chain C2 residue 68 LYS Chi-restraints excluded: chain C2 residue 108 LYS Chi-restraints excluded: chain C2 residue 157 SER Chi-restraints excluded: chain C2 residue 160 THR Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 88 GLU Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain D2 residue 176 ASP Chi-restraints excluded: chain E2 residue 10 SER Chi-restraints excluded: chain E2 residue 65 THR Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 73 ILE Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 125 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 175 ILE Chi-restraints excluded: chain E2 residue 176 ASP Chi-restraints excluded: chain E2 residue 189 THR Chi-restraints excluded: chain E2 residue 197 GLU Chi-restraints excluded: chain F2 residue 44 ILE Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 85 ILE Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 144 ASP Chi-restraints excluded: chain F2 residue 159 THR Chi-restraints excluded: chain F2 residue 162 SER Chi-restraints excluded: chain G2 residue 2 SER Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 34 THR Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 131 ILE Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain H2 residue 85 VAL Chi-restraints excluded: chain I2 residue 13 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 93 ILE Chi-restraints excluded: chain J2 residue 140 LEU Chi-restraints excluded: chain K2 residue 6 THR Chi-restraints excluded: chain K2 residue 25 LEU Chi-restraints excluded: chain K2 residue 35 VAL Chi-restraints excluded: chain K2 residue 61 VAL Chi-restraints excluded: chain K2 residue 118 LEU Chi-restraints excluded: chain L2 residue 5 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 40 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 46 VAL Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 117 THR Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain L2 residue 142 ILE Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 54 THR Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 88 ASN Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 6 SER Chi-restraints excluded: chain N2 residue 15 SER Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 53 THR Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 70 THR Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 97 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 12 THR Chi-restraints excluded: chain O2 residue 49 VAL Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 7 GLN Chi-restraints excluded: chain P2 residue 26 VAL Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 29 LYS Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 63 LYS Chi-restraints excluded: chain P2 residue 78 SER Chi-restraints excluded: chain P2 residue 85 SER Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 18 LEU Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 80 ILE Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain Q2 residue 104 VAL Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain R2 residue 99 THR Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain S2 residue 85 ILE Chi-restraints excluded: chain S2 residue 95 ARG Chi-restraints excluded: chain T2 residue 4 GLU Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 27 SER Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 55 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 60 THR Chi-restraints excluded: chain T2 residue 66 LYS Chi-restraints excluded: chain T2 residue 74 ILE Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 21 LYS Chi-restraints excluded: chain U2 residue 68 SER Chi-restraints excluded: chain V2 residue 3 THR Chi-restraints excluded: chain V2 residue 8 VAL Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 34 LYS Chi-restraints excluded: chain V2 residue 45 ASP Chi-restraints excluded: chain V2 residue 53 LYS Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 38 VAL Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain W2 residue 75 LYS Chi-restraints excluded: chain X2 residue 2 SER Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 11 VAL Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 4 THR Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain Z2 residue 52 SER Chi-restraints excluded: chain a2 residue 9 THR Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain a2 residue 29 SER Chi-restraints excluded: chain a2 residue 43 ILE Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 17 THR Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain b2 residue 35 GLU Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 16 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 328 optimal weight: 10.0000 chunk 879 optimal weight: 0.0000 chunk 192 optimal weight: 10.0000 chunk 573 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 977 optimal weight: 0.8980 chunk 811 optimal weight: 0.9980 chunk 452 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 513 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 8 ASN C1 140 ASN ** C1 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 54 GLN E1 12 GLN E1 73 ASN E1 78 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 118 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 73 ASN L1 112 GLN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 57 HIS T1 3 ASN C2 153 GLN D2 130 GLN D2 136 ASN D2 167 ASN E2 41 GLN E2 90 GLN E2 94 GLN E2 163 ASN F2 27 GLN F2 52 ASN ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 88 GLN G2 143 GLN H2 88 HIS J2 67 ASN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN P2 12 GLN R2 18 GLN R2 87 GLN S2 57 ASN S2 61 ASN T2 48 GLN T2 70 HIS U2 74 ASN V2 24 ASN ** W2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN Y2 25 GLN a2 4 GLN c2 13 ASN e2 37 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 156479 Z= 0.184 Angle : 0.626 14.280 234145 Z= 0.332 Chirality : 0.034 0.396 29875 Planarity : 0.006 0.124 12503 Dihedral : 23.099 179.762 78488 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 6.63 % Allowed : 38.83 % Favored : 54.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.14 (0.11), residues: 5626 helix: 0.80 (0.12), residues: 1903 sheet: -0.30 (0.15), residues: 1064 loop : -0.57 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRPB1 23 HIS 0.005 0.001 HISO2 29 PHE 0.031 0.002 PHEH1 49 TYR 0.024 0.002 TYRR2 2 ARG 0.014 0.001 ARGS1 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1971 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1661 time to evaluate : 5.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 197 ASP cc_start: 0.7411 (t0) cc_final: 0.7180 (t0) REVERT: D1 54 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: H1 41 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7500 (tmmm) REVERT: L1 12 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8049 (mmt-90) REVERT: L1 83 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6293 (ptp90) REVERT: O1 67 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7800 (mp) REVERT: T1 68 HIS cc_start: 0.6532 (t-90) cc_final: 0.5649 (t70) REVERT: C2 98 ASP cc_start: 0.8335 (p0) cc_final: 0.7956 (p0) REVERT: C2 111 LYS cc_start: 0.8679 (pmtt) cc_final: 0.8341 (pmtt) REVERT: C2 150 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8750 (tttm) REVERT: C2 153 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: C2 271 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6971 (ptp90) REVERT: E2 24 ASN cc_start: 0.8619 (t0) cc_final: 0.8376 (t0) REVERT: E2 145 ASP cc_start: 0.6756 (t0) cc_final: 0.6478 (t70) REVERT: F2 14 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8999 (pptt) REVERT: F2 27 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.8590 (tp40) REVERT: F2 42 GLU cc_start: 0.8336 (pp20) cc_final: 0.8038 (pp20) REVERT: F2 85 ILE cc_start: 0.8261 (tt) cc_final: 0.7968 (pp) REVERT: F2 98 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7696 (pp20) REVERT: F2 125 ARG cc_start: 0.9274 (mmm-85) cc_final: 0.8374 (mmm-85) REVERT: F2 142 ASP cc_start: 0.7857 (p0) cc_final: 0.6578 (p0) REVERT: F2 144 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8171 (p0) REVERT: F2 154 ILE cc_start: 0.9544 (mt) cc_final: 0.9255 (mm) REVERT: F2 163 ASP cc_start: 0.8592 (m-30) cc_final: 0.8290 (t70) REVERT: F2 165 GLU cc_start: 0.8561 (mp0) cc_final: 0.8091 (mp0) REVERT: G2 2 SER cc_start: 0.7895 (OUTLIER) cc_final: 0.7537 (p) REVERT: G2 130 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: G2 163 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.7367 (ptp90) REVERT: I2 117 MET cc_start: -0.0486 (mmp) cc_final: -0.1544 (ttt) REVERT: J2 31 GLU cc_start: 0.7562 (tp30) cc_final: 0.7276 (tp30) REVERT: J2 34 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8249 (ttp80) REVERT: K2 92 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: K2 106 GLU cc_start: 0.8330 (mp0) cc_final: 0.7941 (mp0) REVERT: M2 17 ASN cc_start: 0.8496 (t0) cc_final: 0.8198 (t0) REVERT: M2 45 GLN cc_start: 0.8773 (mt0) cc_final: 0.8323 (mt0) REVERT: N2 57 THR cc_start: 0.8788 (m) cc_final: 0.8435 (p) REVERT: O2 76 LYS cc_start: 0.9246 (ttpm) cc_final: 0.8744 (ttpp) REVERT: O2 84 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: O2 99 TYR cc_start: 0.9055 (t80) cc_final: 0.8441 (t80) REVERT: O2 104 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8284 (tm-30) REVERT: P2 37 LYS cc_start: 0.7761 (mppt) cc_final: 0.7473 (mmtt) REVERT: Q2 5 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8858 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8319 (t80) cc_final: 0.7999 (t80) REVERT: Q2 51 ARG cc_start: 0.8422 (mpt90) cc_final: 0.7600 (mpt90) REVERT: R2 31 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7519 (tm-30) REVERT: R2 49 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8868 (pt) REVERT: R2 79 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8044 (ptt90) REVERT: R2 97 LYS cc_start: 0.9269 (ttpt) cc_final: 0.8850 (ttpt) REVERT: T2 3 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8388 (mtp85) REVERT: U2 26 LYS cc_start: 0.8706 (mmtp) cc_final: 0.7563 (mptp) REVERT: U2 37 GLU cc_start: 0.8319 (pm20) cc_final: 0.7590 (pm20) REVERT: U2 74 ASN cc_start: 0.8053 (t0) cc_final: 0.7747 (m-40) REVERT: V2 2 PHE cc_start: 0.8000 (m-80) cc_final: 0.7773 (m-80) REVERT: V2 25 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8558 (mtpp) REVERT: W2 68 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8660 (ttmm) REVERT: X2 32 ASN cc_start: 0.8794 (t0) cc_final: 0.8376 (t0) REVERT: Y2 20 ASN cc_start: 0.8939 (m110) cc_final: 0.8648 (m110) REVERT: Y2 31 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8018 (tp-100) REVERT: b2 49 TYR cc_start: 0.9044 (m-80) cc_final: 0.8726 (m-80) REVERT: d2 42 ARG cc_start: 0.8764 (ttp80) cc_final: 0.8140 (ttm-80) outliers start: 310 outliers final: 167 residues processed: 1805 average time/residue: 2.0329 time to fit residues: 5330.7325 Evaluate side-chains 1782 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1594 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain B1 residue 199 VAL Chi-restraints excluded: chain C1 residue 8 ASN Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 33 LEU Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 119 SER Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 162 ILE Chi-restraints excluded: chain C1 residue 195 VAL Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 53 VAL Chi-restraints excluded: chain D1 residue 54 GLN Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain D1 residue 144 SER Chi-restraints excluded: chain D1 residue 161 LEU Chi-restraints excluded: chain E1 residue 11 LEU Chi-restraints excluded: chain E1 residue 56 VAL Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain F1 residue 36 ILE Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain H1 residue 11 LEU Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain H1 residue 118 GLN Chi-restraints excluded: chain I1 residue 83 ILE Chi-restraints excluded: chain J1 residue 77 VAL Chi-restraints excluded: chain K1 residue 36 ASP Chi-restraints excluded: chain K1 residue 42 LEU Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 12 ARG Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 52 VAL Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain L1 residue 107 VAL Chi-restraints excluded: chain M1 residue 12 HIS Chi-restraints excluded: chain M1 residue 45 ILE Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain M1 residue 49 SER Chi-restraints excluded: chain N1 residue 35 ASN Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 67 LEU Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain P1 residue 26 ASN Chi-restraints excluded: chain P1 residue 29 ASN Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain T1 residue 3 ASN Chi-restraints excluded: chain T1 residue 27 MET Chi-restraints excluded: chain T1 residue 48 GLN Chi-restraints excluded: chain U1 residue 42 THR Chi-restraints excluded: chain U1 residue 44 GLU Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 72 ASP Chi-restraints excluded: chain C2 residue 95 LEU Chi-restraints excluded: chain C2 residue 150 LYS Chi-restraints excluded: chain C2 residue 153 GLN Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 176 ASP Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 27 GLN Chi-restraints excluded: chain F2 residue 37 ASN Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 144 ASP Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 162 SER Chi-restraints excluded: chain G2 residue 2 SER Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 39 ASP Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 30 THR Chi-restraints excluded: chain J2 residue 43 GLU Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 93 ILE Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain J2 residue 142 ILE Chi-restraints excluded: chain K2 residue 42 THR Chi-restraints excluded: chain K2 residue 92 GLU Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 117 THR Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 82 MET Chi-restraints excluded: chain M2 residue 88 ASN Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 56 LYS Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 97 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 49 VAL Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 83 LEU Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 8 LEU Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 78 SER Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 49 ILE Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain S2 residue 57 ASN Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain T2 residue 4 GLU Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 27 SER Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 48 GLN Chi-restraints excluded: chain T2 residue 55 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 74 ILE Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 100 SER Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 12 ASN Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain d2 residue 38 THR Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 942 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 556 optimal weight: 6.9990 chunk 713 optimal weight: 10.0000 chunk 552 optimal weight: 20.0000 chunk 822 optimal weight: 6.9990 chunk 545 optimal weight: 6.9990 chunk 973 optimal weight: 2.9990 chunk 609 optimal weight: 10.0000 chunk 593 optimal weight: 50.0000 chunk 449 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 24 ASN C1 8 ASN C1 140 ASN E1 12 GLN E1 73 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 97 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 6 GLN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 56 GLN S1 57 HIS T1 21 ASN ** T1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 130 GLN D2 167 ASN E2 41 GLN E2 90 GLN E2 94 GLN ** E2 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN H2 88 HIS J2 67 ASN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN L2 104 GLN ** P2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 20 GLN ** Q2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R2 82 HIS S2 61 ASN T2 15 HIS X2 6 GLN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 13 ASN e2 35 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.167 156479 Z= 0.459 Angle : 0.749 15.954 234145 Z= 0.387 Chirality : 0.040 0.477 29875 Planarity : 0.007 0.135 12503 Dihedral : 23.007 179.352 78486 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.28 % Favored : 95.57 % Rotamer: Outliers : 7.87 % Allowed : 38.77 % Favored : 53.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.34 (0.11), residues: 5626 helix: 0.67 (0.12), residues: 1903 sheet: -0.45 (0.15), residues: 1117 loop : -0.71 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRPB1 23 HIS 0.025 0.002 HISB1 94 PHE 0.031 0.002 PHEH1 49 TYR 0.031 0.002 TYRR2 2 ARG 0.014 0.001 ARGS1 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1993 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1625 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G1 4 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5795 (tmm-80) REVERT: G1 97 ASN cc_start: 0.6886 (m-40) cc_final: 0.6380 (m110) REVERT: H1 41 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7524 (tmmm) REVERT: I1 122 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6209 (mmt-90) REVERT: L1 12 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7842 (mmt-90) REVERT: L1 83 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6534 (ptp90) REVERT: O1 67 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7841 (mp) REVERT: C2 43 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.6943 (mtm-85) REVERT: C2 98 ASP cc_start: 0.8338 (p0) cc_final: 0.7943 (p0) REVERT: C2 108 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8734 (tppp) REVERT: C2 111 LYS cc_start: 0.8636 (pmtt) cc_final: 0.8306 (pmtt) REVERT: C2 271 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7116 (ptp90) REVERT: D2 165 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7473 (ttp) REVERT: E2 24 ASN cc_start: 0.8742 (t0) cc_final: 0.8519 (t0) REVERT: E2 111 GLU cc_start: 0.8449 (tp30) cc_final: 0.8028 (tp30) REVERT: E2 145 ASP cc_start: 0.6810 (t0) cc_final: 0.6520 (t0) REVERT: F2 14 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9032 (pptt) REVERT: F2 42 GLU cc_start: 0.8440 (pp20) cc_final: 0.8181 (pp20) REVERT: F2 47 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8747 (pptt) REVERT: F2 85 ILE cc_start: 0.8290 (tt) cc_final: 0.8061 (pp) REVERT: F2 98 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: F2 154 ILE cc_start: 0.9536 (mt) cc_final: 0.9175 (mm) REVERT: F2 163 ASP cc_start: 0.8702 (m-30) cc_final: 0.8397 (t0) REVERT: F2 175 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: G2 2 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7538 (p) REVERT: G2 95 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7622 (ptm160) REVERT: G2 130 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: G2 163 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.7395 (ptp90) REVERT: I2 117 MET cc_start: -0.0656 (mmp) cc_final: -0.1620 (ttt) REVERT: J2 31 GLU cc_start: 0.7695 (tp30) cc_final: 0.7380 (tp30) REVERT: J2 34 ARG cc_start: 0.8552 (ttp80) cc_final: 0.8348 (ttp80) REVERT: L2 142 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8784 (pp) REVERT: M2 17 ASN cc_start: 0.8573 (t0) cc_final: 0.8227 (t0) REVERT: M2 45 GLN cc_start: 0.8852 (mt0) cc_final: 0.8401 (mt0) REVERT: N2 57 THR cc_start: 0.8944 (m) cc_final: 0.8590 (p) REVERT: O2 84 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8861 (pm20) REVERT: O2 99 TYR cc_start: 0.9084 (t80) cc_final: 0.8561 (t80) REVERT: O2 104 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8368 (tm-30) REVERT: P2 37 LYS cc_start: 0.7806 (mppt) cc_final: 0.7530 (mmtt) REVERT: Q2 5 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8897 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8545 (t80) cc_final: 0.8212 (t80) REVERT: Q2 51 ARG cc_start: 0.8625 (mpt90) cc_final: 0.7379 (mpt90) REVERT: R2 21 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8488 (ttm-80) REVERT: R2 31 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7677 (tm-30) REVERT: R2 79 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8061 (ptt90) REVERT: R2 97 LYS cc_start: 0.9288 (ttpt) cc_final: 0.8850 (ttpt) REVERT: S2 83 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (mptp) REVERT: T2 3 ARG cc_start: 0.8833 (mmm-85) cc_final: 0.8510 (mtp85) REVERT: U2 26 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8561 (mptt) REVERT: U2 73 PHE cc_start: 0.8319 (t80) cc_final: 0.7962 (t80) REVERT: V2 2 PHE cc_start: 0.7998 (m-80) cc_final: 0.7701 (m-80) REVERT: V2 25 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8385 (mmmm) REVERT: V2 51 GLN cc_start: 0.8856 (pp30) cc_final: 0.8149 (tm-30) REVERT: V2 57 TYR cc_start: 0.8866 (m-80) cc_final: 0.7890 (m-10) REVERT: W2 68 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: X2 32 ASN cc_start: 0.8800 (t0) cc_final: 0.8320 (t0) REVERT: Y2 20 ASN cc_start: 0.8945 (m110) cc_final: 0.8635 (m110) REVERT: Y2 31 GLN cc_start: 0.8722 (mm-40) cc_final: 0.7950 (tp-100) REVERT: d2 16 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8618 (tppp) REVERT: d2 45 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8216 (ttp80) outliers start: 368 outliers final: 230 residues processed: 1768 average time/residue: 2.0149 time to fit residues: 5197.3392 Evaluate side-chains 1838 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1582 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 9 MET Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 106 THR Chi-restraints excluded: chain B1 residue 107 VAL Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain C1 residue 8 ASN Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 128 VAL Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 162 ILE Chi-restraints excluded: chain C1 residue 186 THR Chi-restraints excluded: chain C1 residue 191 THR Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain C1 residue 200 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 74 ASN Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain D1 residue 144 SER Chi-restraints excluded: chain E1 residue 21 VAL Chi-restraints excluded: chain E1 residue 24 THR Chi-restraints excluded: chain E1 residue 34 THR Chi-restraints excluded: chain E1 residue 38 VAL Chi-restraints excluded: chain E1 residue 56 VAL Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain F1 residue 64 VAL Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 4 ARG Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 31 MET Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain H1 residue 11 LEU Chi-restraints excluded: chain H1 residue 34 VAL Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 83 ILE Chi-restraints excluded: chain I1 residue 122 ARG Chi-restraints excluded: chain J1 residue 25 ILE Chi-restraints excluded: chain K1 residue 26 SER Chi-restraints excluded: chain K1 residue 36 ASP Chi-restraints excluded: chain K1 residue 42 LEU Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain K1 residue 121 CYS Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 12 ARG Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 83 ARG Chi-restraints excluded: chain L1 residue 107 VAL Chi-restraints excluded: chain M1 residue 9 ILE Chi-restraints excluded: chain M1 residue 25 VAL Chi-restraints excluded: chain M1 residue 45 ILE Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain N1 residue 35 ASN Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain N1 residue 64 CYS Chi-restraints excluded: chain O1 residue 3 LEU Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain O1 residue 52 SER Chi-restraints excluded: chain O1 residue 60 VAL Chi-restraints excluded: chain O1 residue 67 LEU Chi-restraints excluded: chain O1 residue 75 VAL Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain P1 residue 29 ASN Chi-restraints excluded: chain P1 residue 35 ARG Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain Q1 residue 33 ILE Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 59 ILE Chi-restraints excluded: chain R1 residue 65 LEU Chi-restraints excluded: chain S1 residue 63 THR Chi-restraints excluded: chain U1 residue 42 THR Chi-restraints excluded: chain U1 residue 44 GLU Chi-restraints excluded: chain U1 residue 56 HIS Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 43 ARG Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 72 ASP Chi-restraints excluded: chain C2 residue 108 LYS Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 191 THR Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 50 VAL Chi-restraints excluded: chain D2 residue 52 THR Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain D2 residue 165 MET Chi-restraints excluded: chain D2 residue 176 ASP Chi-restraints excluded: chain D2 residue 207 VAL Chi-restraints excluded: chain E2 residue 10 SER Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 72 SER Chi-restraints excluded: chain E2 residue 73 ILE Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 175 ILE Chi-restraints excluded: chain E2 residue 179 SER Chi-restraints excluded: chain E2 residue 189 THR Chi-restraints excluded: chain E2 residue 197 GLU Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 44 ILE Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 144 ASP Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 159 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 2 SER Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 39 ASP Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 72 LEU Chi-restraints excluded: chain G2 residue 95 ARG Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 107 LEU Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain H2 residue 85 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 30 THR Chi-restraints excluded: chain J2 residue 43 GLU Chi-restraints excluded: chain J2 residue 52 ASP Chi-restraints excluded: chain J2 residue 58 ASN Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain K2 residue 6 THR Chi-restraints excluded: chain K2 residue 104 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 46 VAL Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 106 GLU Chi-restraints excluded: chain L2 residue 117 THR Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain L2 residue 142 ILE Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 54 THR Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 88 ASN Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain M2 residue 136 MET Chi-restraints excluded: chain N2 residue 6 SER Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 53 THR Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 75 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 12 THR Chi-restraints excluded: chain O2 residue 49 VAL Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 83 LEU Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 8 LEU Chi-restraints excluded: chain P2 residue 26 VAL Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 63 LYS Chi-restraints excluded: chain P2 residue 78 SER Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain P2 residue 85 SER Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 75 VAL Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain S2 residue 83 LYS Chi-restraints excluded: chain T2 residue 4 GLU Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 55 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 60 THR Chi-restraints excluded: chain T2 residue 63 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 21 LYS Chi-restraints excluded: chain U2 residue 41 LEU Chi-restraints excluded: chain U2 residue 58 ILE Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 3 THR Chi-restraints excluded: chain V2 residue 24 ASN Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 42 LEU Chi-restraints excluded: chain V2 residue 45 ASP Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 12 ASN Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 31 VAL Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 43 THR Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain W2 residue 68 LYS Chi-restraints excluded: chain X2 residue 2 SER Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 22 LEU Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 4 THR Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 9 THR Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain a2 residue 43 ILE Chi-restraints excluded: chain b2 residue 13 SER Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 16 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain d2 residue 38 THR Chi-restraints excluded: chain d2 residue 45 ARG Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 602 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 581 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 618 optimal weight: 5.9990 chunk 663 optimal weight: 7.9990 chunk 481 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 765 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 140 ASN ** D1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 12 GLN E1 73 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 56 GLN S1 57 HIS T1 3 ASN ** T1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1 48 GLN ** T1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 153 GLN D2 130 GLN D2 167 ASN E2 41 GLN E2 90 GLN E2 94 GLN ** E2 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN J2 67 ASN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN ** P2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 56 GLN R2 18 GLN R2 87 GLN S2 61 ASN T2 15 HIS T2 48 GLN ** W2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN a2 4 GLN c2 13 ASN e2 35 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 156479 Z= 0.286 Angle : 0.675 16.190 234145 Z= 0.354 Chirality : 0.036 0.415 29875 Planarity : 0.006 0.129 12503 Dihedral : 23.049 179.808 78486 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.89 % Rotamer: Outliers : 6.42 % Allowed : 40.86 % Favored : 52.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.25 (0.11), residues: 5626 helix: 0.78 (0.12), residues: 1899 sheet: -0.37 (0.16), residues: 1074 loop : -0.69 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPB1 23 HIS 0.021 0.001 HISB1 94 PHE 0.031 0.002 PHEU2 95 TYR 0.038 0.002 TYRR2 2 ARG 0.016 0.001 ARGS1 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1923 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1623 time to evaluate : 6.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 93 ASN cc_start: 0.7501 (p0) cc_final: 0.7249 (p0) REVERT: H1 41 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7501 (tmmm) REVERT: L1 12 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8010 (mmt-90) REVERT: C2 43 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.6980 (mtm-85) REVERT: C2 98 ASP cc_start: 0.8403 (p0) cc_final: 0.7960 (p0) REVERT: C2 271 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7095 (ptp90) REVERT: E2 24 ASN cc_start: 0.8665 (t0) cc_final: 0.8425 (t0) REVERT: E2 111 GLU cc_start: 0.8474 (tp30) cc_final: 0.8248 (tp30) REVERT: E2 115 GLN cc_start: 0.8712 (mt0) cc_final: 0.8282 (mt0) REVERT: E2 145 ASP cc_start: 0.6808 (t0) cc_final: 0.6505 (t70) REVERT: E2 197 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: E2 198 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8490 (tm-30) REVERT: F2 14 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8979 (pptt) REVERT: F2 42 GLU cc_start: 0.8415 (pp20) cc_final: 0.8147 (pp20) REVERT: F2 47 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8704 (pptt) REVERT: F2 85 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7981 (pp) REVERT: F2 98 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7759 (pp20) REVERT: F2 142 ASP cc_start: 0.7919 (p0) cc_final: 0.6718 (p0) REVERT: F2 144 ASP cc_start: 0.8647 (m-30) cc_final: 0.8244 (p0) REVERT: F2 154 ILE cc_start: 0.9517 (mt) cc_final: 0.8979 (pp) REVERT: F2 163 ASP cc_start: 0.8679 (m-30) cc_final: 0.8400 (t70) REVERT: F2 175 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: G2 2 SER cc_start: 0.7834 (OUTLIER) cc_final: 0.7547 (p) REVERT: G2 88 GLN cc_start: 0.8391 (pt0) cc_final: 0.7693 (pp30) REVERT: G2 95 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7645 (ptm160) REVERT: G2 130 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: G2 163 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.7227 (ptp90) REVERT: H2 38 MET cc_start: 0.3669 (ptm) cc_final: 0.3293 (pp-130) REVERT: I2 117 MET cc_start: -0.0395 (mmp) cc_final: -0.1537 (ttt) REVERT: J2 31 GLU cc_start: 0.7646 (tp30) cc_final: 0.7318 (tp30) REVERT: J2 108 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: M2 17 ASN cc_start: 0.8513 (t0) cc_final: 0.8212 (t0) REVERT: M2 40 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8267 (mtt90) REVERT: M2 45 GLN cc_start: 0.8798 (mt0) cc_final: 0.8336 (mt0) REVERT: N2 57 THR cc_start: 0.8864 (m) cc_final: 0.8542 (p) REVERT: N2 82 GLU cc_start: 0.8519 (mp0) cc_final: 0.8103 (mp0) REVERT: O2 84 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8798 (pm20) REVERT: O2 99 TYR cc_start: 0.9062 (t80) cc_final: 0.8482 (t80) REVERT: O2 104 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Q2 5 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8892 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8527 (t80) cc_final: 0.8162 (t80) REVERT: Q2 51 ARG cc_start: 0.8530 (mpt90) cc_final: 0.7541 (mpt90) REVERT: R2 31 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7530 (tm-30) REVERT: R2 79 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8090 (ptt90) REVERT: R2 97 LYS cc_start: 0.9275 (ttpt) cc_final: 0.8856 (ttpt) REVERT: S2 83 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8483 (mptp) REVERT: T2 3 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8577 (mtp85) REVERT: U2 26 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8546 (mptt) REVERT: U2 74 ASN cc_start: 0.8019 (t0) cc_final: 0.7621 (t0) REVERT: V2 25 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8355 (mmmm) REVERT: V2 50 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (ppp) REVERT: V2 51 GLN cc_start: 0.8750 (pp30) cc_final: 0.8181 (tm-30) REVERT: V2 57 TYR cc_start: 0.8889 (m-80) cc_final: 0.8140 (m-10) REVERT: W2 68 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8530 (ttmm) REVERT: X2 32 ASN cc_start: 0.8800 (t0) cc_final: 0.8366 (t0) REVERT: Y2 20 ASN cc_start: 0.8930 (m110) cc_final: 0.8581 (m110) REVERT: Y2 31 GLN cc_start: 0.8703 (mm-40) cc_final: 0.7950 (tp-100) REVERT: Y2 56 LEU cc_start: 0.9530 (mm) cc_final: 0.9278 (mm) REVERT: c2 19 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8077 (mtm-85) REVERT: d2 16 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8585 (tppp) REVERT: d2 19 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9001 (mtmm) REVERT: d2 42 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8039 (ttm-80) outliers start: 300 outliers final: 202 residues processed: 1755 average time/residue: 2.0088 time to fit residues: 5138.8713 Evaluate side-chains 1810 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1585 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 111 ILE Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 153 ASP Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain B1 residue 199 VAL Chi-restraints excluded: chain B1 residue 207 ILE Chi-restraints excluded: chain C1 residue 15 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 134 MET Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 162 ILE Chi-restraints excluded: chain C1 residue 186 THR Chi-restraints excluded: chain C1 residue 191 THR Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain D1 residue 144 SER Chi-restraints excluded: chain E1 residue 24 THR Chi-restraints excluded: chain E1 residue 38 VAL Chi-restraints excluded: chain E1 residue 56 VAL Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 30 THR Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 31 MET Chi-restraints excluded: chain G1 residue 38 THR Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 95 ARG Chi-restraints excluded: chain H1 residue 11 LEU Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 83 ILE Chi-restraints excluded: chain I1 residue 104 VAL Chi-restraints excluded: chain K1 residue 36 ASP Chi-restraints excluded: chain K1 residue 42 LEU Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain L1 residue 8 VAL Chi-restraints excluded: chain L1 residue 12 ARG Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 79 VAL Chi-restraints excluded: chain M1 residue 25 VAL Chi-restraints excluded: chain M1 residue 45 ILE Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain N1 residue 35 ASN Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain O1 residue 3 LEU Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 36 ILE Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain O1 residue 40 GLN Chi-restraints excluded: chain O1 residue 75 VAL Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain P1 residue 29 ASN Chi-restraints excluded: chain P1 residue 35 ARG Chi-restraints excluded: chain P1 residue 78 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 65 LEU Chi-restraints excluded: chain T1 residue 3 ASN Chi-restraints excluded: chain T1 residue 39 ILE Chi-restraints excluded: chain U1 residue 42 THR Chi-restraints excluded: chain U1 residue 44 GLU Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 43 ARG Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 72 ASP Chi-restraints excluded: chain C2 residue 120 VAL Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 191 THR Chi-restraints excluded: chain C2 residue 257 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 50 VAL Chi-restraints excluded: chain D2 residue 52 THR Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain E2 residue 10 SER Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 175 ILE Chi-restraints excluded: chain E2 residue 176 ASP Chi-restraints excluded: chain E2 residue 179 SER Chi-restraints excluded: chain E2 residue 189 THR Chi-restraints excluded: chain E2 residue 195 GLN Chi-restraints excluded: chain E2 residue 197 GLU Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 34 ILE Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 85 ILE Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 108 VAL Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 2 SER Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 39 ASP Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 95 ARG Chi-restraints excluded: chain G2 residue 98 VAL Chi-restraints excluded: chain G2 residue 107 LEU Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain H2 residue 85 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 30 THR Chi-restraints excluded: chain J2 residue 44 TYR Chi-restraints excluded: chain J2 residue 52 ASP Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 108 MET Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain J2 residue 142 ILE Chi-restraints excluded: chain K2 residue 104 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 30 THR Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 40 ARG Chi-restraints excluded: chain M2 residue 54 THR Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 88 ASN Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 6 SER Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 56 LYS Chi-restraints excluded: chain N2 residue 59 SER Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 75 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 12 THR Chi-restraints excluded: chain O2 residue 49 VAL Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 83 LEU Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 7 GLN Chi-restraints excluded: chain P2 residue 8 LEU Chi-restraints excluded: chain P2 residue 26 VAL Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 63 LYS Chi-restraints excluded: chain P2 residue 78 SER Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 75 VAL Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain S2 residue 24 ILE Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain S2 residue 83 LYS Chi-restraints excluded: chain T2 residue 4 GLU Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 55 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 12 ILE Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 3 THR Chi-restraints excluded: chain V2 residue 24 ASN Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 42 LEU Chi-restraints excluded: chain V2 residue 45 ASP Chi-restraints excluded: chain V2 residue 50 MET Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 12 ASN Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 38 VAL Chi-restraints excluded: chain W2 residue 43 THR Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 9 THR Chi-restraints excluded: chain a2 residue 11 SER Chi-restraints excluded: chain a2 residue 46 ASP Chi-restraints excluded: chain b2 residue 14 SER Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 16 LYS Chi-restraints excluded: chain d2 residue 19 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain d2 residue 38 THR Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 885 optimal weight: 2.9990 chunk 932 optimal weight: 2.9990 chunk 850 optimal weight: 5.9990 chunk 907 optimal weight: 6.9990 chunk 546 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 712 optimal weight: 1.9990 chunk 278 optimal weight: 30.0000 chunk 819 optimal weight: 0.5980 chunk 857 optimal weight: 3.9990 chunk 903 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 24 ASN C1 8 ASN C1 140 ASN D1 59 GLN D1 85 ASN ** D1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 12 GLN E1 73 ASN G1 97 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 126 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 56 GLN S1 57 HIS ** T1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 153 GLN D2 130 GLN D2 173 GLN E2 41 GLN E2 90 GLN E2 94 GLN ** E2 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN J2 67 ASN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN P2 3 ASN P2 7 GLN ** Q2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 56 GLN R2 18 GLN R2 43 ASN R2 87 GLN S2 57 ASN S2 61 ASN T2 15 HIS ** T2 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 70 HIS V2 49 ASN ** W2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN a2 4 GLN c2 13 ASN e2 35 GLN ** e2 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 156479 Z= 0.196 Angle : 0.640 16.238 234145 Z= 0.337 Chirality : 0.034 0.369 29875 Planarity : 0.006 0.125 12503 Dihedral : 23.052 179.939 78486 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.57 % Favored : 96.29 % Rotamer: Outliers : 5.20 % Allowed : 42.64 % Favored : 52.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.19 (0.11), residues: 5626 helix: 0.76 (0.12), residues: 1911 sheet: -0.27 (0.16), residues: 1087 loop : -0.64 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPB1 23 HIS 0.020 0.001 HISB1 94 PHE 0.033 0.002 PHEH1 66 TYR 0.036 0.002 TYRR2 2 ARG 0.018 0.001 ARGS1 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1898 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1655 time to evaluate : 8.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 42 ASN cc_start: 0.7589 (t0) cc_final: 0.7170 (t0) REVERT: H1 41 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7474 (tmmm) REVERT: L1 12 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8006 (mmt-90) REVERT: C2 98 ASP cc_start: 0.8432 (p0) cc_final: 0.7981 (p0) REVERT: C2 214 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8246 (mtt90) REVERT: C2 271 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.6931 (ptp90) REVERT: E2 24 ASN cc_start: 0.8618 (t0) cc_final: 0.8378 (t0) REVERT: E2 111 GLU cc_start: 0.8364 (tp30) cc_final: 0.8153 (tp30) REVERT: E2 115 GLN cc_start: 0.8694 (mt0) cc_final: 0.8200 (mt0) REVERT: E2 147 LEU cc_start: 0.9063 (tt) cc_final: 0.8787 (tt) REVERT: E2 198 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8425 (tm-30) REVERT: F2 14 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8920 (pptt) REVERT: F2 27 GLN cc_start: 0.9477 (mt0) cc_final: 0.8637 (tp40) REVERT: F2 42 GLU cc_start: 0.8433 (pp20) cc_final: 0.8055 (pp20) REVERT: F2 47 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8723 (pptt) REVERT: F2 98 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: F2 154 ILE cc_start: 0.9537 (mt) cc_final: 0.9071 (pp) REVERT: F2 165 GLU cc_start: 0.8549 (mp0) cc_final: 0.8330 (mp0) REVERT: F2 175 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: G2 25 THR cc_start: 0.7676 (m) cc_final: 0.7101 (p) REVERT: G2 69 ARG cc_start: 0.8397 (tpt90) cc_final: 0.8108 (tpt90) REVERT: G2 88 GLN cc_start: 0.8311 (pt0) cc_final: 0.7638 (pp30) REVERT: G2 95 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7657 (ptm160) REVERT: G2 130 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: G2 163 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7267 (ptp90) REVERT: H2 38 MET cc_start: 0.3708 (ptm) cc_final: 0.3409 (pp-130) REVERT: I2 117 MET cc_start: -0.0343 (mmp) cc_final: -0.1643 (ttt) REVERT: J2 1 MET cc_start: 0.7826 (ppp) cc_final: 0.7611 (ppp) REVERT: J2 108 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: K2 106 GLU cc_start: 0.8345 (mp0) cc_final: 0.7964 (mp0) REVERT: M2 17 ASN cc_start: 0.8467 (t0) cc_final: 0.8153 (t0) REVERT: M2 40 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8202 (mtt90) REVERT: M2 45 GLN cc_start: 0.8778 (mt0) cc_final: 0.8345 (mt0) REVERT: N2 5 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8821 (mttm) REVERT: N2 57 THR cc_start: 0.8836 (m) cc_final: 0.8546 (p) REVERT: N2 78 LYS cc_start: 0.8922 (tttt) cc_final: 0.8707 (tptm) REVERT: N2 82 GLU cc_start: 0.8444 (mp0) cc_final: 0.7936 (mp0) REVERT: O2 76 LYS cc_start: 0.9262 (tmmm) cc_final: 0.8320 (tmmt) REVERT: O2 84 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8763 (pm20) REVERT: O2 99 TYR cc_start: 0.9052 (t80) cc_final: 0.8482 (t80) REVERT: O2 104 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8213 (tm-30) REVERT: P2 7 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: P2 37 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7733 (mppt) REVERT: Q2 5 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8440 (t80) cc_final: 0.8075 (t80) REVERT: Q2 51 ARG cc_start: 0.8392 (mpt90) cc_final: 0.7575 (mpt90) REVERT: R2 31 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7487 (tm-30) REVERT: R2 79 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8036 (ptt90) REVERT: R2 85 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: U2 74 ASN cc_start: 0.7581 (t0) cc_final: 0.7229 (t0) REVERT: V2 20 LEU cc_start: 0.9055 (mm) cc_final: 0.8778 (tp) REVERT: V2 25 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8654 (mtpp) REVERT: V2 50 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7882 (ppp) REVERT: V2 51 GLN cc_start: 0.8639 (pp30) cc_final: 0.8138 (tm-30) REVERT: X2 32 ASN cc_start: 0.8793 (t0) cc_final: 0.8362 (t0) REVERT: Y2 20 ASN cc_start: 0.8925 (m110) cc_final: 0.8588 (m110) REVERT: Y2 31 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8057 (tp-100) REVERT: b2 33 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8739 (mmmm) REVERT: c2 6 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: d2 19 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8985 (mtmm) REVERT: d2 42 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8021 (ttm-80) outliers start: 243 outliers final: 149 residues processed: 1760 average time/residue: 1.9972 time to fit residues: 5142.0371 Evaluate side-chains 1779 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1609 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 9 MET Chi-restraints excluded: chain B1 residue 14 VAL Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 196 VAL Chi-restraints excluded: chain B1 residue 199 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain E1 residue 24 THR Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 45 SER Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 83 ILE Chi-restraints excluded: chain I1 residue 104 VAL Chi-restraints excluded: chain K1 residue 42 LEU Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain L1 residue 12 ARG Chi-restraints excluded: chain L1 residue 14 ARG Chi-restraints excluded: chain L1 residue 79 VAL Chi-restraints excluded: chain M1 residue 12 HIS Chi-restraints excluded: chain M1 residue 25 VAL Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain M1 residue 104 THR Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain P1 residue 29 ASN Chi-restraints excluded: chain P1 residue 78 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 59 ILE Chi-restraints excluded: chain T1 residue 39 ILE Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 191 THR Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 50 VAL Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain D2 residue 207 VAL Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 176 ASP Chi-restraints excluded: chain E2 residue 179 SER Chi-restraints excluded: chain E2 residue 195 GLN Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 34 ILE Chi-restraints excluded: chain F2 residue 37 ASN Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 39 ASP Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 95 ARG Chi-restraints excluded: chain G2 residue 107 LEU Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain H2 residue 85 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 30 THR Chi-restraints excluded: chain J2 residue 44 TYR Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 93 ILE Chi-restraints excluded: chain J2 residue 108 MET Chi-restraints excluded: chain K2 residue 42 THR Chi-restraints excluded: chain K2 residue 104 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 40 ARG Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 5 LYS Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 56 LYS Chi-restraints excluded: chain N2 residue 73 ASN Chi-restraints excluded: chain N2 residue 75 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 7 GLN Chi-restraints excluded: chain P2 residue 25 THR Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 71 GLN Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain R2 residue 2 TYR Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 43 ASN Chi-restraints excluded: chain R2 residue 75 VAL Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 85 LYS Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain S2 residue 55 ILE Chi-restraints excluded: chain S2 residue 57 ASN Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 24 ASN Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 42 LEU Chi-restraints excluded: chain V2 residue 45 ASP Chi-restraints excluded: chain V2 residue 50 MET Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 12 ASN Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 38 VAL Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 10 SER Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain b2 residue 13 SER Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain c2 residue 6 GLN Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 19 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 595 optimal weight: 50.0000 chunk 959 optimal weight: 5.9990 chunk 585 optimal weight: 5.9990 chunk 455 optimal weight: 6.9990 chunk 666 optimal weight: 10.0000 chunk 1006 optimal weight: 9.9990 chunk 926 optimal weight: 0.9980 chunk 801 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 618 optimal weight: 8.9990 chunk 491 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 140 ASN ** D1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 73 ASN G1 97 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN L1 112 GLN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 56 GLN S1 57 HIS T1 20 HIS ** T1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 153 GLN D2 126 ASN D2 130 GLN D2 167 ASN D2 173 GLN E2 41 GLN E2 90 GLN E2 94 GLN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN J2 67 ASN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 93 GLN L2 99 ASN ** P2 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 20 GLN Q2 56 GLN R2 43 ASN R2 87 GLN S2 40 ASN S2 57 ASN S2 61 ASN T2 15 HIS V2 49 ASN ** W2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN a2 4 GLN c2 13 ASN e2 35 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 156479 Z= 0.322 Angle : 0.699 16.095 234145 Z= 0.364 Chirality : 0.037 0.535 29875 Planarity : 0.007 0.130 12503 Dihedral : 22.992 179.901 78486 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.05 % Favored : 95.81 % Rotamer: Outliers : 4.90 % Allowed : 43.54 % Favored : 51.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.29 (0.11), residues: 5626 helix: 0.66 (0.12), residues: 1905 sheet: -0.25 (0.16), residues: 1064 loop : -0.71 (0.12), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRPB1 23 HIS 0.033 0.001 HISB1 94 PHE 0.071 0.002 PHEY2 26 TYR 0.033 0.002 TYRJ2 44 ARG 0.023 0.001 ARGF1 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1844 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1615 time to evaluate : 6.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 42 ASN cc_start: 0.7315 (t0) cc_final: 0.7082 (t0) REVERT: F1 17 GLN cc_start: 0.6816 (pm20) cc_final: 0.6209 (pm20) REVERT: H1 41 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7468 (tmmm) REVERT: J1 88 MET cc_start: 0.6332 (pmm) cc_final: 0.5827 (tmm) REVERT: L1 12 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7966 (mmt-90) REVERT: C2 98 ASP cc_start: 0.8433 (p0) cc_final: 0.7969 (p0) REVERT: C2 271 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.6971 (ptp90) REVERT: D2 161 MET cc_start: 0.8608 (ptm) cc_final: 0.8377 (ptp) REVERT: E2 24 ASN cc_start: 0.8691 (t0) cc_final: 0.8470 (t0) REVERT: E2 111 GLU cc_start: 0.8439 (tp30) cc_final: 0.8165 (tp30) REVERT: E2 115 GLN cc_start: 0.8722 (mt0) cc_final: 0.8201 (mt0) REVERT: E2 198 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8613 (tp30) REVERT: F2 14 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8927 (pptt) REVERT: F2 27 GLN cc_start: 0.9483 (mt0) cc_final: 0.8691 (tp40) REVERT: F2 42 GLU cc_start: 0.8475 (pp20) cc_final: 0.8016 (pp20) REVERT: F2 47 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8745 (pptt) REVERT: F2 98 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: F2 154 ILE cc_start: 0.9531 (mt) cc_final: 0.9016 (pp) REVERT: F2 165 GLU cc_start: 0.8508 (mp0) cc_final: 0.7849 (mp0) REVERT: F2 175 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: G2 69 ARG cc_start: 0.8396 (tpt90) cc_final: 0.8138 (tpt90) REVERT: G2 88 GLN cc_start: 0.8305 (pt0) cc_final: 0.7636 (pp30) REVERT: G2 95 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7650 (ptm160) REVERT: G2 130 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: G2 163 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7227 (ptp90) REVERT: H2 38 MET cc_start: 0.3689 (ptm) cc_final: 0.3434 (pp-130) REVERT: I2 117 MET cc_start: -0.0343 (mmp) cc_final: -0.1665 (ttp) REVERT: K2 54 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8432 (ttmm) REVERT: K2 106 GLU cc_start: 0.8348 (mp0) cc_final: 0.7953 (mp0) REVERT: L2 128 THR cc_start: 0.8717 (t) cc_final: 0.8460 (t) REVERT: M2 17 ASN cc_start: 0.8534 (t0) cc_final: 0.8162 (t0) REVERT: M2 40 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8216 (mtt90) REVERT: M2 45 GLN cc_start: 0.8788 (mt0) cc_final: 0.8313 (mt0) REVERT: N2 5 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8880 (mttm) REVERT: N2 57 THR cc_start: 0.8883 (m) cc_final: 0.8584 (p) REVERT: N2 78 LYS cc_start: 0.8937 (tttt) cc_final: 0.8709 (tptm) REVERT: N2 82 GLU cc_start: 0.8486 (mp0) cc_final: 0.7961 (mp0) REVERT: O2 84 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: O2 99 TYR cc_start: 0.9065 (t80) cc_final: 0.8488 (t80) REVERT: O2 104 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8249 (tm-30) REVERT: P2 37 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7709 (mppt) REVERT: Q2 5 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8912 (mtmm) REVERT: Q2 47 TYR cc_start: 0.8557 (t80) cc_final: 0.8201 (t80) REVERT: Q2 51 ARG cc_start: 0.8555 (mpt90) cc_final: 0.7523 (mpt90) REVERT: R2 31 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7735 (tm-30) REVERT: R2 79 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8040 (ptt90) REVERT: R2 85 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8105 (ttmm) REVERT: T2 3 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8553 (mtp85) REVERT: U2 40 ASN cc_start: 0.8490 (t0) cc_final: 0.7911 (t0) REVERT: U2 74 ASN cc_start: 0.7554 (t0) cc_final: 0.7255 (t0) REVERT: U2 96 PHE cc_start: 0.8669 (m-10) cc_final: 0.8409 (m-10) REVERT: V2 25 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8622 (mtpp) REVERT: V2 50 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7823 (ppp) REVERT: V2 51 GLN cc_start: 0.8670 (pp30) cc_final: 0.8190 (tm-30) REVERT: X2 32 ASN cc_start: 0.8784 (t0) cc_final: 0.8358 (t0) REVERT: Y2 20 ASN cc_start: 0.8947 (m110) cc_final: 0.8579 (m110) REVERT: Y2 31 GLN cc_start: 0.8713 (mm-40) cc_final: 0.7975 (tp-100) REVERT: c2 6 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: d2 19 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.9000 (mtmm) REVERT: d2 42 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8038 (ttm-80) outliers start: 229 outliers final: 154 residues processed: 1722 average time/residue: 1.9731 time to fit residues: 4970.4433 Evaluate side-chains 1749 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1575 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B1 residue 9 MET Chi-restraints excluded: chain B1 residue 38 VAL Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 136 MET Chi-restraints excluded: chain B1 residue 199 VAL Chi-restraints excluded: chain C1 residue 52 VAL Chi-restraints excluded: chain C1 residue 56 VAL Chi-restraints excluded: chain C1 residue 121 THR Chi-restraints excluded: chain C1 residue 124 LEU Chi-restraints excluded: chain C1 residue 151 VAL Chi-restraints excluded: chain C1 residue 198 VAL Chi-restraints excluded: chain D1 residue 15 GLU Chi-restraints excluded: chain D1 residue 28 ILE Chi-restraints excluded: chain D1 residue 143 VAL Chi-restraints excluded: chain E1 residue 24 THR Chi-restraints excluded: chain E1 residue 64 MET Chi-restraints excluded: chain E1 residue 161 VAL Chi-restraints excluded: chain F1 residue 73 GLU Chi-restraints excluded: chain G1 residue 23 LEU Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain H1 residue 41 LYS Chi-restraints excluded: chain H1 residue 72 VAL Chi-restraints excluded: chain H1 residue 79 SER Chi-restraints excluded: chain H1 residue 107 SER Chi-restraints excluded: chain H1 residue 112 THR Chi-restraints excluded: chain I1 residue 83 ILE Chi-restraints excluded: chain I1 residue 104 VAL Chi-restraints excluded: chain J1 residue 25 ILE Chi-restraints excluded: chain K1 residue 42 LEU Chi-restraints excluded: chain K1 residue 46 THR Chi-restraints excluded: chain L1 residue 3 THR Chi-restraints excluded: chain L1 residue 12 ARG Chi-restraints excluded: chain L1 residue 19 SER Chi-restraints excluded: chain L1 residue 79 VAL Chi-restraints excluded: chain M1 residue 12 HIS Chi-restraints excluded: chain M1 residue 25 VAL Chi-restraints excluded: chain M1 residue 47 GLU Chi-restraints excluded: chain M1 residue 104 THR Chi-restraints excluded: chain N1 residue 42 TRP Chi-restraints excluded: chain O1 residue 22 THR Chi-restraints excluded: chain O1 residue 39 LEU Chi-restraints excluded: chain O1 residue 56 LEU Chi-restraints excluded: chain P1 residue 20 VAL Chi-restraints excluded: chain P1 residue 29 ASN Chi-restraints excluded: chain P1 residue 78 VAL Chi-restraints excluded: chain Q1 residue 7 THR Chi-restraints excluded: chain Q1 residue 13 VAL Chi-restraints excluded: chain R1 residue 33 ILE Chi-restraints excluded: chain R1 residue 59 ILE Chi-restraints excluded: chain T1 residue 39 ILE Chi-restraints excluded: chain C2 residue 3 VAL Chi-restraints excluded: chain C2 residue 49 ILE Chi-restraints excluded: chain C2 residue 95 LEU Chi-restraints excluded: chain C2 residue 160 THR Chi-restraints excluded: chain C2 residue 162 VAL Chi-restraints excluded: chain C2 residue 191 THR Chi-restraints excluded: chain C2 residue 203 ARG Chi-restraints excluded: chain C2 residue 271 ARG Chi-restraints excluded: chain D2 residue 50 VAL Chi-restraints excluded: chain D2 residue 58 ASN Chi-restraints excluded: chain D2 residue 61 THR Chi-restraints excluded: chain D2 residue 92 VAL Chi-restraints excluded: chain D2 residue 95 SER Chi-restraints excluded: chain D2 residue 207 VAL Chi-restraints excluded: chain E2 residue 70 SER Chi-restraints excluded: chain E2 residue 75 SER Chi-restraints excluded: chain E2 residue 150 THR Chi-restraints excluded: chain E2 residue 176 ASP Chi-restraints excluded: chain E2 residue 179 SER Chi-restraints excluded: chain E2 residue 195 GLN Chi-restraints excluded: chain F2 residue 14 LYS Chi-restraints excluded: chain F2 residue 34 ILE Chi-restraints excluded: chain F2 residue 37 ASN Chi-restraints excluded: chain F2 residue 74 VAL Chi-restraints excluded: chain F2 residue 98 GLU Chi-restraints excluded: chain F2 residue 103 LEU Chi-restraints excluded: chain F2 residue 113 ASP Chi-restraints excluded: chain F2 residue 127 ASN Chi-restraints excluded: chain F2 residue 158 THR Chi-restraints excluded: chain F2 residue 175 PHE Chi-restraints excluded: chain G2 residue 11 VAL Chi-restraints excluded: chain G2 residue 39 ASP Chi-restraints excluded: chain G2 residue 49 THR Chi-restraints excluded: chain G2 residue 95 ARG Chi-restraints excluded: chain G2 residue 107 LEU Chi-restraints excluded: chain G2 residue 113 VAL Chi-restraints excluded: chain G2 residue 127 THR Chi-restraints excluded: chain G2 residue 129 THR Chi-restraints excluded: chain G2 residue 130 GLU Chi-restraints excluded: chain G2 residue 163 ARG Chi-restraints excluded: chain H2 residue 85 VAL Chi-restraints excluded: chain I2 residue 33 VAL Chi-restraints excluded: chain I2 residue 70 VAL Chi-restraints excluded: chain I2 residue 98 VAL Chi-restraints excluded: chain J2 residue 30 THR Chi-restraints excluded: chain J2 residue 52 ASP Chi-restraints excluded: chain J2 residue 70 THR Chi-restraints excluded: chain J2 residue 131 ASN Chi-restraints excluded: chain K2 residue 40 LYS Chi-restraints excluded: chain K2 residue 42 THR Chi-restraints excluded: chain K2 residue 54 LYS Chi-restraints excluded: chain K2 residue 104 THR Chi-restraints excluded: chain L2 residue 25 SER Chi-restraints excluded: chain L2 residue 30 THR Chi-restraints excluded: chain L2 residue 42 SER Chi-restraints excluded: chain L2 residue 93 ASN Chi-restraints excluded: chain L2 residue 118 THR Chi-restraints excluded: chain M2 residue 7 THR Chi-restraints excluded: chain M2 residue 27 SER Chi-restraints excluded: chain M2 residue 40 ARG Chi-restraints excluded: chain M2 residue 57 VAL Chi-restraints excluded: chain M2 residue 126 ILE Chi-restraints excluded: chain M2 residue 132 THR Chi-restraints excluded: chain N2 residue 5 LYS Chi-restraints excluded: chain N2 residue 37 THR Chi-restraints excluded: chain N2 residue 56 LYS Chi-restraints excluded: chain N2 residue 75 ILE Chi-restraints excluded: chain N2 residue 100 CYS Chi-restraints excluded: chain O2 residue 65 THR Chi-restraints excluded: chain O2 residue 84 GLU Chi-restraints excluded: chain P2 residue 27 GLU Chi-restraints excluded: chain P2 residue 30 VAL Chi-restraints excluded: chain P2 residue 33 VAL Chi-restraints excluded: chain P2 residue 60 THR Chi-restraints excluded: chain P2 residue 80 VAL Chi-restraints excluded: chain P2 residue 92 VAL Chi-restraints excluded: chain Q2 residue 5 LYS Chi-restraints excluded: chain Q2 residue 8 VAL Chi-restraints excluded: chain Q2 residue 29 SER Chi-restraints excluded: chain Q2 residue 75 SER Chi-restraints excluded: chain Q2 residue 88 VAL Chi-restraints excluded: chain R2 residue 27 ILE Chi-restraints excluded: chain R2 residue 75 VAL Chi-restraints excluded: chain R2 residue 79 ARG Chi-restraints excluded: chain R2 residue 85 LYS Chi-restraints excluded: chain R2 residue 94 THR Chi-restraints excluded: chain S2 residue 57 ASN Chi-restraints excluded: chain S2 residue 81 SER Chi-restraints excluded: chain T2 residue 4 GLU Chi-restraints excluded: chain T2 residue 16 VAL Chi-restraints excluded: chain T2 residue 31 VAL Chi-restraints excluded: chain T2 residue 58 VAL Chi-restraints excluded: chain T2 residue 93 LEU Chi-restraints excluded: chain U2 residue 102 THR Chi-restraints excluded: chain V2 residue 8 VAL Chi-restraints excluded: chain V2 residue 24 ASN Chi-restraints excluded: chain V2 residue 25 LYS Chi-restraints excluded: chain V2 residue 42 LEU Chi-restraints excluded: chain V2 residue 45 ASP Chi-restraints excluded: chain V2 residue 50 MET Chi-restraints excluded: chain V2 residue 92 VAL Chi-restraints excluded: chain W2 residue 12 ASN Chi-restraints excluded: chain W2 residue 30 SER Chi-restraints excluded: chain W2 residue 35 SER Chi-restraints excluded: chain W2 residue 38 VAL Chi-restraints excluded: chain W2 residue 67 VAL Chi-restraints excluded: chain X2 residue 5 CYS Chi-restraints excluded: chain X2 residue 22 LEU Chi-restraints excluded: chain X2 residue 48 THR Chi-restraints excluded: chain X2 residue 52 SER Chi-restraints excluded: chain X2 residue 58 VAL Chi-restraints excluded: chain X2 residue 71 LEU Chi-restraints excluded: chain Y2 residue 40 SER Chi-restraints excluded: chain Z2 residue 49 ASN Chi-restraints excluded: chain a2 residue 9 THR Chi-restraints excluded: chain b2 residue 13 SER Chi-restraints excluded: chain b2 residue 24 THR Chi-restraints excluded: chain c2 residue 1 MET Chi-restraints excluded: chain c2 residue 6 GLN Chi-restraints excluded: chain d2 residue 6 THR Chi-restraints excluded: chain d2 residue 7 VAL Chi-restraints excluded: chain d2 residue 19 LYS Chi-restraints excluded: chain d2 residue 32 ILE Chi-restraints excluded: chain e2 residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1010 random chunks: chunk 636 optimal weight: 5.9990 chunk 853 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 738 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 802 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 824 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 chunk 147 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 140 ASN D1 85 ASN ** D1 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 73 ASN E1 135 ASN G1 97 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 5 ASN ** N1 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 56 GLN S1 57 HIS T1 3 ASN ** T1 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 117 GLN C2 153 GLN D2 130 GLN D2 167 ASN E2 41 GLN E2 90 GLN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 143 GLN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN Q2 20 GLN Q2 56 GLN R2 43 ASN R2 87 GLN S2 40 ASN S2 61 ASN T2 15 HIS V2 49 ASN ** W2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN a2 4 GLN a2 5 GLN c2 13 ASN e2 35 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088412 restraints weight = 353682.546| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.00 r_work: 0.3066 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 156479 Z= 0.351 Angle : 0.720 20.083 234145 Z= 0.373 Chirality : 0.038 0.371 29875 Planarity : 0.007 0.131 12503 Dihedral : 23.003 179.927 78486 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 4.96 % Allowed : 43.73 % Favored : 51.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.04 % 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: -0.36 (0.11), residues: 5626 helix: 0.57 (0.12), residues: 1914 sheet: -0.26 (0.16), residues: 1060 loop : -0.75 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRPB1 23 HIS 0.035 0.001 HISB1 94 PHE 0.055 0.002 PHEB1 50 TYR 0.034 0.002 TYRR2 2 ARG 0.017 0.001 ARGF1 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 74217.58 seconds wall clock time: 1274 minutes 31.88 seconds (76471.88 seconds total)