Starting phenix.real_space_refine on Wed Apr 10 06:33:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7asp_11903/04_2024/7asp_11903.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 4282 5.49 5 S 83 5.16 5 C 64103 2.51 5 N 23926 2.21 5 O 36434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "2 ARG 42": "NH1" <-> "NH2" Residue "2 ARG 57": "NH1" <-> "NH2" Residue "4 GLU 28": "OE1" <-> "OE2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a GLU 23": "OE1" <-> "OE2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 63": "OE1" <-> "OE2" Residue "a GLU 66": "OE1" <-> "OE2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ARG 111": "NH1" <-> "NH2" Residue "b ARG 122": "NH1" <-> "NH2" Residue "b ARG 128": "NH1" <-> "NH2" Residue "c ARG 9": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ARG 69": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "d ARG 11": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 66": "OE1" <-> "OE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 71": "NH1" <-> "NH2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d ARG 98": "NH1" <-> "NH2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "e GLU 20": "OE1" <-> "OE2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e ARG 26": "NH1" <-> "NH2" Residue "e ARG 29": "NH1" <-> "NH2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "e ARG 57": "NH1" <-> "NH2" Residue "f ARG 7": "NH1" <-> "NH2" Residue "f GLU 14": "OE1" <-> "OE2" Residue "f ARG 16": "NH1" <-> "NH2" Residue "f GLU 26": "OE1" <-> "OE2" Residue "f ARG 54": "NH1" <-> "NH2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "g ARG 26": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "h ARG 39": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "i GLU 40": "OE1" <-> "OE2" Residue "i ARG 47": "NH1" <-> "NH2" Residue "i ARG 66": "NH1" <-> "NH2" Residue "j ARG 10": "NH1" <-> "NH2" Residue "j GLU 15": "OE1" <-> "OE2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "k GLU 19": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 48": "OE1" <-> "OE2" Residue "k GLU 55": "OE1" <-> "OE2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k ARG 87": "NH1" <-> "NH2" Residue "k ARG 113": "NH1" <-> "NH2" Residue "k ARG 121": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k ARG 139": "NH1" <-> "NH2" Residue "k ARG 163": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ARG 110": "NH1" <-> "NH2" Residue "l ARG 58": "NH1" <-> "NH2" Residue "m GLU 10": "OE1" <-> "OE2" Residue "m GLU 13": "OE1" <-> "OE2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 32": "NH1" <-> "NH2" Residue "m GLU 65": "OE1" <-> "OE2" Residue "m GLU 116": "OE1" <-> "OE2" Residue "m ARG 157": "NH1" <-> "NH2" Residue "m GLU 162": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "n GLU 5": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n GLU 16": "OE1" <-> "OE2" Residue "n GLU 24": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n GLU 51": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 75": "OE1" <-> "OE2" Residue "n ARG 78": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "o GLU 23": "OE1" <-> "OE2" Residue "o GLU 26": "OE1" <-> "OE2" Residue "o GLU 43": "OE1" <-> "OE2" Residue "o ARG 61": "NH1" <-> "NH2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "o ARG 72": "NH1" <-> "NH2" Residue "o GLU 93": "OE1" <-> "OE2" Residue "o GLU 110": "OE1" <-> "OE2" Residue "o ARG 119": "NH1" <-> "NH2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "p ARG 10": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p GLU 60": "OE1" <-> "OE2" Residue "p GLU 64": "OE1" <-> "OE2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "p GLU 94": "OE1" <-> "OE2" Residue "p ARG 96": "NH1" <-> "NH2" Residue "p ARG 111": "NH1" <-> "NH2" Residue "p GLU 117": "OE1" <-> "OE2" Residue "p GLU 139": "OE1" <-> "OE2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 29": "OE1" <-> "OE2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 82": "NH1" <-> "NH2" Residue "q GLU 91": "OE1" <-> "OE2" Residue "q GLU 114": "OE1" <-> "OE2" Residue "q ARG 115": "NH1" <-> "NH2" Residue "q ARG 125": "NH1" <-> "NH2" Residue "Q GLU 2": "OE1" <-> "OE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 59": "OE1" <-> "OE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 84": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "T ARG 9": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U GLU 25": "OE1" <-> "OE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "V ARG 37": "NH1" <-> "NH2" Residue "W GLU 5": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 39": "OE1" <-> "OE2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W GLU 59": "OE1" <-> "OE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "1 ARG 10": "NH1" <-> "NH2" Residue "1 GLU 17": "OE1" <-> "OE2" Residue "1 GLU 57": "OE1" <-> "OE2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "Z ARG 7": "NH1" <-> "NH2" Residue "Z GLU 29": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 128828 Number of models: 1 Model: "" Number of chains: 47 Chain: "Y" Number of atoms: 58376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2723, 58376 Classifications: {'RNA': 2723} Modifications used: {'rna2p_pur': 306, 'rna2p_pyr': 177, 'rna3p_pur': 1257, 'rna3p_pyr': 982} Link IDs: {'rna2p': 483, 'rna3p': 2239} Chain breaks: 13 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 31009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1447, 31009 Inner-chain residues flagged as termini: ['pdbres=" U X 494 "', 'pdbres=" G X 855 "'] Classifications: {'RNA': 1447} Modifications used: {'5*END': 2, 'rna2p_pur': 188, 'rna2p_pyr': 132, 'rna3p_pur': 636, 'rna3p_pyr': 491} Link IDs: {'rna2p': 320, 'rna3p': 1126} Chain breaks: 8 Chain: "3" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "A" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "2" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 826 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "c" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 976 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "d" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 828 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1627 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 713 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "g" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 537 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1184 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1143 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 520 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "j" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 498 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 76} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1086 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "k" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1071 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1058 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 579 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 326 Chain: "m" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1153 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 882 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "n" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "o" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1007 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "p" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1155 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 57 Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 790 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "q" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 975 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 715 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 770 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 597 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 355 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 765 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 469 Unresolved non-hydrogen angles: 591 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 225 Time building chain proxies: 47.37, per 1000 atoms: 0.37 Number of scatterers: 128828 At special positions: 0 Unit cell: (285.6, 265.2, 236.3, 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 83 16.00 P 4282 15.00 O 36434 8.00 N 23926 7.00 C 64103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 12 " - pdb=" SG CYS A 36 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 40 " distance=2.03 Simple disulfide: pdb=" SG CYS e 27 " - pdb=" SG CYS e 43 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 50.94 Conformation dependent library (CDL) restraints added in 6.0 seconds 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9128 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 61 sheets defined 23.0% alpha, 12.0% beta 674 base pairs and 1810 stacking pairs defined. Time for finding SS restraints: 36.75 Creating SS restraints... Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 25 through 39 removed outlier: 3.715A pdb=" N ARG B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing helix chain '2' and resid 38 through 44 Processing helix chain '2' and resid 51 through 58 removed outlier: 3.538A pdb=" N ARG 2 57 " --> pdb=" O SER 2 53 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 33 removed outlier: 4.085A pdb=" N LYS 4 33 " --> pdb=" O PRO 4 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 14 through 32 removed outlier: 3.507A pdb=" N GLU a 23 " --> pdb=" O ASP a 19 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 71 removed outlier: 3.719A pdb=" N ALA b 63 " --> pdb=" O THR b 59 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN b 64 " --> pdb=" O PRO b 60 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR b 69 " --> pdb=" O MET b 65 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 95 Processing helix chain 'b' and resid 96 through 102 removed outlier: 3.725A pdb=" N GLN b 101 " --> pdb=" O ILE b 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.670A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.684A pdb=" N VAL C 224 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET C 225 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 225' Processing helix chain 'd' and resid 14 through 16 No H-bonds generated for 'chain 'd' and resid 14 through 16' Processing helix chain 'd' and resid 17 through 22 removed outlier: 3.689A pdb=" N TYR d 21 " --> pdb=" O ILE d 17 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE d 22 " --> pdb=" O SER d 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 17 through 22' Processing helix chain 'd' and resid 52 through 63 removed outlier: 3.578A pdb=" N ILE d 56 " --> pdb=" O GLU d 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP d 61 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 75 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 71 through 79 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.661A pdb=" N HIS D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 42 Processing helix chain 'E' and resid 102 through 119 Processing helix chain 'E' and resid 135 through 146 Processing helix chain 'E' and resid 196 through 206 Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 40 through 48 Processing helix chain 'f' and resid 4 through 7 Processing helix chain 'f' and resid 8 through 16 removed outlier: 4.298A pdb=" N ILE f 12 " --> pdb=" O LYS f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 39 Processing helix chain 'f' and resid 41 through 46 removed outlier: 4.226A pdb=" N THR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS f 46 " --> pdb=" O HIS f 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 41 through 46' Processing helix chain 'f' and resid 52 through 74 removed outlier: 3.821A pdb=" N LEU f 57 " --> pdb=" O ARG f 53 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS f 65 " --> pdb=" O GLY f 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS f 73 " --> pdb=" O TYR f 69 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 77 removed outlier: 3.540A pdb=" N LYS g 77 " --> pdb=" O ASN g 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.843A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.739A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 96 removed outlier: 3.701A pdb=" N ARG H 95 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 108 removed outlier: 4.077A pdb=" N LEU H 101 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'i' and resid 55 through 66 removed outlier: 4.128A pdb=" N MET i 59 " --> pdb=" O LYS i 55 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 32 Processing helix chain 'j' and resid 36 through 41 Processing helix chain 'j' and resid 68 through 78 removed outlier: 3.557A pdb=" N ILE j 74 " --> pdb=" O LYS j 70 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN j 77 " --> pdb=" O ARG j 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU j 78 " --> pdb=" O ILE j 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 83 removed outlier: 3.544A pdb=" N GLN J 81 " --> pdb=" O ASN J 78 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU J 82 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN J 83 " --> pdb=" O ASP J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 78 through 83' Processing helix chain 'J' and resid 92 through 99 Processing helix chain 'J' and resid 129 through 140 removed outlier: 4.029A pdb=" N GLU J 134 " --> pdb=" O ALA J 130 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 47 removed outlier: 4.514A pdb=" N SER k 30 " --> pdb=" O LYS k 26 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE k 41 " --> pdb=" O LYS k 37 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS k 47 " --> pdb=" O ASP k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 94 removed outlier: 3.604A pdb=" N LYS k 89 " --> pdb=" O LYS k 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU k 93 " --> pdb=" O LYS k 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 144 Processing helix chain 'K' and resid 43 through 59 removed outlier: 3.860A pdb=" N TYR K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 122 removed outlier: 3.634A pdb=" N ARG K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 125 No H-bonds generated for 'chain 'K' and resid 123 through 125' Processing helix chain 'L' and resid 9 through 27 removed outlier: 3.816A pdb=" N SER L 27 " --> pdb=" O SER L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 38 Processing helix chain 'L' and resid 43 through 54 removed outlier: 3.601A pdb=" N GLY L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 63 Processing helix chain 'L' and resid 81 through 86 Processing helix chain 'L' and resid 87 through 93 Processing helix chain 'l' and resid 45 through 61 removed outlier: 3.760A pdb=" N GLN l 50 " --> pdb=" O GLU l 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU l 60 " --> pdb=" O LYS l 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 75 Processing helix chain 'l' and resid 84 through 89 Processing helix chain 'l' and resid 94 through 99 removed outlier: 3.744A pdb=" N VAL l 98 " --> pdb=" O LEU l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 107 through 112 Processing helix chain 'l' and resid 191 through 198 Processing helix chain 'm' and resid 55 through 61 removed outlier: 3.527A pdb=" N LYS m 61 " --> pdb=" O PRO m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 61 through 67 Processing helix chain 'm' and resid 137 through 145 Processing helix chain 'm' and resid 149 through 158 removed outlier: 3.522A pdb=" N VAL m 153 " --> pdb=" O ASN m 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU m 156 " --> pdb=" O ASP m 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG m 157 " --> pdb=" O VAL m 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 160 through 164 removed outlier: 4.040A pdb=" N LEU m 164 " --> pdb=" O VAL m 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 19 removed outlier: 3.942A pdb=" N VAL M 10 " --> pdb=" O ASP M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 87 removed outlier: 3.714A pdb=" N THR M 74 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 114 removed outlier: 3.521A pdb=" N ALA M 107 " --> pdb=" O GLY M 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA M 112 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG M 113 " --> pdb=" O ALA M 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 15 through 31 Processing helix chain 'n' and resid 74 through 80 removed outlier: 3.917A pdb=" N ARG n 78 " --> pdb=" O ASP n 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.928A pdb=" N LEU N 102 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG N 103 " --> pdb=" O TYR N 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 103' Processing helix chain 'o' and resid 7 through 18 removed outlier: 3.510A pdb=" N THR o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL o 14 " --> pdb=" O MET o 10 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG o 15 " --> pdb=" O LEU o 11 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN o 16 " --> pdb=" O THR o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 117 through 122 Processing helix chain 'O' and resid 9 through 21 removed outlier: 3.531A pdb=" N ARG O 13 " --> pdb=" O VAL O 9 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 50 Processing helix chain 'O' and resid 52 through 70 removed outlier: 3.955A pdb=" N ARG O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 71 through 73 No H-bonds generated for 'chain 'O' and resid 71 through 73' Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 91 through 101 Processing helix chain 'O' and resid 102 through 116 removed outlier: 3.668A pdb=" N PHE O 106 " --> pdb=" O ASP O 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 30 Processing helix chain 'p' and resid 36 through 44 Processing helix chain 'p' and resid 46 through 53 Processing helix chain 'p' and resid 57 through 62 Processing helix chain 'p' and resid 79 through 83 removed outlier: 4.374A pdb=" N GLY p 82 " --> pdb=" O ARG p 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 102 removed outlier: 3.968A pdb=" N THR p 97 " --> pdb=" O PRO p 93 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR p 98 " --> pdb=" O GLU p 94 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG p 102 " --> pdb=" O THR p 98 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 125 removed outlier: 4.149A pdb=" N ALA p 121 " --> pdb=" O GLU p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 135 through 143 removed outlier: 4.195A pdb=" N GLU p 139 " --> pdb=" O VAL p 135 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS p 142 " --> pdb=" O ARG p 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 35 Processing helix chain 'q' and resid 51 through 58 removed outlier: 4.032A pdb=" N ASP q 55 " --> pdb=" O ASN q 51 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL q 56 " --> pdb=" O GLN q 52 " (cutoff:3.500A) Processing helix chain 'q' and resid 59 through 61 No H-bonds generated for 'chain 'q' and resid 59 through 61' Processing helix chain 'q' and resid 80 through 93 removed outlier: 3.603A pdb=" N GLU q 91 " --> pdb=" O ARG q 87 " (cutoff:3.500A) Processing helix chain 'q' and resid 93 through 100 removed outlier: 4.481A pdb=" N ARG q 97 " --> pdb=" O ASP q 93 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY q 98 " --> pdb=" O PRO q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 18 Processing helix chain 'Q' and resid 28 through 37 Processing helix chain 'Q' and resid 43 through 61 Processing helix chain 'R' and resid 13 through 20 Processing helix chain 'R' and resid 34 through 43 removed outlier: 3.843A pdb=" N GLU R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 24 Processing helix chain 'T' and resid 45 through 50 Processing helix chain 'W' and resid 11 through 34 Processing helix chain 'W' and resid 41 through 64 removed outlier: 3.821A pdb=" N THR W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) Processing helix chain '1' and resid 16 through 27 removed outlier: 3.680A pdb=" N GLY 1 27 " --> pdb=" O VAL 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 50 removed outlier: 3.709A pdb=" N GLN 1 46 " --> pdb=" O ALA 1 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 17 removed outlier: 3.696A pdb=" N ARG Z 17 " --> pdb=" O LYS Z 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.523A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.503A pdb=" N MET A 32 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 23 through 24 removed outlier: 3.986A pdb=" N ARG 2 48 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 17 through 18 Processing sheet with id=AA4, first strand: chain 'b' and resid 22 through 23 removed outlier: 3.989A pdb=" N THR b 33 " --> pdb=" O HIS b 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 46 through 47 removed outlier: 3.521A pdb=" N ARG c 69 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE c 76 " --> pdb=" O VAL c 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.672A pdb=" N ILE C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 93 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.552A pdb=" N LEU C 130 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG C 189 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE C 144 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 144 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.552A pdb=" N LEU C 130 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ARG C 189 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE C 144 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 182 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 177 through 180 removed outlier: 4.908A pdb=" N VAL D 121 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU D 208 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS D 198 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 185 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.554A pdb=" N ILE D 49 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA D 48 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN D 33 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 13 through 18 removed outlier: 4.027A pdb=" N GLY E 15 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 10.758A pdb=" N LEU E 123 " --> pdb=" O ASN E 3 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP E 5 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 125 " --> pdb=" O ASP E 5 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 195 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E 152 " --> pdb=" O GLN E 174 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N THR E 176 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL E 154 " --> pdb=" O THR E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 5 through 7 removed outlier: 8.336A pdb=" N ILE g 20 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN g 36 " --> pdb=" O ILE g 20 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL g 22 " --> pdb=" O ILE g 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 11 through 12 removed outlier: 4.296A pdb=" N SER g 12 " --> pdb=" O ASN g 15 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN g 15 " --> pdb=" O SER g 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'g' and resid 39 through 40 Processing sheet with id=AB9, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AC1, first strand: chain 'G' and resid 84 through 87 removed outlier: 3.910A pdb=" N LYS G 85 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 133 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=AC3, first strand: chain 'H' and resid 55 through 57 Processing sheet with id=AC4, first strand: chain 'H' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'h' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'h' and resid 23 through 26 removed outlier: 3.613A pdb=" N ILE h 23 " --> pdb=" O THR h 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 29 through 32 removed outlier: 3.820A pdb=" N LYS h 31 " --> pdb=" O VAL h 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 7 through 10 removed outlier: 3.699A pdb=" N VAL I 10 " --> pdb=" O ARG I 17 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG I 17 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA I 16 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA I 46 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU I 18 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL I 40 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL I 24 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL I 38 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE I 62 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL I 85 " --> pdb=" O ILE I 62 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N CYS I 84 " --> pdb=" O ARG I 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS I 9 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE I 86 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 69 through 70 removed outlier: 4.014A pdb=" N VAL I 69 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE I 77 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE N 76 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE N 61 " --> pdb=" O PHE N 76 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR N 60 " --> pdb=" O ARG N 52 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG N 52 " --> pdb=" O THR N 60 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR N 62 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE N 66 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLU N 46 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR N 27 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'J' and resid 75 through 77 removed outlier: 6.047A pdb=" N ALA J 75 " --> pdb=" O LYS J 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS J 127 " --> pdb=" O ILE J 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'k' and resid 20 through 21 removed outlier: 3.848A pdb=" N ALA k 66 " --> pdb=" O GLU k 55 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 147 through 149 Processing sheet with id=AD5, first strand: chain 'K' and resid 63 through 66 removed outlier: 6.431A pdb=" N LEU K 34 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU K 105 " --> pdb=" O PHE K 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE K 32 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 40 through 41 removed outlier: 3.519A pdb=" N SER K 40 " --> pdb=" O VAL K 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 72 through 75 removed outlier: 6.718A pdb=" N THR K 72 " --> pdb=" O TRP K 93 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TRP K 93 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR K 74 " --> pdb=" O GLU K 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.341A pdb=" N SER L 116 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AE1, first strand: chain 'm' and resid 13 through 14 removed outlier: 3.539A pdb=" N ASN m 19 " --> pdb=" O THR m 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 13 through 14 Processing sheet with id=AE3, first strand: chain 'm' and resid 22 through 23 removed outlier: 3.763A pdb=" N LYS m 23 " --> pdb=" O ARG m 30 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG m 30 " --> pdb=" O LYS m 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'm' and resid 95 through 98 removed outlier: 3.732A pdb=" N LYS m 97 " --> pdb=" O LEU m 124 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 51 through 52 removed outlier: 3.629A pdb=" N VAL M 51 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 51 through 52 removed outlier: 3.629A pdb=" N VAL M 51 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'p' and resid 73 through 76 removed outlier: 3.612A pdb=" N VAL p 87 " --> pdb=" O LYS p 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 12 through 15 removed outlier: 6.446A pdb=" N PHE P 2 " --> pdb=" O VAL P 41 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL P 41 " --> pdb=" O PHE P 2 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE P 4 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 19 through 23 removed outlier: 6.719A pdb=" N LYS P 94 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR P 59 " --> pdb=" O ASP P 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 71 through 76 Processing sheet with id=AF2, first strand: chain 'q' and resid 24 through 25 removed outlier: 3.666A pdb=" N ASP q 64 " --> pdb=" O VAL q 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 2 through 7 removed outlier: 5.751A pdb=" N HIS Q 102 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA Q 76 " --> pdb=" O HIS Q 102 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR Q 104 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA Q 74 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL Q 106 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 82 through 87 removed outlier: 3.514A pdb=" N ARG Q 86 " --> pdb=" O SER Q 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 7 through 10 removed outlier: 6.659A pdb=" N ASP R 28 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N THR R 26 " --> pdb=" O PRO R 10 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG R 75 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN R 57 " --> pdb=" O ARG R 75 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS R 77 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE R 55 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE R 79 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL R 53 " --> pdb=" O ILE R 79 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR R 81 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS R 49 " --> pdb=" O LYS R 83 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 62 through 63 removed outlier: 3.726A pdb=" N GLY R 70 " --> pdb=" O LYS R 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 63 through 64 removed outlier: 4.152A pdb=" N ALA S 25 " --> pdb=" O VAL S 34 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 40 through 43 removed outlier: 3.734A pdb=" N THR S 59 " --> pdb=" O MET S 41 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 82 through 85 removed outlier: 3.985A pdb=" N VAL S 91 " --> pdb=" O LYS S 84 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 4 through 5 removed outlier: 7.593A pdb=" N LEU T 4 " --> pdb=" O GLY T 64 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL T 74 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU T 92 " --> pdb=" O VAL T 74 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP T 76 " --> pdb=" O ASP T 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS T 88 " --> pdb=" O GLN T 78 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP T 80 " --> pdb=" O ILE T 86 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE T 86 " --> pdb=" O ASP T 80 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N LYS T 26 " --> pdb=" O THR T 87 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N ILE T 89 " --> pdb=" O LYS T 26 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N PHE T 91 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL T 30 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA T 93 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR T 32 " --> pdb=" O ALA T 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL T 43 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY T 33 " --> pdb=" O LYS T 37 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LYS T 37 " --> pdb=" O GLY T 33 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 30 through 31 removed outlier: 6.645A pdb=" N LEU U 67 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 38 through 39 removed outlier: 3.539A pdb=" N VAL U 74 " --> pdb=" O TYR U 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 14 through 16 removed outlier: 3.763A pdb=" N ARG V 27 " --> pdb=" O GLY V 15 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 33 through 38 Processing sheet with id=AG6, first strand: chain '1' and resid 34 through 38 removed outlier: 3.517A pdb=" N GLU 1 57 " --> pdb=" O GLN 1 5 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.623A pdb=" N VAL F 35 " --> pdb=" O VAL F 155 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1584 hydrogen bonds 2618 hydrogen bond angles 0 basepair planarities 674 basepair parallelities 1810 stacking parallelities Total time for adding SS restraints: 153.18 Time building geometry restraints manager: 55.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16580 1.33 - 1.45: 60099 1.45 - 1.57: 54898 1.57 - 1.69: 8540 1.69 - 1.81: 150 Bond restraints: 140267 Sorted by residual: bond pdb=" N ILE c 80 " pdb=" CA ILE c 80 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.30e-03 1.88e+04 2.12e+01 bond pdb=" N LYS b 125 " pdb=" CA LYS b 125 " ideal model delta sigma weight residual 1.457 1.485 -0.029 6.40e-03 2.44e+04 2.04e+01 bond pdb=" N GLY P 66 " pdb=" CA GLY P 66 " ideal model delta sigma weight residual 1.442 1.477 -0.035 7.70e-03 1.69e+04 2.04e+01 bond pdb=" N GLY o 125 " pdb=" CA GLY o 125 " ideal model delta sigma weight residual 1.442 1.476 -0.035 7.70e-03 1.69e+04 2.01e+01 bond pdb=" N GLY o 102 " pdb=" CA GLY o 102 " ideal model delta sigma weight residual 1.442 1.476 -0.035 7.70e-03 1.69e+04 2.01e+01 ... (remaining 140262 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.35: 25067 106.35 - 113.35: 85260 113.35 - 120.34: 54196 120.34 - 127.33: 37078 127.33 - 134.32: 9054 Bond angle restraints: 210655 Sorted by residual: angle pdb=" O3' U Y1897 " pdb=" C3' U Y1897 " pdb=" C2' U Y1897 " ideal model delta sigma weight residual 109.50 123.13 -13.63 1.50e+00 4.44e-01 8.26e+01 angle pdb=" C4' U X 99 " pdb=" C3' U X 99 " pdb=" O3' U X 99 " ideal model delta sigma weight residual 109.40 122.72 -13.32 1.50e+00 4.44e-01 7.89e+01 angle pdb=" C4' C X 353 " pdb=" C3' C X 353 " pdb=" O3' C X 353 " ideal model delta sigma weight residual 109.40 122.37 -12.97 1.50e+00 4.44e-01 7.47e+01 angle pdb=" O3' A Y2591 " pdb=" C3' A Y2591 " pdb=" C2' A Y2591 " ideal model delta sigma weight residual 113.70 126.20 -12.50 1.50e+00 4.44e-01 6.95e+01 angle pdb=" O3' C 3 26 " pdb=" C3' C 3 26 " pdb=" C2' C 3 26 " ideal model delta sigma weight residual 113.70 126.20 -12.50 1.50e+00 4.44e-01 6.95e+01 ... (remaining 210650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 75342 35.88 - 71.76: 12345 71.76 - 107.65: 1507 107.65 - 143.53: 132 143.53 - 179.41: 108 Dihedral angle restraints: 89434 sinusoidal: 75263 harmonic: 14171 Sorted by residual: dihedral pdb=" C4' A Y2338 " pdb=" C3' A Y2338 " pdb=" C2' A Y2338 " pdb=" C1' A Y2338 " ideal model delta sinusoidal sigma weight residual 36.34 86.65 -50.30 1 3.10e+00 1.04e-01 3.61e+02 dihedral pdb=" C5' A X1250 " pdb=" C4' A X1250 " pdb=" C3' A X1250 " pdb=" O3' A X1250 " ideal model delta sinusoidal sigma weight residual 82.00 152.78 -70.78 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' A X1250 " pdb=" C4' A X1250 " pdb=" C3' A X1250 " pdb=" C2' A X1250 " ideal model delta sinusoidal sigma weight residual -35.00 32.44 -67.44 1 8.00e+00 1.56e-02 9.25e+01 ... (remaining 89431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 23300 0.155 - 0.311: 3870 0.311 - 0.466: 16 0.466 - 0.621: 12 0.621 - 0.777: 6 Chirality restraints: 27204 Sorted by residual: chirality pdb=" C3' A X 695 " pdb=" C4' A X 695 " pdb=" O3' A X 695 " pdb=" C2' A X 695 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C3' A X 756 " pdb=" C4' A X 756 " pdb=" O3' A X 756 " pdb=" C2' A X 756 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C3' C 3 40 " pdb=" C4' C 3 40 " pdb=" O3' C 3 40 " pdb=" C2' C 3 40 " both_signs ideal model delta sigma weight residual False -2.74 -2.04 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 27201 not shown) Planarity restraints: 10799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 141 " 0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ILE F 141 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE F 141 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP F 142 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 158 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C THR F 158 " 0.057 2.00e-02 2.50e+03 pdb=" O THR F 158 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 159 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 93 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C GLY F 93 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY F 93 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU F 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 10796 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 233 2.42 - 3.04: 70381 3.04 - 3.66: 230940 3.66 - 4.28: 343754 4.28 - 4.90: 493313 Nonbonded interactions: 1138621 Sorted by model distance: nonbonded pdb=" N1 A Y 722 " pdb=" O6 G Y 846 " model vdw 1.802 2.496 nonbonded pdb=" C2 A Y 722 " pdb=" O6 G Y 846 " model vdw 1.955 3.340 nonbonded pdb=" O2' A X 571 " pdb=" O2' G X 574 " model vdw 2.037 2.440 nonbonded pdb=" O2' U X 426 " pdb=" O2' G X 548 " model vdw 2.038 2.440 nonbonded pdb=" O2' A X 581 " pdb=" O2' C X 892 " model vdw 2.041 2.440 ... (remaining 1138616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 25.960 Check model and map are aligned: 1.360 Set scattering table: 0.910 Process input model: 377.660 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.300 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 424.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.008 0.057 140267 Z= 0.533 Angle : 1.049 13.634 210655 Z= 0.765 Chirality : 0.100 0.777 27204 Planarity : 0.002 0.036 10799 Dihedral : 27.275 179.410 80291 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 2.83 % Allowed : 14.84 % Favored : 82.33 % Rotamer: Outliers : 24.23 % Allowed : 23.12 % Favored : 52.65 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.09), residues: 4878 helix: -3.30 (0.11), residues: 1134 sheet: -3.21 (0.18), residues: 575 loop : -3.81 (0.08), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 250 HIS 0.004 0.000 HIS e 31 PHE 0.008 0.000 PHE p 151 TYR 0.008 0.000 TYR E 99 ARG 0.003 0.000 ARG m 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 874 poor density : 842 time to evaluate : 5.364 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 TARDY: cannot create tardy model for: "LYS d 114 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 2 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7191 (tpt170) REVERT: A 39 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8475 (mt) REVERT: 2 21 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8390 (mm110) REVERT: 2 29 THR cc_start: 0.9355 (p) cc_final: 0.9142 (p) REVERT: 4 8 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9091 (ptpp) REVERT: 4 13 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.6726 (pttp) REVERT: a 53 ARG cc_start: 0.3064 (OUTLIER) cc_final: 0.2440 (tpm170) REVERT: a 69 THR cc_start: 0.1739 (OUTLIER) cc_final: 0.1462 (p) REVERT: a 74 ILE cc_start: 0.2533 (OUTLIER) cc_final: 0.2156 (mm) REVERT: b 53 LYS cc_start: -0.0954 (OUTLIER) cc_final: -0.1563 (mmpt) REVERT: b 105 LEU cc_start: -0.0596 (OUTLIER) cc_final: -0.1361 (pt) REVERT: c 7 LEU cc_start: -0.2082 (OUTLIER) cc_final: -0.2393 (mt) REVERT: C 87 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7830 (ttm-80) REVERT: d 87 ARG cc_start: 0.0978 (OUTLIER) cc_final: 0.0055 (tpm170) REVERT: D 67 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8651 (ttpt) REVERT: D 173 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8303 (ptt) REVERT: E 17 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9208 (tt) REVERT: E 41 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7981 (ttp80) REVERT: E 84 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8267 (ttt-90) REVERT: E 127 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7812 (p0) REVERT: E 164 GLU cc_start: 0.7531 (pp20) cc_final: 0.7199 (pp20) REVERT: e 6 MET cc_start: 0.0895 (OUTLIER) cc_final: -0.0032 (mmp) REVERT: e 40 CYS cc_start: 0.4036 (OUTLIER) cc_final: 0.3513 (p) REVERT: f 58 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5297 (mmmt) REVERT: f 59 MET cc_start: 0.4601 (mtt) cc_final: 0.3528 (tpt) REVERT: g 12 SER cc_start: -0.3063 (OUTLIER) cc_final: -0.3364 (m) REVERT: g 14 ARG cc_start: -0.0079 (OUTLIER) cc_final: -0.3220 (tpt170) REVERT: g 20 ILE cc_start: 0.5547 (pt) cc_final: 0.5298 (pt) REVERT: g 29 ARG cc_start: -0.3183 (OUTLIER) cc_final: -0.3460 (mtm-85) REVERT: g 73 ASN cc_start: -0.0620 (OUTLIER) cc_final: -0.1324 (t0) REVERT: G 98 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8696 (ttm) REVERT: G 119 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8723 (mp0) REVERT: G 124 SER cc_start: 0.6326 (OUTLIER) cc_final: 0.5987 (m) REVERT: G 155 GLU cc_start: 0.5318 (pt0) cc_final: 0.4821 (pp20) REVERT: G 163 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6812 (ppp80) REVERT: G 170 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5476 (tpm170) REVERT: H 95 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8044 (mtm110) REVERT: h 45 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6882 (mmtm) REVERT: i 36 ARG cc_start: 0.1721 (OUTLIER) cc_final: 0.1193 (ptt180) REVERT: i 58 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.4632 (mtt180) REVERT: i 70 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.4175 (ppp) REVERT: i 75 TYR cc_start: 0.0558 (OUTLIER) cc_final: 0.0115 (m-80) REVERT: j 20 ARG cc_start: -0.0145 (OUTLIER) cc_final: -0.0377 (tpp-160) REVERT: j 68 SER cc_start: 0.0044 (OUTLIER) cc_final: -0.0403 (m) REVERT: J 104 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8389 (p0) REVERT: k 4 LYS cc_start: -0.3882 (OUTLIER) cc_final: -0.4609 (tttm) REVERT: k 6 ASN cc_start: 0.1467 (OUTLIER) cc_final: 0.1165 (m-40) REVERT: k 96 LYS cc_start: -0.3160 (OUTLIER) cc_final: -0.3618 (mptt) REVERT: k 114 LEU cc_start: 0.6613 (mm) cc_final: 0.6078 (pt) REVERT: k 119 ILE cc_start: -0.3560 (OUTLIER) cc_final: -0.4339 (pp) REVERT: k 174 LEU cc_start: -0.1484 (OUTLIER) cc_final: -0.3240 (tp) REVERT: k 175 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.6171 (t-90) REVERT: k 176 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.6789 (t) REVERT: k 178 ARG cc_start: 0.0973 (OUTLIER) cc_final: -0.0032 (pmt170) REVERT: k 194 LYS cc_start: 0.3157 (OUTLIER) cc_final: 0.2647 (ttpp) REVERT: K 68 ILE cc_start: 0.9140 (pt) cc_final: 0.8934 (pt) REVERT: K 113 VAL cc_start: 0.9478 (OUTLIER) cc_final: 0.9277 (t) REVERT: L 13 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: l 58 ARG cc_start: -0.0334 (tpp-160) cc_final: -0.1715 (tmm160) REVERT: l 69 ARG cc_start: 0.7788 (ptt-90) cc_final: 0.7362 (ptp-170) REVERT: m 54 GLN cc_start: 0.1982 (OUTLIER) cc_final: 0.1547 (mp10) REVERT: m 61 LYS cc_start: 0.7385 (pptt) cc_final: 0.7001 (pptt) REVERT: m 65 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.5875 (pp20) REVERT: M 12 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.8858 (mm) REVERT: M 28 LYS cc_start: 0.9538 (OUTLIER) cc_final: 0.9288 (mtpp) REVERT: M 48 ASN cc_start: 0.9641 (t0) cc_final: 0.9434 (t0) REVERT: M 59 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9075 (ttmm) REVERT: M 119 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8554 (p90) REVERT: n 2 ARG cc_start: 0.5463 (OUTLIER) cc_final: 0.4531 (mtp180) REVERT: n 42 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.7051 (t0) REVERT: n 48 LEU cc_start: -0.0847 (OUTLIER) cc_final: -0.2623 (pt) REVERT: n 78 ARG cc_start: -0.0788 (OUTLIER) cc_final: -0.3486 (mtt180) REVERT: o 15 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5813 (tpm170) REVERT: o 33 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4463 (mttt) REVERT: o 54 ASP cc_start: 0.4524 (OUTLIER) cc_final: 0.3308 (p0) REVERT: o 119 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7117 (mmm160) REVERT: o 121 ARG cc_start: 0.2599 (OUTLIER) cc_final: 0.2342 (mtm110) REVERT: o 127 ILE cc_start: 0.1680 (OUTLIER) cc_final: 0.1267 (mm) REVERT: O 52 GLN cc_start: 0.8104 (mt0) cc_final: 0.7772 (mt0) REVERT: O 70 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8306 (mtt-85) REVERT: p 21 LYS cc_start: 0.5282 (mmtm) cc_final: 0.4949 (mmtp) REVERT: p 29 LYS cc_start: 0.1195 (mptt) cc_final: 0.0008 (pptt) REVERT: p 31 MET cc_start: 0.0182 (ptm) cc_final: -0.0084 (ttp) REVERT: p 64 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: p 66 ILE cc_start: -0.4495 (OUTLIER) cc_final: -0.5530 (tt) REVERT: p 69 ILE cc_start: -0.6717 (OUTLIER) cc_final: -0.7412 (pt) REVERT: p 72 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.6051 (t) REVERT: p 107 TYR cc_start: -0.1231 (OUTLIER) cc_final: -0.1456 (m-80) REVERT: p 149 LYS cc_start: 0.4531 (pptt) cc_final: 0.4219 (pmtt) REVERT: q 11 THR cc_start: 0.2701 (OUTLIER) cc_final: 0.2043 (p) REVERT: q 36 ASP cc_start: -0.1123 (OUTLIER) cc_final: -0.3517 (m-30) REVERT: q 55 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6431 (p0) REVERT: q 87 ARG cc_start: 0.4065 (OUTLIER) cc_final: 0.3323 (tpt-90) REVERT: Q 2 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7183 (mt-10) REVERT: Q 64 MET cc_start: 0.7965 (mtp) cc_final: 0.6980 (mtp) REVERT: R 15 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9124 (tttt) REVERT: R 18 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: S 4 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8134 (mmtt) REVERT: S 41 MET cc_start: 0.7819 (mmt) cc_final: 0.7484 (mmm) REVERT: S 67 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8438 (t0) REVERT: T 12 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8708 (tppt) REVERT: T 17 ASP cc_start: 0.8900 (m-30) cc_final: 0.8661 (m-30) REVERT: T 26 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8508 (mmmt) REVERT: T 50 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9123 (ttmm) REVERT: T 80 ASP cc_start: 0.9494 (t0) cc_final: 0.9265 (t0) REVERT: U 22 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8283 (mtm180) REVERT: U 79 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (ptm160) REVERT: W 21 SER cc_start: 0.9550 (m) cc_final: 0.9284 (p) REVERT: W 27 ASN cc_start: 0.9000 (m-40) cc_final: 0.8541 (m-40) REVERT: W 31 GLN cc_start: 0.9059 (mp10) cc_final: 0.8784 (mp10) outliers start: 874 outliers final: 274 residues processed: 1492 average time/residue: 1.9971 time to fit residues: 4155.5330 Evaluate side-chains 1094 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 736 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 30 LYS Chi-restraints excluded: chain 2 residue 46 LYS Chi-restraints excluded: chain 2 residue 53 SER Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain a residue 23 GLU Chi-restraints excluded: chain a residue 24 LYS Chi-restraints excluded: chain a residue 30 LYS Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 68 GLU Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain c residue 34 LYS Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 49 ARG Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain d residue 11 ARG Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 57 ARG Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain d residue 87 ARG Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain d residue 114 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 187 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain e residue 3 LYS Chi-restraints excluded: chain e residue 6 MET Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 26 ARG Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 54 ARG Chi-restraints excluded: chain f residue 58 LYS Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 13 LYS Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 29 ARG Chi-restraints excluded: chain g residue 73 ASN Chi-restraints excluded: chain g residue 83 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 98 MET Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain h residue 45 LYS Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 33 LEU Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 70 MET Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 5 LYS Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 16 LYS Chi-restraints excluded: chain j residue 20 ARG Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain j residue 79 MET Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain k residue 4 LYS Chi-restraints excluded: chain k residue 6 ASN Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain k residue 58 ARG Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 96 LYS Chi-restraints excluded: chain k residue 101 ASN Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 119 ILE Chi-restraints excluded: chain k residue 174 LEU Chi-restraints excluded: chain k residue 175 HIS Chi-restraints excluded: chain k residue 176 THR Chi-restraints excluded: chain k residue 178 ARG Chi-restraints excluded: chain k residue 194 LYS Chi-restraints excluded: chain k residue 198 LYS Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 52 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 42 LYS Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 70 ASP Chi-restraints excluded: chain m residue 76 ARG Chi-restraints excluded: chain m residue 85 ILE Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 96 MET Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 155 LYS Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 41 TYR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 119 PHE Chi-restraints excluded: chain n residue 2 ARG Chi-restraints excluded: chain n residue 19 LYS Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 46 ARG Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 88 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 113 GLN Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 15 ARG Chi-restraints excluded: chain o residue 21 ARG Chi-restraints excluded: chain o residue 33 LYS Chi-restraints excluded: chain o residue 42 SER Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 71 GLU Chi-restraints excluded: chain o residue 72 ARG Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 103 ILE Chi-restraints excluded: chain o residue 119 ARG Chi-restraints excluded: chain o residue 121 ARG Chi-restraints excluded: chain o residue 127 ILE Chi-restraints excluded: chain O residue 22 LYS Chi-restraints excluded: chain O residue 41 LYS Chi-restraints excluded: chain O residue 70 ARG Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 104 LYS Chi-restraints excluded: chain p residue 17 ILE Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 48 ASP Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 64 GLU Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 69 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 76 LYS Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 136 LYS Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 24 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 45 SER Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 36 ASP Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 85 ILE Chi-restraints excluded: chain q residue 87 ARG Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 102 ARG Chi-restraints excluded: chain q residue 121 LYS Chi-restraints excluded: chain q residue 124 ARG Chi-restraints excluded: chain q residue 130 SER Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 86 ARG Chi-restraints excluded: chain Q residue 99 ARG Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 4 ARG Chi-restraints excluded: chain R residue 8 LYS Chi-restraints excluded: chain R residue 15 LYS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 86 VAL Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain S residue 89 LYS Chi-restraints excluded: chain S residue 101 ILE Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 22 ARG Chi-restraints excluded: chain U residue 70 LYS Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 19 LYS Chi-restraints excluded: chain W residue 40 THR Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 59 LYS Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 23 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 762 optimal weight: 0.7980 chunk 684 optimal weight: 1.9990 chunk 379 optimal weight: 50.0000 chunk 233 optimal weight: 10.0000 chunk 461 optimal weight: 40.0000 chunk 365 optimal weight: 50.0000 chunk 707 optimal weight: 40.0000 chunk 273 optimal weight: 50.0000 chunk 430 optimal weight: 7.9990 chunk 526 optimal weight: 4.9990 chunk 820 optimal weight: 20.0000 overall best weight: 5.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN a 67 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN D 33 ASN D 70 ASN D 128 GLN D 143 HIS D 176 ASN D 192 ASN D 200 ASN E 162 ASN E 179 GLN ** f 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 57 GLN J 17 ASN J 27 ASN K 35 GLN L 12 GLN L 106 GLN l 67 GLN ** n 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 ASN N 14 GLN o 22 HIS O 37 GLN O 71 GLN P 81 ASN P 88 HIS Q 61 ASN T 13 GLN T 85 GLN V 34 GLN ** W 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 140267 Z= 0.295 Angle : 0.704 10.315 210655 Z= 0.363 Chirality : 0.039 0.414 27204 Planarity : 0.005 0.061 10799 Dihedral : 26.623 179.966 72618 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.09 % Favored : 88.60 % Rotamer: Outliers : 10.40 % Allowed : 31.91 % Favored : 57.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.10), residues: 4878 helix: -1.42 (0.14), residues: 1173 sheet: -2.49 (0.17), residues: 698 loop : -3.37 (0.09), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP k 18 HIS 0.007 0.001 HIS M 102 PHE 0.019 0.002 PHE J 50 TYR 0.022 0.002 TYR a 58 ARG 0.011 0.001 ARG U 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 748 time to evaluate : 5.334 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: 2 3 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9007 (mtmt) REVERT: 4 13 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6854 (pttm) REVERT: 4 24 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7263 (mtm) REVERT: a 46 LYS cc_start: 0.4861 (OUTLIER) cc_final: 0.1657 (mtmm) REVERT: a 55 VAL cc_start: -0.0545 (OUTLIER) cc_final: -0.0814 (m) REVERT: a 69 THR cc_start: 0.2048 (OUTLIER) cc_final: 0.0163 (t) REVERT: a 74 ILE cc_start: 0.2137 (OUTLIER) cc_final: 0.1785 (mt) REVERT: c 7 LEU cc_start: -0.1794 (OUTLIER) cc_final: -0.1995 (mt) REVERT: c 44 ARG cc_start: 0.4261 (mmm160) cc_final: 0.3782 (mmm160) REVERT: C 150 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8561 (tttt) REVERT: C 170 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6510 (mmtt) REVERT: d 86 TYR cc_start: -0.3068 (OUTLIER) cc_final: -0.4111 (t80) REVERT: d 87 ARG cc_start: 0.1234 (OUTLIER) cc_final: -0.0468 (tpt170) REVERT: D 205 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8497 (mmtp) REVERT: E 40 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: E 54 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5644 (pmt170) REVERT: E 127 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8073 (p0) REVERT: E 164 GLU cc_start: 0.7816 (pp20) cc_final: 0.7500 (pp20) REVERT: E 185 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7022 (p0) REVERT: e 6 MET cc_start: 0.1065 (OUTLIER) cc_final: 0.0184 (mmp) REVERT: e 40 CYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4472 (p) REVERT: e 57 ARG cc_start: 0.2156 (OUTLIER) cc_final: 0.0086 (mmp-170) REVERT: f 59 MET cc_start: 0.4553 (mtt) cc_final: 0.3423 (tpt) REVERT: f 62 ARG cc_start: 0.2243 (OUTLIER) cc_final: 0.2009 (tmt170) REVERT: g 14 ARG cc_start: -0.0476 (OUTLIER) cc_final: -0.3378 (tpt170) REVERT: G 71 LEU cc_start: 0.9532 (tm) cc_final: 0.9176 (tt) REVERT: G 87 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6909 (tt) REVERT: G 119 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8923 (mp0) REVERT: H 100 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7823 (ttp-170) REVERT: h 62 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8262 (mmpt) REVERT: I 1 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7800 (mtm) REVERT: i 28 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: i 57 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: i 58 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.4789 (mtt180) REVERT: i 70 MET cc_start: 0.6224 (mmt) cc_final: 0.4045 (tmm) REVERT: i 75 TYR cc_start: 0.0503 (OUTLIER) cc_final: 0.0019 (m-80) REVERT: J 33 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8670 (mtt-85) REVERT: J 39 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8577 (mtpp) REVERT: J 104 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8146 (p0) REVERT: k 96 LYS cc_start: -0.3346 (OUTLIER) cc_final: -0.3591 (mptt) REVERT: k 114 LEU cc_start: 0.6137 (mm) cc_final: 0.5879 (pt) REVERT: k 121 ARG cc_start: 0.0675 (OUTLIER) cc_final: 0.0097 (mmp-170) REVERT: k 175 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.6385 (t-90) REVERT: k 176 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7220 (t) REVERT: K 45 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: L 70 GLU cc_start: 0.8353 (mp0) cc_final: 0.8111 (mp0) REVERT: m 54 GLN cc_start: 0.1828 (OUTLIER) cc_final: 0.1552 (mp10) REVERT: n 42 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6846 (t0) REVERT: n 78 ARG cc_start: -0.2052 (OUTLIER) cc_final: -0.4209 (mtt180) REVERT: o 54 ASP cc_start: 0.3137 (OUTLIER) cc_final: 0.2118 (OUTLIER) REVERT: o 93 GLU cc_start: 0.5603 (pp20) cc_final: 0.5152 (mt-10) REVERT: o 94 MET cc_start: 0.4566 (OUTLIER) cc_final: 0.4045 (tmt) REVERT: p 21 LYS cc_start: 0.5514 (mmtm) cc_final: 0.5059 (mmtp) REVERT: p 29 LYS cc_start: 0.1538 (mptt) cc_final: 0.0055 (pptt) REVERT: p 36 ARG cc_start: 0.3500 (OUTLIER) cc_final: 0.3195 (mpp-170) REVERT: p 66 ILE cc_start: -0.4497 (OUTLIER) cc_final: -0.5346 (tt) REVERT: p 149 LYS cc_start: 0.4395 (pptt) cc_final: 0.4166 (pmtt) REVERT: q 8 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.5034 (m-80) REVERT: q 36 ASP cc_start: -0.2571 (OUTLIER) cc_final: -0.3521 (m-30) REVERT: R 32 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8335 (mtp180) REVERT: R 64 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7597 (ttm110) REVERT: R 69 GLN cc_start: 0.8469 (mm110) cc_final: 0.7393 (mm110) REVERT: S 41 MET cc_start: 0.7819 (mmt) cc_final: 0.7589 (mmm) REVERT: S 100 GLU cc_start: 0.9305 (pp20) cc_final: 0.8800 (pp20) REVERT: T 12 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8727 (tppt) REVERT: T 23 LYS cc_start: 0.9476 (tppp) cc_final: 0.9236 (tppp) REVERT: T 80 ASP cc_start: 0.9482 (t0) cc_final: 0.9155 (t0) REVERT: U 48 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: U 82 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6657 (ttm170) REVERT: W 17 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8677 (tp40) REVERT: W 27 ASN cc_start: 0.8862 (m-40) cc_final: 0.8575 (m110) REVERT: Z 27 MET cc_start: 0.8749 (ppp) cc_final: 0.8298 (ppp) outliers start: 375 outliers final: 154 residues processed: 1026 average time/residue: 1.9978 time to fit residues: 2926.5660 Evaluate side-chains 887 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 683 time to evaluate : 5.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 35 ASN Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 24 LYS Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 46 LYS Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 188 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain d residue 87 ARG Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain e residue 6 MET Chi-restraints excluded: chain e residue 23 ARG Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 57 ARG Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 80 GLU Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 171 ARG Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 22 THR Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 57 GLN Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 14 THR Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 33 ARG Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 96 LYS Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 121 ARG Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 141 MET Chi-restraints excluded: chain k residue 148 ILE Chi-restraints excluded: chain k residue 153 SER Chi-restraints excluded: chain k residue 175 HIS Chi-restraints excluded: chain k residue 176 THR Chi-restraints excluded: chain k residue 183 TYR Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain l residue 61 TYR Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 77 GLN Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 85 LYS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 21 ARG Chi-restraints excluded: chain o residue 42 SER Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 72 ARG Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain p residue 51 GLU Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 76 LYS Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 135 VAL Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 36 ASP Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 32 ARG Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 43 SER Chi-restraints excluded: chain U residue 48 GLN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 455 optimal weight: 0.0030 chunk 254 optimal weight: 7.9990 chunk 682 optimal weight: 4.9990 chunk 558 optimal weight: 50.0000 chunk 226 optimal weight: 10.0000 chunk 821 optimal weight: 5.9990 chunk 887 optimal weight: 7.9990 chunk 731 optimal weight: 0.2980 chunk 814 optimal weight: 10.0000 chunk 280 optimal weight: 50.0000 chunk 659 optimal weight: 50.0000 overall best weight: 3.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 60 GLN b 18 ASN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN E 148 GLN ** f 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 HIS I 4 GLN i 25 HIS i 57 GLN J 17 ASN J 27 ASN k 6 ASN k 118 ASN k 151 GLN k 175 HIS L 79 GLN ** m 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 ASN O 71 GLN P 63 ASN q 16 ASN Q 61 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 ASN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 140267 Z= 0.232 Angle : 0.638 11.170 210655 Z= 0.327 Chirality : 0.037 0.369 27204 Planarity : 0.005 0.062 10799 Dihedral : 26.396 179.846 71947 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.62 % Favored : 89.18 % Rotamer: Outliers : 7.96 % Allowed : 34.38 % Favored : 57.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.11), residues: 4878 helix: -0.43 (0.15), residues: 1168 sheet: -2.03 (0.18), residues: 725 loop : -3.09 (0.09), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 48 HIS 0.007 0.001 HIS a 56 PHE 0.018 0.001 PHE o 63 TYR 0.018 0.001 TYR a 58 ARG 0.015 0.001 ARG e 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 748 time to evaluate : 5.232 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9264 (tm) cc_final: 0.9014 (mp) REVERT: 2 3 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8984 (mtmt) REVERT: 4 24 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7348 (mtm) REVERT: 4 26 ILE cc_start: 0.8031 (tt) cc_final: 0.7534 (pp) REVERT: a 74 ILE cc_start: 0.2214 (OUTLIER) cc_final: 0.1905 (mt) REVERT: c 53 MET cc_start: 0.1441 (tmm) cc_final: 0.1047 (tmm) REVERT: c 56 LYS cc_start: 0.2479 (OUTLIER) cc_final: 0.2182 (tptt) REVERT: c 96 ARG cc_start: 0.4885 (tpm170) cc_final: 0.4546 (tpm170) REVERT: C 150 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8620 (tttt) REVERT: d 31 GLN cc_start: 0.2784 (OUTLIER) cc_final: 0.2559 (tt0) REVERT: d 81 MET cc_start: -0.4495 (ttt) cc_final: -0.4836 (ttt) REVERT: d 87 ARG cc_start: 0.0889 (OUTLIER) cc_final: -0.0069 (mmt180) REVERT: E 164 GLU cc_start: 0.7881 (pp20) cc_final: 0.7614 (pp20) REVERT: E 185 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7165 (p0) REVERT: e 6 MET cc_start: 0.1242 (mtt) cc_final: 0.0583 (mmp) REVERT: e 40 CYS cc_start: 0.5717 (OUTLIER) cc_final: 0.4631 (p) REVERT: e 42 ILE cc_start: -0.4532 (OUTLIER) cc_final: -0.4794 (pt) REVERT: e 43 CYS cc_start: -0.1829 (OUTLIER) cc_final: -0.3332 (t) REVERT: f 59 MET cc_start: 0.4571 (mtt) cc_final: 0.3497 (tpt) REVERT: g 14 ARG cc_start: -0.0150 (OUTLIER) cc_final: -0.3132 (tpt170) REVERT: g 70 THR cc_start: -0.1317 (OUTLIER) cc_final: -0.1691 (m) REVERT: G 27 LYS cc_start: 0.9074 (tppt) cc_final: 0.8042 (tppt) REVERT: G 41 MET cc_start: 0.7453 (mtt) cc_final: 0.6517 (ttt) REVERT: G 71 LEU cc_start: 0.9614 (tm) cc_final: 0.9411 (tt) REVERT: G 119 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: G 140 GLN cc_start: 0.9207 (tm-30) cc_final: 0.9000 (tm-30) REVERT: G 144 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9295 (pp) REVERT: H 100 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7798 (ttp-170) REVERT: h 38 LYS cc_start: 0.6309 (tppt) cc_final: 0.5609 (mmpt) REVERT: h 62 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8351 (mmpt) REVERT: i 38 ILE cc_start: 0.4022 (OUTLIER) cc_final: 0.3351 (mm) REVERT: i 52 THR cc_start: -0.0829 (OUTLIER) cc_final: -0.1285 (p) REVERT: i 57 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: i 58 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.4878 (mtt180) REVERT: i 70 MET cc_start: 0.6253 (mmt) cc_final: 0.4180 (tmm) REVERT: i 75 TYR cc_start: 0.0644 (OUTLIER) cc_final: 0.0099 (m-80) REVERT: j 16 LYS cc_start: 0.7662 (mmmm) cc_final: 0.7395 (mtpp) REVERT: J 47 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8520 (ttp-110) REVERT: J 87 ASP cc_start: 0.8380 (t0) cc_final: 0.8119 (t70) REVERT: J 104 ASN cc_start: 0.8706 (t0) cc_final: 0.8098 (p0) REVERT: k 121 ARG cc_start: 0.0585 (OUTLIER) cc_final: 0.0027 (mmp-170) REVERT: k 139 ARG cc_start: -0.2535 (OUTLIER) cc_final: -0.3254 (ppt90) REVERT: k 174 LEU cc_start: -0.1935 (OUTLIER) cc_final: -0.3761 (tp) REVERT: K 45 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7785 (mtp85) REVERT: K 82 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7746 (ptp90) REVERT: L 70 GLU cc_start: 0.8388 (mp0) cc_final: 0.8147 (mp0) REVERT: l 69 ARG cc_start: 0.7652 (pmt170) cc_final: 0.6743 (mmp-170) REVERT: m 54 GLN cc_start: 0.2054 (OUTLIER) cc_final: 0.1754 (mp10) REVERT: m 138 ARG cc_start: 0.2773 (OUTLIER) cc_final: 0.2485 (ttt-90) REVERT: n 42 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6995 (t0) REVERT: n 78 ARG cc_start: -0.1798 (OUTLIER) cc_final: -0.3945 (mtt180) REVERT: o 54 ASP cc_start: 0.3472 (OUTLIER) cc_final: 0.2365 (OUTLIER) REVERT: o 94 MET cc_start: 0.4191 (OUTLIER) cc_final: 0.3883 (tmt) REVERT: o 110 GLU cc_start: 0.4756 (mp0) cc_final: 0.3468 (pm20) REVERT: p 21 LYS cc_start: 0.5606 (mmtm) cc_final: 0.5118 (mmtp) REVERT: p 29 LYS cc_start: 0.1301 (mptt) cc_final: 0.1079 (mmtp) REVERT: p 35 LYS cc_start: 0.5796 (pttm) cc_final: 0.5401 (pttt) REVERT: p 36 ARG cc_start: 0.3265 (OUTLIER) cc_final: 0.2855 (mtm110) REVERT: p 66 ILE cc_start: -0.4533 (OUTLIER) cc_final: -0.5434 (tt) REVERT: P 26 ASP cc_start: 0.7653 (t70) cc_final: 0.7433 (t0) REVERT: q 8 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.5001 (m-80) REVERT: S 100 GLU cc_start: 0.9268 (pp20) cc_final: 0.8808 (pp20) REVERT: T 12 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8805 (tppt) REVERT: T 26 LYS cc_start: 0.9226 (mmtp) cc_final: 0.9009 (mmtm) REVERT: T 44 ASP cc_start: 0.8177 (t0) cc_final: 0.7967 (t0) REVERT: T 71 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8784 (mmmt) REVERT: T 80 ASP cc_start: 0.9470 (t0) cc_final: 0.9093 (t0) REVERT: U 79 ARG cc_start: 0.7882 (ptp-170) cc_final: 0.7593 (ptm-80) REVERT: U 82 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6638 (ttm170) REVERT: W 27 ASN cc_start: 0.8797 (m-40) cc_final: 0.8466 (m110) REVERT: Z 27 MET cc_start: 0.8716 (ppp) cc_final: 0.8322 (ppp) outliers start: 287 outliers final: 132 residues processed: 962 average time/residue: 1.9069 time to fit residues: 2605.3819 Evaluate side-chains 844 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 675 time to evaluate : 5.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 24 LYS Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 87 ARG Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 38 ILE Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 57 GLN Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 14 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 15 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 121 ARG Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 148 ILE Chi-restraints excluded: chain k residue 174 LEU Chi-restraints excluded: chain k residue 183 TYR Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain l residue 154 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 85 ILE Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 138 ARG Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 42 SER Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 72 ARG Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 51 GLU Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 135 VAL Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 94 SER Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 43 SER Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 811 optimal weight: 7.9990 chunk 617 optimal weight: 10.0000 chunk 426 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 392 optimal weight: 60.0000 chunk 551 optimal weight: 9.9990 chunk 824 optimal weight: 10.0000 chunk 872 optimal weight: 4.9990 chunk 430 optimal weight: 9.9990 chunk 781 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 60 GLN ** a 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** f 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN k 6 ASN k 151 GLN L 79 GLN O 71 GLN P 81 ASN q 83 HIS S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 140267 Z= 0.380 Angle : 0.700 17.856 210655 Z= 0.355 Chirality : 0.041 0.360 27204 Planarity : 0.005 0.068 10799 Dihedral : 26.319 179.962 71838 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.82 % Favored : 90.02 % Rotamer: Outliers : 7.96 % Allowed : 34.74 % Favored : 57.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 4878 helix: -0.21 (0.15), residues: 1188 sheet: -1.87 (0.18), residues: 741 loop : -2.93 (0.09), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 93 HIS 0.005 0.001 HIS O 29 PHE 0.017 0.001 PHE J 50 TYR 0.018 0.001 TYR E 99 ARG 0.012 0.001 ARG q 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 673 time to evaluate : 5.323 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 31 GLU cc_start: 0.7931 (tp30) cc_final: 0.7455 (tp30) REVERT: A 39 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8959 (mp) REVERT: 2 3 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.8972 (mtmt) REVERT: 4 26 ILE cc_start: 0.8090 (tt) cc_final: 0.7723 (pp) REVERT: a 74 ILE cc_start: 0.2202 (OUTLIER) cc_final: 0.1935 (mt) REVERT: c 56 LYS cc_start: 0.2870 (OUTLIER) cc_final: 0.2093 (tptt) REVERT: c 96 ARG cc_start: 0.4801 (tpm170) cc_final: 0.4490 (tpm170) REVERT: C 66 ASP cc_start: 0.8152 (t0) cc_final: 0.7863 (t0) REVERT: C 150 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8739 (tttt) REVERT: C 247 MET cc_start: 0.8801 (mmm) cc_final: 0.8133 (mtp) REVERT: d 81 MET cc_start: -0.4497 (ttt) cc_final: -0.4943 (ttt) REVERT: d 87 ARG cc_start: 0.0687 (OUTLIER) cc_final: 0.0232 (mmt180) REVERT: D 205 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8504 (mmtp) REVERT: E 40 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: e 6 MET cc_start: 0.1380 (mtt) cc_final: 0.0738 (mmp) REVERT: e 40 CYS cc_start: 0.5702 (OUTLIER) cc_final: 0.4540 (p) REVERT: e 42 ILE cc_start: -0.4521 (OUTLIER) cc_final: -0.4752 (pt) REVERT: e 43 CYS cc_start: -0.1829 (OUTLIER) cc_final: -0.3329 (t) REVERT: f 5 GLN cc_start: -0.1554 (OUTLIER) cc_final: -0.1844 (tt0) REVERT: f 59 MET cc_start: 0.4514 (mtt) cc_final: 0.3511 (tpt) REVERT: g 14 ARG cc_start: -0.0237 (OUTLIER) cc_final: -0.3166 (tpt170) REVERT: G 41 MET cc_start: 0.7460 (mtt) cc_final: 0.6573 (ttt) REVERT: G 71 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9379 (tt) REVERT: G 119 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: G 152 ARG cc_start: 0.5102 (OUTLIER) cc_final: 0.4855 (ttt180) REVERT: H 62 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8644 (mmtp) REVERT: H 100 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7799 (ttp-170) REVERT: h 38 LYS cc_start: 0.6590 (tppt) cc_final: 0.5939 (mmpt) REVERT: h 45 LYS cc_start: 0.7543 (mmmt) cc_final: 0.7113 (mmmt) REVERT: h 62 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8319 (mmpt) REVERT: i 28 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: i 36 ARG cc_start: 0.1895 (OUTLIER) cc_final: 0.1477 (ptt180) REVERT: i 52 THR cc_start: -0.0631 (OUTLIER) cc_final: -0.1005 (p) REVERT: i 58 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.4980 (mtt180) REVERT: i 70 MET cc_start: 0.6251 (mmt) cc_final: 0.4228 (tmm) REVERT: i 75 TYR cc_start: 0.0573 (OUTLIER) cc_final: 0.0171 (m-80) REVERT: J 47 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8584 (ttp-110) REVERT: J 64 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8579 (ttm-80) REVERT: J 87 ASP cc_start: 0.8256 (t0) cc_final: 0.7997 (t0) REVERT: J 104 ASN cc_start: 0.8724 (t0) cc_final: 0.8116 (p0) REVERT: k 71 LYS cc_start: 0.3017 (OUTLIER) cc_final: 0.2657 (mtmt) REVERT: k 121 ARG cc_start: 0.0321 (OUTLIER) cc_final: -0.0186 (mmp-170) REVERT: k 139 ARG cc_start: -0.2868 (OUTLIER) cc_final: -0.3449 (ppt170) REVERT: K 45 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7847 (mtp85) REVERT: K 82 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: K 110 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8029 (p) REVERT: L 70 GLU cc_start: 0.8449 (mp0) cc_final: 0.8195 (mp0) REVERT: m 54 GLN cc_start: 0.2173 (OUTLIER) cc_final: 0.1899 (mp10) REVERT: n 42 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7143 (t0) REVERT: n 76 PHE cc_start: -0.5568 (OUTLIER) cc_final: -0.5973 (t80) REVERT: n 78 ARG cc_start: -0.1755 (OUTLIER) cc_final: -0.3763 (mtt180) REVERT: N 4 HIS cc_start: 0.5292 (OUTLIER) cc_final: 0.4367 (m-70) REVERT: o 42 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7647 (t) REVERT: o 43 GLU cc_start: 0.3012 (tm-30) cc_final: 0.2704 (tp30) REVERT: o 54 ASP cc_start: 0.3533 (OUTLIER) cc_final: 0.2522 (OUTLIER) REVERT: o 94 MET cc_start: 0.4209 (OUTLIER) cc_final: 0.3799 (tmt) REVERT: p 21 LYS cc_start: 0.5511 (mmtm) cc_final: 0.4996 (mmtp) REVERT: p 29 LYS cc_start: 0.1226 (mptt) cc_final: -0.0191 (pptt) REVERT: p 66 ILE cc_start: -0.4527 (OUTLIER) cc_final: -0.5474 (tt) REVERT: q 8 TYR cc_start: 0.5337 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: R 14 GLU cc_start: 0.6941 (tm-30) cc_final: 0.5647 (tm-30) REVERT: S 16 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8320 (p0) REVERT: S 100 GLU cc_start: 0.9263 (pp20) cc_final: 0.8747 (pp20) REVERT: T 12 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (tppt) REVERT: T 80 ASP cc_start: 0.9428 (t0) cc_final: 0.9034 (t0) REVERT: U 79 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7537 (ptm-80) REVERT: V 38 ILE cc_start: 0.9154 (tp) cc_final: 0.8474 (pp) REVERT: W 27 ASN cc_start: 0.8809 (m-40) cc_final: 0.8509 (m110) REVERT: Z 27 MET cc_start: 0.8726 (ppp) cc_final: 0.8066 (ppp) outliers start: 287 outliers final: 158 residues processed: 888 average time/residue: 1.9211 time to fit residues: 2411.5579 Evaluate side-chains 830 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 630 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 24 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 87 ARG Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 5 GLN Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 11 VAL Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 14 THR Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 15 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 121 ARG Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 178 ARG Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 8 LYS Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 106 ILE Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 42 ASP Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 42 SER Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 135 VAL Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 36 ASP Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 726 optimal weight: 0.2980 chunk 495 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 649 optimal weight: 9.9990 chunk 360 optimal weight: 50.0000 chunk 744 optimal weight: 20.0000 chunk 603 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 445 optimal weight: 9.9990 chunk 783 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** f 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN k 151 GLN L 79 GLN O 71 GLN P 81 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN 1 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 140267 Z= 0.241 Angle : 0.635 12.671 210655 Z= 0.323 Chirality : 0.037 0.362 27204 Planarity : 0.004 0.066 10799 Dihedral : 26.253 179.995 71827 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.70 % Favored : 90.16 % Rotamer: Outliers : 6.88 % Allowed : 36.51 % Favored : 56.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.11), residues: 4878 helix: 0.12 (0.16), residues: 1179 sheet: -1.59 (0.18), residues: 717 loop : -2.80 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 48 HIS 0.004 0.001 HIS i 25 PHE 0.021 0.001 PHE o 63 TYR 0.026 0.001 TYR D 59 ARG 0.011 0.000 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 700 time to evaluate : 5.186 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8986 (mp) REVERT: 2 3 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.8994 (mtmt) REVERT: 4 26 ILE cc_start: 0.8032 (tt) cc_final: 0.7681 (pp) REVERT: a 74 ILE cc_start: 0.2112 (OUTLIER) cc_final: 0.1879 (mt) REVERT: c 44 ARG cc_start: 0.4140 (mmm160) cc_final: 0.3641 (mmm160) REVERT: c 53 MET cc_start: 0.1236 (tmm) cc_final: 0.0886 (tmm) REVERT: c 56 LYS cc_start: 0.2717 (OUTLIER) cc_final: 0.2462 (tptt) REVERT: c 96 ARG cc_start: 0.4870 (tpm170) cc_final: 0.4354 (tpm170) REVERT: c 107 ARG cc_start: 0.4326 (mmt180) cc_final: 0.4025 (mmt180) REVERT: C 66 ASP cc_start: 0.8168 (t0) cc_final: 0.7806 (t0) REVERT: C 150 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8779 (tttt) REVERT: C 247 MET cc_start: 0.8787 (mmm) cc_final: 0.8261 (mtp) REVERT: d 81 MET cc_start: -0.4531 (ttt) cc_final: -0.4964 (ttt) REVERT: E 40 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: e 6 MET cc_start: 0.1325 (mtt) cc_final: 0.0690 (mmp) REVERT: e 40 CYS cc_start: 0.5642 (OUTLIER) cc_final: 0.4498 (p) REVERT: e 42 ILE cc_start: -0.4370 (OUTLIER) cc_final: -0.4592 (pt) REVERT: e 43 CYS cc_start: -0.1959 (OUTLIER) cc_final: -0.3378 (t) REVERT: f 59 MET cc_start: 0.4497 (mtt) cc_final: 0.3525 (tpt) REVERT: f 62 ARG cc_start: 0.1912 (OUTLIER) cc_final: 0.1559 (tmt170) REVERT: g 14 ARG cc_start: -0.0107 (OUTLIER) cc_final: -0.3089 (tpt170) REVERT: g 70 THR cc_start: -0.1067 (OUTLIER) cc_final: -0.1365 (m) REVERT: g 71 VAL cc_start: 0.3706 (OUTLIER) cc_final: 0.3402 (t) REVERT: G 32 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8111 (mp0) REVERT: G 41 MET cc_start: 0.7531 (mtt) cc_final: 0.6610 (ttt) REVERT: G 75 MET cc_start: 0.9131 (ttp) cc_final: 0.8693 (tpt) REVERT: G 119 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: G 152 ARG cc_start: 0.5147 (OUTLIER) cc_final: 0.4891 (ttt180) REVERT: H 100 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7705 (ttp-170) REVERT: h 38 LYS cc_start: 0.6727 (tppt) cc_final: 0.6122 (mmpt) REVERT: h 45 LYS cc_start: 0.7682 (mmmt) cc_final: 0.7159 (mmmt) REVERT: h 62 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8323 (mmpt) REVERT: I 82 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.9071 (m110) REVERT: i 28 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: i 52 THR cc_start: -0.0723 (OUTLIER) cc_final: -0.1051 (p) REVERT: i 58 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5028 (mtt180) REVERT: i 70 MET cc_start: 0.6251 (mmt) cc_final: 0.4196 (tmm) REVERT: i 75 TYR cc_start: 0.0533 (OUTLIER) cc_final: 0.0246 (m-80) REVERT: J 47 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8549 (ttp-110) REVERT: J 64 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8414 (ttm-80) REVERT: J 87 ASP cc_start: 0.8240 (t70) cc_final: 0.8024 (t0) REVERT: J 104 ASN cc_start: 0.8708 (t0) cc_final: 0.8139 (p0) REVERT: k 40 LYS cc_start: -0.2943 (OUTLIER) cc_final: -0.3554 (ptmt) REVERT: k 71 LYS cc_start: 0.2952 (OUTLIER) cc_final: 0.2585 (mtmt) REVERT: k 143 LEU cc_start: 0.0373 (OUTLIER) cc_final: -0.0073 (tt) REVERT: k 174 LEU cc_start: -0.1765 (OUTLIER) cc_final: -0.3702 (tp) REVERT: K 45 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7844 (mtp85) REVERT: K 82 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7782 (ptp90) REVERT: L 70 GLU cc_start: 0.8421 (mp0) cc_final: 0.8188 (mp0) REVERT: l 69 ARG cc_start: 0.7730 (pmt170) cc_final: 0.6843 (mmp-170) REVERT: m 54 GLN cc_start: 0.2133 (OUTLIER) cc_final: 0.1869 (mp10) REVERT: m 96 MET cc_start: 0.5908 (ppp) cc_final: 0.3098 (mmt) REVERT: n 76 PHE cc_start: -0.5597 (OUTLIER) cc_final: -0.5984 (t80) REVERT: n 78 ARG cc_start: -0.1660 (OUTLIER) cc_final: -0.3613 (mtt180) REVERT: N 4 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.4422 (m-70) REVERT: o 54 ASP cc_start: 0.3685 (OUTLIER) cc_final: 0.2665 (OUTLIER) REVERT: o 94 MET cc_start: 0.4099 (OUTLIER) cc_final: 0.3771 (tmt) REVERT: o 110 GLU cc_start: 0.4915 (mp0) cc_final: 0.3676 (pm20) REVERT: o 126 GLU cc_start: 0.1655 (OUTLIER) cc_final: 0.0830 (mt-10) REVERT: p 21 LYS cc_start: 0.5570 (mmtm) cc_final: 0.5047 (mmtp) REVERT: p 29 LYS cc_start: 0.1172 (mptt) cc_final: -0.0287 (pptt) REVERT: p 31 MET cc_start: -0.0805 (OUTLIER) cc_final: -0.1629 (ttt) REVERT: p 35 LYS cc_start: 0.6519 (pttp) cc_final: 0.5943 (ptmt) REVERT: p 36 ARG cc_start: 0.3466 (OUTLIER) cc_final: 0.1813 (mtm110) REVERT: p 66 ILE cc_start: -0.4572 (OUTLIER) cc_final: -0.5513 (tt) REVERT: P 36 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7880 (p0) REVERT: q 8 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.5026 (m-80) REVERT: S 16 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8417 (p0) REVERT: S 100 GLU cc_start: 0.9224 (pp20) cc_final: 0.8810 (pp20) REVERT: T 80 ASP cc_start: 0.9427 (t0) cc_final: 0.9029 (t0) REVERT: U 79 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.7538 (ptm-80) REVERT: U 82 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6780 (ttm170) REVERT: V 38 ILE cc_start: 0.9092 (tp) cc_final: 0.8446 (pp) REVERT: W 27 ASN cc_start: 0.8800 (m-40) cc_final: 0.8492 (m110) REVERT: Z 27 MET cc_start: 0.8760 (ppp) cc_final: 0.8392 (ppp) outliers start: 248 outliers final: 140 residues processed: 878 average time/residue: 1.9117 time to fit residues: 2370.7503 Evaluate side-chains 841 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 659 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain a residue 24 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 74 ILE Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain e residue 25 GLU Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 82 ASN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 14 THR Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain k residue 15 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 141 MET Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 174 LEU Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 106 ILE Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain o residue 126 GLU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 31 MET Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 135 VAL Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 82 ARG Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 293 optimal weight: 50.0000 chunk 786 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 512 optimal weight: 0.0570 chunk 215 optimal weight: 10.0000 chunk 873 optimal weight: 20.0000 chunk 725 optimal weight: 50.0000 chunk 404 optimal weight: 50.0000 chunk 72 optimal weight: 8.9990 chunk 289 optimal weight: 50.0000 chunk 458 optimal weight: 50.0000 overall best weight: 6.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 GLN E 179 GLN f 5 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 151 GLN O 52 GLN P 81 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 140267 Z= 0.339 Angle : 0.672 12.370 210655 Z= 0.340 Chirality : 0.039 0.348 27204 Planarity : 0.005 0.071 10799 Dihedral : 26.197 179.852 71802 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.84 % Favored : 90.02 % Rotamer: Outliers : 7.76 % Allowed : 35.82 % Favored : 56.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 4878 helix: 0.18 (0.16), residues: 1186 sheet: -1.59 (0.18), residues: 742 loop : -2.69 (0.10), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP k 200 HIS 0.005 0.001 HIS O 29 PHE 0.016 0.001 PHE o 45 TYR 0.026 0.001 TYR D 59 ARG 0.011 0.001 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 675 time to evaluate : 5.454 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8952 (mp) REVERT: 2 3 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9029 (mtmt) REVERT: 4 26 ILE cc_start: 0.8042 (tt) cc_final: 0.7716 (pp) REVERT: a 46 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.1488 (mtmm) REVERT: c 44 ARG cc_start: 0.4124 (mmm160) cc_final: 0.3435 (mmm160) REVERT: c 53 MET cc_start: 0.1567 (tmm) cc_final: 0.1118 (tmm) REVERT: c 56 LYS cc_start: 0.2645 (OUTLIER) cc_final: 0.2264 (tptt) REVERT: c 96 ARG cc_start: 0.4944 (tpm170) cc_final: 0.4396 (tpm170) REVERT: C 150 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8776 (tttt) REVERT: d 32 LYS cc_start: -0.1415 (OUTLIER) cc_final: -0.2406 (mttt) REVERT: d 102 THR cc_start: 0.3913 (OUTLIER) cc_final: 0.3478 (m) REVERT: D 205 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8478 (mmtp) REVERT: E 40 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: e 6 MET cc_start: 0.1211 (mtt) cc_final: 0.0490 (mmp) REVERT: e 40 CYS cc_start: 0.5600 (OUTLIER) cc_final: 0.2671 (p) REVERT: e 42 ILE cc_start: -0.4324 (OUTLIER) cc_final: -0.4543 (pt) REVERT: e 43 CYS cc_start: -0.1791 (OUTLIER) cc_final: -0.3427 (t) REVERT: e 57 ARG cc_start: 0.1830 (OUTLIER) cc_final: 0.0121 (mmp-170) REVERT: f 5 GLN cc_start: -0.1409 (OUTLIER) cc_final: -0.1615 (tt0) REVERT: f 59 MET cc_start: 0.4387 (mtt) cc_final: 0.3419 (tpt) REVERT: f 62 ARG cc_start: 0.1916 (OUTLIER) cc_final: 0.1644 (ttt-90) REVERT: g 14 ARG cc_start: -0.0024 (OUTLIER) cc_final: -0.2981 (tpt170) REVERT: g 70 THR cc_start: -0.1039 (OUTLIER) cc_final: -0.1360 (m) REVERT: g 71 VAL cc_start: 0.4091 (OUTLIER) cc_final: 0.3799 (t) REVERT: G 41 MET cc_start: 0.7598 (mtt) cc_final: 0.6637 (ttt) REVERT: G 75 MET cc_start: 0.9128 (ttp) cc_final: 0.8695 (tpt) REVERT: G 119 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: G 144 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9306 (pp) REVERT: G 152 ARG cc_start: 0.5057 (OUTLIER) cc_final: 0.4811 (ttt180) REVERT: H 100 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7710 (ttp-170) REVERT: h 38 LYS cc_start: 0.6796 (tppt) cc_final: 0.6263 (mmpt) REVERT: h 62 LYS cc_start: 0.8790 (tmtt) cc_final: 0.8345 (mmpt) REVERT: i 28 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: i 36 ARG cc_start: 0.1787 (OUTLIER) cc_final: 0.1358 (ptt180) REVERT: i 52 THR cc_start: -0.0444 (OUTLIER) cc_final: -0.0781 (p) REVERT: i 58 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.4997 (mtt180) REVERT: i 70 MET cc_start: 0.6264 (mmt) cc_final: 0.4248 (tmm) REVERT: i 75 TYR cc_start: 0.0579 (OUTLIER) cc_final: 0.0317 (m-80) REVERT: j 16 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7991 (mtpp) REVERT: J 47 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8552 (ttp-110) REVERT: J 64 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8268 (ttm-80) REVERT: J 104 ASN cc_start: 0.8726 (t0) cc_final: 0.8195 (p0) REVERT: k 40 LYS cc_start: -0.2888 (OUTLIER) cc_final: -0.3479 (ptmt) REVERT: k 71 LYS cc_start: 0.2856 (OUTLIER) cc_final: 0.2472 (mtmt) REVERT: k 139 ARG cc_start: -0.2745 (OUTLIER) cc_final: -0.3326 (ppt170) REVERT: k 143 LEU cc_start: 0.0356 (OUTLIER) cc_final: -0.0074 (tt) REVERT: k 151 GLN cc_start: 0.0366 (OUTLIER) cc_final: -0.0696 (mm-40) REVERT: k 178 ARG cc_start: 0.0463 (OUTLIER) cc_final: -0.0016 (pmt170) REVERT: K 45 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7859 (mtp85) REVERT: K 82 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7836 (ptp90) REVERT: L 70 GLU cc_start: 0.8457 (mp0) cc_final: 0.8213 (mp0) REVERT: l 69 ARG cc_start: 0.7737 (pmt170) cc_final: 0.6874 (mmp-170) REVERT: m 65 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5685 (pp20) REVERT: m 96 MET cc_start: 0.5880 (ppp) cc_final: 0.3078 (mmt) REVERT: n 76 PHE cc_start: -0.5542 (OUTLIER) cc_final: -0.5944 (t80) REVERT: n 78 ARG cc_start: -0.1613 (OUTLIER) cc_final: -0.3473 (mtt180) REVERT: N 4 HIS cc_start: 0.5475 (OUTLIER) cc_final: 0.4714 (m-70) REVERT: o 54 ASP cc_start: 0.3843 (OUTLIER) cc_final: 0.2897 (OUTLIER) REVERT: o 94 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3942 (tpt) REVERT: o 126 GLU cc_start: 0.1867 (OUTLIER) cc_final: 0.1098 (mt-10) REVERT: p 21 LYS cc_start: 0.5725 (mmtm) cc_final: 0.5185 (mmtp) REVERT: p 29 LYS cc_start: 0.1231 (mptt) cc_final: -0.0238 (pptt) REVERT: p 31 MET cc_start: -0.0864 (ttt) cc_final: -0.1740 (ttt) REVERT: p 35 LYS cc_start: 0.6393 (pttp) cc_final: 0.5803 (pttp) REVERT: p 36 ARG cc_start: 0.3543 (OUTLIER) cc_final: 0.1954 (mtm110) REVERT: p 66 ILE cc_start: -0.4451 (OUTLIER) cc_final: -0.5436 (tt) REVERT: P 26 ASP cc_start: 0.7733 (t70) cc_final: 0.7530 (t0) REVERT: P 36 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (p0) REVERT: q 8 TYR cc_start: 0.5247 (OUTLIER) cc_final: 0.4945 (m-80) REVERT: S 100 GLU cc_start: 0.9259 (pp20) cc_final: 0.8753 (pp20) REVERT: T 5 LYS cc_start: 0.8793 (tppt) cc_final: 0.8580 (tppt) REVERT: T 26 LYS cc_start: 0.9248 (mmtp) cc_final: 0.8950 (mmtm) REVERT: T 80 ASP cc_start: 0.9430 (t0) cc_final: 0.9023 (t0) REVERT: U 48 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: U 79 ARG cc_start: 0.7995 (ptp-170) cc_final: 0.7586 (ptm-80) REVERT: V 38 ILE cc_start: 0.9094 (tp) cc_final: 0.8464 (pp) REVERT: W 27 ASN cc_start: 0.8737 (m-40) cc_final: 0.8467 (m110) REVERT: Z 27 MET cc_start: 0.8753 (ppp) cc_final: 0.8092 (ppp) outliers start: 280 outliers final: 167 residues processed: 882 average time/residue: 2.0061 time to fit residues: 2522.9048 Evaluate side-chains 864 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 649 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 46 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 57 ARG Chi-restraints excluded: chain f residue 5 GLN Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 15 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 141 MET Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 151 GLN Chi-restraints excluded: chain k residue 178 ARG Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 52 LYS Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 85 ILE Chi-restraints excluded: chain m residue 89 TYR Chi-restraints excluded: chain m residue 106 ILE Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 160 THR Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 102 HIS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain o residue 126 GLU Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 48 GLN Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 842 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 497 optimal weight: 5.9990 chunk 638 optimal weight: 50.0000 chunk 494 optimal weight: 4.9990 chunk 735 optimal weight: 20.0000 chunk 487 optimal weight: 8.9990 chunk 870 optimal weight: 9.9990 chunk 544 optimal weight: 6.9990 chunk 530 optimal weight: 0.9990 chunk 401 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 43 GLN 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 5 GLN G 81 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN i 25 HIS ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 34 ASN ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 151 GLN l 50 GLN M 37 ASN n 53 ASN ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN P 81 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN T 85 GLN W 31 GLN W 36 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 140267 Z= 0.286 Angle : 0.647 11.789 210655 Z= 0.328 Chirality : 0.038 0.357 27204 Planarity : 0.004 0.071 10799 Dihedral : 26.160 179.839 71784 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.57 % Favored : 90.28 % Rotamer: Outliers : 6.88 % Allowed : 37.45 % Favored : 55.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.11), residues: 4878 helix: 0.34 (0.16), residues: 1171 sheet: -1.42 (0.18), residues: 748 loop : -2.64 (0.10), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP k 200 HIS 0.004 0.001 HIS O 29 PHE 0.019 0.001 PHE o 63 TYR 0.039 0.001 TYR D 59 ARG 0.013 0.000 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 684 time to evaluate : 5.310 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 175 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8957 (mp) REVERT: 2 3 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9059 (mtmt) REVERT: 4 26 ILE cc_start: 0.7994 (tt) cc_final: 0.7643 (pp) REVERT: c 53 MET cc_start: 0.1611 (tmm) cc_final: 0.0842 (tmm) REVERT: c 56 LYS cc_start: 0.2647 (OUTLIER) cc_final: 0.2270 (tptt) REVERT: c 63 ARG cc_start: -0.0860 (mpt180) cc_final: -0.1172 (mpt180) REVERT: c 96 ARG cc_start: 0.4947 (tpm170) cc_final: 0.4349 (tpm170) REVERT: c 107 ARG cc_start: 0.4284 (mmt180) cc_final: 0.1117 (tpt-90) REVERT: C 20 ASP cc_start: 0.8404 (t70) cc_final: 0.7796 (p0) REVERT: C 247 MET cc_start: 0.8806 (mmm) cc_final: 0.8280 (mtp) REVERT: E 40 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: e 6 MET cc_start: 0.1290 (mtt) cc_final: 0.0552 (mmp) REVERT: e 40 CYS cc_start: 0.3837 (OUTLIER) cc_final: 0.2693 (p) REVERT: e 42 ILE cc_start: -0.4309 (OUTLIER) cc_final: -0.4522 (pt) REVERT: e 43 CYS cc_start: -0.2044 (OUTLIER) cc_final: -0.3514 (t) REVERT: f 59 MET cc_start: 0.4401 (mtt) cc_final: 0.3419 (tpt) REVERT: f 62 ARG cc_start: 0.1943 (OUTLIER) cc_final: 0.1682 (ttt-90) REVERT: g 14 ARG cc_start: 0.0033 (OUTLIER) cc_final: -0.2983 (tpt170) REVERT: g 70 THR cc_start: -0.0951 (OUTLIER) cc_final: -0.1286 (m) REVERT: g 71 VAL cc_start: 0.4108 (OUTLIER) cc_final: 0.3830 (t) REVERT: G 41 MET cc_start: 0.7618 (mtt) cc_final: 0.7400 (mtt) REVERT: G 75 MET cc_start: 0.9163 (ttp) cc_final: 0.8883 (tmt) REVERT: G 119 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: G 144 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9316 (pp) REVERT: G 152 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4780 (ttt180) REVERT: H 100 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7686 (ttp-170) REVERT: h 38 LYS cc_start: 0.6805 (tppt) cc_final: 0.6311 (mmpt) REVERT: h 45 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7497 (tppt) REVERT: h 62 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8364 (mmpt) REVERT: I 82 ASN cc_start: 0.9331 (OUTLIER) cc_final: 0.9082 (m110) REVERT: i 28 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: i 36 ARG cc_start: 0.2063 (OUTLIER) cc_final: 0.1628 (ptt180) REVERT: i 52 THR cc_start: -0.0400 (OUTLIER) cc_final: -0.0724 (p) REVERT: i 58 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5002 (mtt180) REVERT: i 70 MET cc_start: 0.6287 (mmt) cc_final: 0.4280 (tmm) REVERT: i 75 TYR cc_start: 0.0564 (OUTLIER) cc_final: 0.0278 (m-80) REVERT: J 47 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8547 (ttp-110) REVERT: J 64 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8376 (ttm-80) REVERT: J 104 ASN cc_start: 0.8718 (t0) cc_final: 0.8201 (p0) REVERT: k 40 LYS cc_start: -0.2868 (OUTLIER) cc_final: -0.3463 (ptmt) REVERT: k 71 LYS cc_start: 0.2786 (OUTLIER) cc_final: 0.2391 (mtmt) REVERT: k 139 ARG cc_start: -0.2793 (OUTLIER) cc_final: -0.3449 (ppt170) REVERT: k 143 LEU cc_start: 0.0408 (OUTLIER) cc_final: -0.0025 (tt) REVERT: k 151 GLN cc_start: 0.0519 (OUTLIER) cc_final: -0.0521 (mm-40) REVERT: K 45 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7819 (mtp85) REVERT: K 82 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7810 (ptp90) REVERT: L 70 GLU cc_start: 0.8401 (mp0) cc_final: 0.8172 (mp0) REVERT: l 69 ARG cc_start: 0.7733 (pmt170) cc_final: 0.6921 (mmp-170) REVERT: m 65 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5702 (pp20) REVERT: m 96 MET cc_start: 0.5858 (ppp) cc_final: 0.3244 (mmt) REVERT: m 136 MET cc_start: 0.4159 (pp-130) cc_final: 0.3671 (tmt) REVERT: M 37 ASN cc_start: 0.9300 (t0) cc_final: 0.8716 (t0) REVERT: n 76 PHE cc_start: -0.5519 (OUTLIER) cc_final: -0.5967 (t80) REVERT: n 78 ARG cc_start: -0.1683 (OUTLIER) cc_final: -0.3372 (mtt180) REVERT: N 4 HIS cc_start: 0.5328 (OUTLIER) cc_final: 0.4592 (m-70) REVERT: o 54 ASP cc_start: 0.3923 (OUTLIER) cc_final: 0.2960 (OUTLIER) REVERT: o 71 GLU cc_start: 0.3270 (pp20) cc_final: 0.2687 (pm20) REVERT: o 94 MET cc_start: 0.4166 (OUTLIER) cc_final: 0.3744 (tpt) REVERT: o 110 GLU cc_start: 0.4829 (mp0) cc_final: 0.3701 (pm20) REVERT: p 21 LYS cc_start: 0.5630 (mmtm) cc_final: 0.5085 (mmtp) REVERT: p 29 LYS cc_start: 0.0972 (mptt) cc_final: -0.0447 (pptt) REVERT: p 31 MET cc_start: -0.0772 (ttt) cc_final: -0.1366 (ttt) REVERT: p 36 ARG cc_start: 0.3562 (OUTLIER) cc_final: 0.3182 (mpp-170) REVERT: p 66 ILE cc_start: -0.4367 (OUTLIER) cc_final: -0.5340 (tt) REVERT: P 36 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7894 (p0) REVERT: q 36 ASP cc_start: -0.0239 (OUTLIER) cc_final: -0.1464 (m-30) REVERT: S 100 GLU cc_start: 0.9250 (pp20) cc_final: 0.8748 (pp20) REVERT: T 5 LYS cc_start: 0.8790 (tppt) cc_final: 0.8560 (tppt) REVERT: T 26 LYS cc_start: 0.9277 (mmtp) cc_final: 0.9020 (mmtm) REVERT: T 80 ASP cc_start: 0.9445 (t0) cc_final: 0.9045 (t0) REVERT: U 48 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: U 79 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7591 (ptm-80) REVERT: V 38 ILE cc_start: 0.9094 (tp) cc_final: 0.8472 (pp) REVERT: W 27 ASN cc_start: 0.8650 (m-40) cc_final: 0.8267 (m110) REVERT: Z 27 MET cc_start: 0.8803 (ppp) cc_final: 0.8113 (ppp) outliers start: 248 outliers final: 153 residues processed: 870 average time/residue: 1.9655 time to fit residues: 2411.0535 Evaluate side-chains 855 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 662 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 82 ASN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 141 MET Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 151 GLN Chi-restraints excluded: chain k residue 183 TYR Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 106 ILE Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 102 HIS Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 104 SER Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 36 ARG Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 138 ARG Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 36 ASP Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 58 ASN Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 48 GLN Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 538 optimal weight: 1.9990 chunk 347 optimal weight: 50.0000 chunk 519 optimal weight: 7.9990 chunk 262 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 553 optimal weight: 0.6980 chunk 592 optimal weight: 40.0000 chunk 430 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 684 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 43 GLN 2 60 GLN 4 34 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN P 81 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 ASN T 85 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 140267 Z= 0.248 Angle : 0.636 21.157 210655 Z= 0.322 Chirality : 0.037 0.353 27204 Planarity : 0.004 0.068 10799 Dihedral : 26.102 179.910 71778 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.25 % Favored : 90.61 % Rotamer: Outliers : 6.29 % Allowed : 38.51 % Favored : 55.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.11), residues: 4878 helix: 0.40 (0.16), residues: 1162 sheet: -1.26 (0.18), residues: 738 loop : -2.57 (0.10), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.005 0.001 HIS O 29 PHE 0.013 0.001 PHE J 50 TYR 0.031 0.001 TYR D 59 ARG 0.021 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 685 time to evaluate : 5.250 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU Q 112 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 11 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7650 (ttt180) REVERT: 2 3 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9033 (mtmt) REVERT: 4 24 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7477 (mtm) REVERT: 4 26 ILE cc_start: 0.7960 (tt) cc_final: 0.7566 (pp) REVERT: a 46 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.1288 (mtmm) REVERT: c 56 LYS cc_start: 0.2666 (OUTLIER) cc_final: 0.2277 (tptt) REVERT: c 96 ARG cc_start: 0.4868 (tpm170) cc_final: 0.4153 (tpm170) REVERT: c 107 ARG cc_start: 0.4298 (mmt180) cc_final: 0.1220 (tpt-90) REVERT: C 247 MET cc_start: 0.8799 (mmm) cc_final: 0.8272 (mtp) REVERT: d 102 THR cc_start: 0.4262 (OUTLIER) cc_final: 0.3861 (m) REVERT: D 205 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8462 (mmtp) REVERT: E 40 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: e 40 CYS cc_start: 0.3754 (OUTLIER) cc_final: 0.2614 (p) REVERT: e 42 ILE cc_start: -0.4264 (OUTLIER) cc_final: -0.4480 (pt) REVERT: e 43 CYS cc_start: -0.1782 (OUTLIER) cc_final: -0.3262 (t) REVERT: f 59 MET cc_start: 0.4406 (mtt) cc_final: 0.3441 (tpt) REVERT: f 62 ARG cc_start: 0.1901 (OUTLIER) cc_final: 0.1628 (ttt-90) REVERT: g 14 ARG cc_start: 0.0022 (OUTLIER) cc_final: -0.3006 (tpt170) REVERT: g 70 THR cc_start: -0.0756 (OUTLIER) cc_final: -0.1104 (m) REVERT: g 71 VAL cc_start: 0.4037 (OUTLIER) cc_final: 0.3771 (t) REVERT: G 41 MET cc_start: 0.7669 (mtt) cc_final: 0.7411 (mtt) REVERT: G 119 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: G 140 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8879 (pp30) REVERT: G 152 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.4771 (ttt180) REVERT: H 100 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7683 (ttp-170) REVERT: h 38 LYS cc_start: 0.6852 (tppt) cc_final: 0.6367 (mppt) REVERT: h 45 LYS cc_start: 0.7995 (mmtt) cc_final: 0.6633 (mmmt) REVERT: h 62 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8364 (mmpt) REVERT: I 82 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.9085 (m110) REVERT: i 28 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6283 (m-10) REVERT: i 36 ARG cc_start: 0.1791 (OUTLIER) cc_final: 0.1437 (ptt180) REVERT: i 52 THR cc_start: -0.0294 (OUTLIER) cc_final: -0.0603 (p) REVERT: i 58 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5067 (mtt180) REVERT: i 70 MET cc_start: 0.6399 (mmt) cc_final: 0.4331 (tmm) REVERT: i 75 TYR cc_start: 0.0571 (OUTLIER) cc_final: 0.0309 (m-80) REVERT: J 47 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8495 (ttp-110) REVERT: J 64 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8519 (ttm-80) REVERT: J 104 ASN cc_start: 0.8713 (t0) cc_final: 0.8228 (p0) REVERT: k 40 LYS cc_start: -0.2753 (OUTLIER) cc_final: -0.3360 (ptmt) REVERT: k 71 LYS cc_start: 0.2837 (OUTLIER) cc_final: 0.2432 (mtmt) REVERT: k 139 ARG cc_start: -0.2887 (OUTLIER) cc_final: -0.3467 (ppt170) REVERT: k 178 ARG cc_start: 0.0633 (OUTLIER) cc_final: 0.0158 (pmt170) REVERT: K 45 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7862 (mtp85) REVERT: K 82 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7798 (ptp90) REVERT: l 69 ARG cc_start: 0.7703 (pmt170) cc_final: 0.6856 (mmp-170) REVERT: m 65 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: m 96 MET cc_start: 0.5848 (ppp) cc_final: 0.3316 (mmt) REVERT: m 138 ARG cc_start: 0.2074 (OUTLIER) cc_final: 0.1798 (ttt-90) REVERT: M 37 ASN cc_start: 0.9288 (t0) cc_final: 0.8745 (t0) REVERT: n 76 PHE cc_start: -0.5500 (OUTLIER) cc_final: -0.5942 (t80) REVERT: n 78 ARG cc_start: -0.1650 (OUTLIER) cc_final: -0.3305 (mtt180) REVERT: N 4 HIS cc_start: 0.5240 (OUTLIER) cc_final: 0.4482 (m-70) REVERT: o 54 ASP cc_start: 0.4117 (OUTLIER) cc_final: 0.3068 (p0) REVERT: o 71 GLU cc_start: 0.3182 (pp20) cc_final: 0.2607 (pm20) REVERT: o 94 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3845 (tpt) REVERT: o 110 GLU cc_start: 0.4882 (mp0) cc_final: 0.3786 (pm20) REVERT: p 21 LYS cc_start: 0.5726 (mmtm) cc_final: 0.5205 (mmtp) REVERT: p 29 LYS cc_start: 0.1270 (mptt) cc_final: -0.0188 (pptt) REVERT: p 66 ILE cc_start: -0.4429 (OUTLIER) cc_final: -0.5447 (tt) REVERT: P 36 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7873 (p0) REVERT: S 100 GLU cc_start: 0.9250 (pp20) cc_final: 0.8768 (pp20) REVERT: T 80 ASP cc_start: 0.9443 (t0) cc_final: 0.9005 (t0) REVERT: U 79 ARG cc_start: 0.7990 (ptp-170) cc_final: 0.7591 (ptm-80) REVERT: U 82 ARG cc_start: 0.7161 (ttm170) cc_final: 0.6898 (tpp-160) REVERT: V 38 ILE cc_start: 0.9108 (tp) cc_final: 0.8441 (pp) REVERT: W 27 ASN cc_start: 0.8694 (m-40) cc_final: 0.8399 (m110) REVERT: Z 27 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8137 (ppp) outliers start: 227 outliers final: 145 residues processed: 856 average time/residue: 2.0025 time to fit residues: 2434.1180 Evaluate side-chains 858 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 670 time to evaluate : 5.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 46 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 80 ILE Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 152 ARG Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain h residue 27 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 82 ASN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 36 ARG Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 141 MET Chi-restraints excluded: chain k residue 151 GLN Chi-restraints excluded: chain k residue 178 ARG Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 138 ARG Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 76 PHE Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 78 GLU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 50 SER Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 27 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 791 optimal weight: 50.0000 chunk 833 optimal weight: 10.0000 chunk 760 optimal weight: 4.9990 chunk 811 optimal weight: 10.0000 chunk 488 optimal weight: 8.9990 chunk 353 optimal weight: 50.0000 chunk 636 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 732 optimal weight: 4.9990 chunk 767 optimal weight: 30.0000 chunk 808 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 43 GLN 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** j 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN P 81 ASN Q 97 ASN R 37 GLN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 85 GLN W 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 140267 Z= 0.388 Angle : 0.701 14.025 210655 Z= 0.353 Chirality : 0.041 0.353 27204 Planarity : 0.005 0.077 10799 Dihedral : 26.101 179.897 71768 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.11 % Favored : 89.75 % Rotamer: Outliers : 6.57 % Allowed : 38.56 % Favored : 54.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 4878 helix: 0.23 (0.16), residues: 1191 sheet: -1.32 (0.19), residues: 719 loop : -2.56 (0.10), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 48 HIS 0.006 0.001 HIS i 25 PHE 0.022 0.001 PHE o 63 TYR 0.040 0.001 TYR D 59 ARG 0.015 0.001 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 662 time to evaluate : 5.370 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 39 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 41 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8085 (mtmm) REVERT: B 11 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7641 (ttt180) REVERT: 2 3 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9018 (mtmt) REVERT: 4 24 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7530 (mtm) REVERT: 4 26 ILE cc_start: 0.8083 (tt) cc_final: 0.7742 (pp) REVERT: a 46 LYS cc_start: 0.4955 (OUTLIER) cc_final: 0.1246 (mtmm) REVERT: b 65 MET cc_start: 0.8398 (mmp) cc_final: 0.7626 (pp-130) REVERT: b 122 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6545 (mtm-85) REVERT: c 53 MET cc_start: 0.1336 (tmm) cc_final: 0.1118 (tpt) REVERT: c 96 ARG cc_start: 0.4826 (tpm170) cc_final: 0.4014 (tpm170) REVERT: c 107 ARG cc_start: 0.4292 (mmt180) cc_final: 0.4049 (mmt180) REVERT: C 20 ASP cc_start: 0.8323 (t70) cc_final: 0.7702 (p0) REVERT: C 247 MET cc_start: 0.8820 (mmm) cc_final: 0.8191 (mtp) REVERT: d 32 LYS cc_start: -0.1671 (OUTLIER) cc_final: -0.3161 (mmtt) REVERT: D 205 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8483 (mmtp) REVERT: E 40 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: E 185 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7293 (p0) REVERT: e 6 MET cc_start: 0.1309 (mtt) cc_final: 0.0694 (mmm) REVERT: e 40 CYS cc_start: 0.3653 (OUTLIER) cc_final: 0.2485 (p) REVERT: e 42 ILE cc_start: -0.4407 (OUTLIER) cc_final: -0.4623 (pt) REVERT: e 43 CYS cc_start: -0.1908 (OUTLIER) cc_final: -0.3438 (t) REVERT: f 59 MET cc_start: 0.4335 (mtt) cc_final: 0.3371 (tpt) REVERT: f 62 ARG cc_start: 0.1816 (OUTLIER) cc_final: 0.1564 (ttt-90) REVERT: g 14 ARG cc_start: -0.0015 (OUTLIER) cc_final: -0.2992 (tpt170) REVERT: g 70 THR cc_start: -0.0741 (OUTLIER) cc_final: -0.1090 (m) REVERT: g 71 VAL cc_start: 0.4371 (OUTLIER) cc_final: 0.4133 (t) REVERT: G 3 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4683 (mpp80) REVERT: G 32 GLU cc_start: 0.8492 (mp0) cc_final: 0.8157 (pm20) REVERT: G 41 MET cc_start: 0.7697 (mtt) cc_final: 0.7220 (mtt) REVERT: H 100 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7707 (ttp-170) REVERT: h 38 LYS cc_start: 0.6938 (tppt) cc_final: 0.6456 (mppt) REVERT: h 45 LYS cc_start: 0.8073 (mmtt) cc_final: 0.6707 (mmmt) REVERT: h 62 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8347 (mmpt) REVERT: i 28 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: i 52 THR cc_start: -0.0096 (OUTLIER) cc_final: -0.0413 (p) REVERT: i 58 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5169 (mtt180) REVERT: i 70 MET cc_start: 0.6338 (mmt) cc_final: 0.4328 (tmm) REVERT: i 75 TYR cc_start: 0.0612 (OUTLIER) cc_final: 0.0371 (m-80) REVERT: J 47 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8563 (ttp-110) REVERT: J 64 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8250 (ttm-80) REVERT: J 104 ASN cc_start: 0.8716 (t0) cc_final: 0.8198 (p0) REVERT: k 40 LYS cc_start: -0.2586 (OUTLIER) cc_final: -0.3174 (ptmt) REVERT: k 71 LYS cc_start: 0.2708 (OUTLIER) cc_final: 0.2289 (mtmt) REVERT: k 139 ARG cc_start: -0.2786 (OUTLIER) cc_final: -0.3325 (ppt170) REVERT: k 143 LEU cc_start: 0.0593 (OUTLIER) cc_final: 0.0188 (tt) REVERT: K 45 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7898 (mtp85) REVERT: K 82 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7848 (ptp90) REVERT: l 69 ARG cc_start: 0.7738 (pmt170) cc_final: 0.6859 (mmp-170) REVERT: m 65 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5658 (pp20) REVERT: m 96 MET cc_start: 0.5936 (ppp) cc_final: 0.3261 (mmt) REVERT: m 138 ARG cc_start: 0.1985 (OUTLIER) cc_final: 0.1728 (ttt-90) REVERT: M 37 ASN cc_start: 0.9332 (t0) cc_final: 0.8818 (t0) REVERT: n 78 ARG cc_start: -0.1532 (OUTLIER) cc_final: -0.3228 (mtt180) REVERT: N 4 HIS cc_start: 0.5347 (OUTLIER) cc_final: 0.4597 (m-70) REVERT: o 35 GLU cc_start: 0.4946 (tp30) cc_final: 0.3815 (tp30) REVERT: o 38 GLU cc_start: 0.4970 (tm-30) cc_final: 0.3595 (tp30) REVERT: o 54 ASP cc_start: 0.4142 (OUTLIER) cc_final: 0.3141 (OUTLIER) REVERT: o 71 GLU cc_start: 0.3385 (pp20) cc_final: 0.2906 (pm20) REVERT: o 94 MET cc_start: 0.3928 (OUTLIER) cc_final: 0.3551 (tpt) REVERT: p 21 LYS cc_start: 0.5806 (mmtm) cc_final: 0.5282 (mmtp) REVERT: p 29 LYS cc_start: 0.1254 (mptt) cc_final: -0.0020 (pptt) REVERT: p 31 MET cc_start: -0.0997 (ttt) cc_final: -0.3166 (tmt) REVERT: p 35 LYS cc_start: 0.6765 (pttp) cc_final: 0.6539 (mtpt) REVERT: p 66 ILE cc_start: -0.4623 (OUTLIER) cc_final: -0.5521 (tt) REVERT: p 76 LYS cc_start: 0.0015 (tptt) cc_final: -0.0248 (tppt) REVERT: P 36 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7875 (p0) REVERT: q 8 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.4732 (m-80) REVERT: T 80 ASP cc_start: 0.9446 (t0) cc_final: 0.8996 (t0) REVERT: U 48 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: U 79 ARG cc_start: 0.8012 (ptp-170) cc_final: 0.7609 (ptm-80) REVERT: W 27 ASN cc_start: 0.8688 (m-40) cc_final: 0.8342 (m110) REVERT: Z 27 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8020 (ppp) outliers start: 237 outliers final: 154 residues processed: 841 average time/residue: 1.9794 time to fit residues: 2340.5016 Evaluate side-chains 837 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 642 time to evaluate : 5.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 46 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 98 ARG Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain h residue 15 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 40 LYS Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 135 GLN Chi-restraints excluded: chain k residue 137 ILE Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 38 VAL Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 138 ARG Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 102 ASP Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 72 VAL Chi-restraints excluded: chain p residue 105 VAL Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 37 LYS Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 85 PHE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 48 GLN Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 23 VAL Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 532 optimal weight: 3.9990 chunk 857 optimal weight: 7.9990 chunk 523 optimal weight: 2.9990 chunk 406 optimal weight: 40.0000 chunk 596 optimal weight: 0.9990 chunk 899 optimal weight: 5.9990 chunk 827 optimal weight: 3.9990 chunk 716 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 553 optimal weight: 5.9990 chunk 439 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 GLN E 49 HIS E 179 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 45 ASN j 24 GLN J 81 GLN ** k 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN P 81 ASN Q 28 ASN S 8 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 85 GLN W 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 140267 Z= 0.226 Angle : 0.645 16.439 210655 Z= 0.325 Chirality : 0.036 0.364 27204 Planarity : 0.004 0.070 10799 Dihedral : 26.074 179.953 71755 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.18 % Favored : 90.67 % Rotamer: Outliers : 5.35 % Allowed : 40.03 % Favored : 54.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 4878 helix: 0.32 (0.16), residues: 1189 sheet: -1.25 (0.19), residues: 732 loop : -2.50 (0.10), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 65 HIS 0.009 0.001 HIS m 83 PHE 0.013 0.001 PHE J 50 TYR 0.019 0.001 TYR K 57 ARG 0.015 0.001 ARG R 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9756 Ramachandran restraints generated. 4878 Oldfield, 0 Emsley, 4878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 682 time to evaluate : 5.454 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 TARDY: cannot create tardy model for: "LYS D 216 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU I 122 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG k 203 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP n 95 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE R 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 1 58 " (corrupted residue). Skipping it. REVERT: A 31 GLU cc_start: 0.8042 (tp30) cc_final: 0.7560 (tp30) REVERT: A 39 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 41 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8039 (mtmm) REVERT: B 11 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7602 (ttt180) REVERT: 2 3 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9043 (mtmt) REVERT: 4 24 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7497 (mtm) REVERT: 4 26 ILE cc_start: 0.8045 (tt) cc_final: 0.7680 (pp) REVERT: a 46 LYS cc_start: 0.4853 (OUTLIER) cc_final: 0.1180 (mtmm) REVERT: b 65 MET cc_start: 0.8266 (mmp) cc_final: 0.7597 (pp-130) REVERT: c 96 ARG cc_start: 0.4733 (tpm170) cc_final: 0.3979 (tpm170) REVERT: c 107 ARG cc_start: 0.4262 (mmt180) cc_final: 0.1189 (tpt-90) REVERT: C 20 ASP cc_start: 0.8249 (t70) cc_final: 0.7693 (p0) REVERT: C 247 MET cc_start: 0.8796 (mmm) cc_final: 0.8258 (mtp) REVERT: d 32 LYS cc_start: -0.1704 (OUTLIER) cc_final: -0.3210 (mmtt) REVERT: d 81 MET cc_start: -0.3835 (ptm) cc_final: -0.4094 (ptm) REVERT: e 6 MET cc_start: 0.1390 (mtt) cc_final: 0.0770 (mmm) REVERT: e 40 CYS cc_start: 0.3655 (OUTLIER) cc_final: 0.2504 (p) REVERT: e 42 ILE cc_start: -0.4284 (OUTLIER) cc_final: -0.4496 (pt) REVERT: e 43 CYS cc_start: -0.1737 (OUTLIER) cc_final: -0.3239 (t) REVERT: f 59 MET cc_start: 0.4443 (mtt) cc_final: 0.3486 (tpt) REVERT: f 62 ARG cc_start: 0.1901 (OUTLIER) cc_final: 0.1642 (ttt-90) REVERT: g 14 ARG cc_start: 0.0046 (OUTLIER) cc_final: -0.2970 (tpt170) REVERT: g 70 THR cc_start: -0.0750 (OUTLIER) cc_final: -0.1101 (m) REVERT: g 71 VAL cc_start: 0.4329 (OUTLIER) cc_final: 0.4098 (t) REVERT: G 32 GLU cc_start: 0.8472 (mp0) cc_final: 0.8143 (pm20) REVERT: G 39 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7372 (mm-30) REVERT: G 41 MET cc_start: 0.7670 (mtt) cc_final: 0.6983 (mtt) REVERT: H 62 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8692 (mttp) REVERT: H 100 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7674 (ttp-170) REVERT: h 38 LYS cc_start: 0.6955 (tppt) cc_final: 0.6410 (mppt) REVERT: h 45 LYS cc_start: 0.8036 (mmtt) cc_final: 0.6661 (mmmt) REVERT: h 62 LYS cc_start: 0.8825 (tmtt) cc_final: 0.8365 (mmpt) REVERT: i 28 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: i 52 THR cc_start: -0.0139 (OUTLIER) cc_final: -0.0446 (p) REVERT: i 58 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5167 (mtt180) REVERT: i 70 MET cc_start: 0.6461 (mmt) cc_final: 0.4387 (tmt) REVERT: i 75 TYR cc_start: 0.0531 (OUTLIER) cc_final: 0.0271 (m-80) REVERT: J 47 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8533 (ttp-110) REVERT: J 64 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8576 (ttm-80) REVERT: J 104 ASN cc_start: 0.8679 (t0) cc_final: 0.8203 (p0) REVERT: k 71 LYS cc_start: 0.2752 (OUTLIER) cc_final: 0.2342 (mtmt) REVERT: k 139 ARG cc_start: -0.2840 (OUTLIER) cc_final: -0.3500 (ppt170) REVERT: k 143 LEU cc_start: 0.0663 (OUTLIER) cc_final: 0.0244 (tt) REVERT: K 45 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7822 (mtp85) REVERT: K 82 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7798 (ptp90) REVERT: l 69 ARG cc_start: 0.7697 (pmt170) cc_final: 0.6872 (mmp-170) REVERT: m 65 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5633 (pp20) REVERT: m 96 MET cc_start: 0.5949 (ppp) cc_final: 0.3338 (mmt) REVERT: m 138 ARG cc_start: 0.2084 (OUTLIER) cc_final: 0.1825 (ttt-90) REVERT: M 37 ASN cc_start: 0.9297 (t0) cc_final: 0.8785 (t0) REVERT: n 78 ARG cc_start: -0.1575 (OUTLIER) cc_final: -0.3188 (mtt180) REVERT: N 4 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4363 (m-70) REVERT: o 38 GLU cc_start: 0.5026 (tm-30) cc_final: 0.3769 (tp30) REVERT: o 54 ASP cc_start: 0.4291 (OUTLIER) cc_final: 0.3364 (OUTLIER) REVERT: o 71 GLU cc_start: 0.3474 (pp20) cc_final: 0.3022 (pm20) REVERT: o 94 MET cc_start: 0.4289 (OUTLIER) cc_final: 0.3977 (tpt) REVERT: o 110 GLU cc_start: 0.4954 (mp0) cc_final: 0.3900 (pm20) REVERT: p 21 LYS cc_start: 0.5903 (mmtm) cc_final: 0.5525 (mmtp) REVERT: p 29 LYS cc_start: 0.1433 (mptt) cc_final: 0.0013 (pptt) REVERT: p 66 ILE cc_start: -0.4739 (OUTLIER) cc_final: -0.5654 (tt) REVERT: p 76 LYS cc_start: -0.0376 (tptt) cc_final: -0.0701 (tppt) REVERT: P 36 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7856 (p0) REVERT: q 8 TYR cc_start: 0.4996 (OUTLIER) cc_final: 0.4696 (m-80) REVERT: S 100 GLU cc_start: 0.9190 (pp20) cc_final: 0.8790 (pp20) REVERT: T 80 ASP cc_start: 0.9443 (t0) cc_final: 0.8982 (t0) REVERT: U 79 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7600 (ptm-80) REVERT: W 27 ASN cc_start: 0.8640 (m-40) cc_final: 0.8330 (m110) REVERT: Z 27 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8279 (ppp) outliers start: 193 outliers final: 132 residues processed: 826 average time/residue: 1.9366 time to fit residues: 2268.2816 Evaluate side-chains 828 residues out of total 4201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 662 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain 2 residue 3 LYS Chi-restraints excluded: chain 2 residue 31 HIS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain a residue 6 ILE Chi-restraints excluded: chain a residue 37 SER Chi-restraints excluded: chain a residue 46 LYS Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 113 VAL Chi-restraints excluded: chain c residue 43 LYS Chi-restraints excluded: chain c residue 67 ARG Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 108 TYR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 86 TYR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 40 CYS Chi-restraints excluded: chain e residue 42 ILE Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 62 ARG Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain f residue 77 ARG Chi-restraints excluded: chain g residue 3 VAL Chi-restraints excluded: chain g residue 14 ARG Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain i residue 28 TYR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 58 ARG Chi-restraints excluded: chain i residue 75 TYR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 69 ASN Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 71 LYS Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain k residue 135 GLN Chi-restraints excluded: chain k residue 139 ARG Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 203 ARG Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 54 GLN Chi-restraints excluded: chain m residue 65 GLU Chi-restraints excluded: chain m residue 138 ARG Chi-restraints excluded: chain m residue 140 THR Chi-restraints excluded: chain m residue 156 LEU Chi-restraints excluded: chain m residue 164 LEU Chi-restraints excluded: chain M residue 3 SER Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 78 ARG Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 91 VAL Chi-restraints excluded: chain n residue 95 ASP Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain o residue 54 ASP Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 87 VAL Chi-restraints excluded: chain o residue 94 MET Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain p residue 66 ILE Chi-restraints excluded: chain p residue 142 HIS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain q residue 8 TYR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 54 PHE Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 109 ASP Chi-restraints excluded: chain Q residue 6 VAL Chi-restraints excluded: chain Q residue 43 SER Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 55 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 85 PHE Chi-restraints excluded: chain S residue 87 ASP Chi-restraints excluded: chain T residue 8 ILE Chi-restraints excluded: chain T residue 13 GLN Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain U residue 83 ASP Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain 1 residue 18 THR Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain Z residue 23 SER Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 27 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 903 random chunks: chunk 569 optimal weight: 50.0000 chunk 763 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 660 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 199 optimal weight: 10.0000 chunk 717 optimal weight: 30.0000 chunk 300 optimal weight: 30.0000 chunk 736 optimal weight: 7.9990 chunk 90 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 43 GLN 2 60 GLN ** c 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 45 ASN J 81 GLN ** k 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN P 81 ASN Q 28 ASN ** S 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.136229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075293 restraints weight = 392488.250| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.62 r_work: 0.2738 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.425 140267 Z= 0.332 Angle : 0.669 65.891 210655 Z= 0.345 Chirality : 0.040 0.485 27204 Planarity : 0.005 0.216 10799 Dihedral : 26.072 179.880 71750 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.25 % Favored : 90.61 % Rotamer: Outliers : 4.99 % Allowed : 40.23 % Favored : 54.78 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.11), residues: 4878 helix: 0.33 (0.16), residues: 1189 sheet: -1.17 (0.19), residues: 748 loop : -2.51 (0.10), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 65 HIS 0.008 0.001 HIS m 83 PHE 0.012 0.001 PHE J 50 TYR 0.034 0.001 TYR h 30 ARG 0.057 0.001 ARG G 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43644.00 seconds wall clock time: 755 minutes 11.86 seconds (45311.86 seconds total)