Starting phenix.real_space_refine on Fri Mar 22 07:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrm_0261/03_2024/6hrm_0261_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4570 5.49 5 Mg 436 5.21 5 S 158 5.16 5 C 72985 2.51 5 N 26975 2.21 5 O 40053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145179 Number of models: 1 Model: "" Number of chains: 64 Chain: "1" Number of atoms: 95544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4450, 95544 Classifications: {'RNA': 4450} Modifications used: {'rna2p': 8, 'rna2p_pur': 418, 'rna2p_pyr': 258, 'rna3p': 25, 'rna3p_pur': 2126, 'rna3p_pyr': 1614} Link IDs: {'rna2p': 683, 'rna3p': 3766} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 422 Unusual residues: {' MG': 422} Classifications: {'undetermined': 422} Link IDs: {None: 421} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0JO7 SG CYS f 11 184.620 127.797 122.688 1.00 20.89 S ATOM A0JOW SG CYS f 14 183.142 124.398 122.012 1.00 16.86 S ATOM A0JRR SG CYS f 27 184.706 124.440 125.764 1.00 13.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 14646 " occ=0.50 Time building chain proxies: 55.16, per 1000 atoms: 0.38 Number of scatterers: 145179 At special positions: 0 Unit cell: (246.98, 287.26, 279.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 158 16.00 P 4570 15.00 Mg 436 11.99 O 40053 8.00 N 26975 7.00 C 72985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " 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: 53.52 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " Number of angles added : 3 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10974 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 179 helices and 72 sheets defined 38.6% alpha, 18.8% beta 1241 base pairs and 2564 stacking pairs defined. Time for finding SS restraints: 68.47 Creating SS restraints... Processing helix chain 'B' and resid 10 through 16 removed outlier: 7.658A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.071A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.514A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.955A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.226A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.274A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.852A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.071A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.585A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.238A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.609A pdb=" N GLN D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.579A pdb=" N ALA D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.527A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.488A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.848A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 183' Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.849A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 4.309A pdb=" N ASP E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 removed outlier: 3.690A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.004A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.653A pdb=" N ASN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.679A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E 104 " --> pdb=" O PHE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.890A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 4.419A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.966A pdb=" N ALA F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.502A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 3.618A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 removed outlier: 3.710A pdb=" N GLN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 48 Processing helix chain 'G' and resid 49 through 73 removed outlier: 5.578A pdb=" N GLU G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.609A pdb=" N GLN H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 12 " --> pdb=" O LYS H 8 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 48 removed outlier: 5.129A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG H 46 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 70 removed outlier: 4.352A pdb=" N GLY H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix Processing helix chain 'H' and resid 96 through 106 removed outlier: 4.357A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA H 102 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 removed outlier: 3.522A pdb=" N ASP H 74 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA H 75 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL H 77 " --> pdb=" O ASP H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 77' Processing helix chain 'I' and resid 33 through 49 removed outlier: 3.973A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE I 41 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.283A pdb=" N LEU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.436A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.664A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 24 removed outlier: 3.983A pdb=" N GLY I 24 " --> pdb=" O PRO I 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 19 through 24' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.778A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.469A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.591A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.167A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.938A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.869A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.632A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.399A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 4.140A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.808A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.750A pdb=" N MET M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.769A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA M 121 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.524A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 58 removed outlier: 3.606A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.533A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.730A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.230A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.501A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 63' Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.915A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 82 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.585A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.837A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.754A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.691A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.795A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 4.197A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN Q 52 " --> pdb=" O ARG Q 48 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.709A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.761A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 removed outlier: 3.522A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.656A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.509A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.962A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.714A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.681A pdb=" N MET T 24 " --> pdb=" O ALA T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.552A pdb=" N VAL T 47 " --> pdb=" O ILE T 43 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.978A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.992A pdb=" N ALA V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.588A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.444A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.573A pdb=" N GLU X 70 " --> pdb=" O THR X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.391A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.603A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.792A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG Y 52 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.698A pdb=" N MET Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 52 removed outlier: 5.129A pdb=" N LYS a 47 " --> pdb=" O PHE a 43 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 65 removed outlier: 3.508A pdb=" N PHE a 60 " --> pdb=" O ARG a 56 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASN a 65 " --> pdb=" O ASN a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.142A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.531A pdb=" N SER d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 24 removed outlier: 3.694A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 removed outlier: 3.669A pdb=" N GLN d 29 " --> pdb=" O LYS d 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.502A pdb=" N ALA e 11 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.753A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.743A pdb=" N ALA e 60 " --> pdb=" O GLY e 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS e 61 " --> pdb=" O LEU e 57 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 3.959A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU g 10 " --> pdb=" O MET g 6 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS g 11 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.872A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 removed outlier: 3.678A pdb=" N THR g 46 " --> pdb=" O ASN g 42 " (cutoff:3.500A) Proline residue: g 48 - end of helix removed outlier: 4.148A pdb=" N ALA g 53 " --> pdb=" O MET g 49 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU g 56 " --> pdb=" O GLU g 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU g 57 " --> pdb=" O ALA g 53 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS g 59 " --> pdb=" O ALA g 55 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.400A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP g 82 " --> pdb=" O GLU g 78 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 3.964A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG g 113 " --> pdb=" O GLN g 109 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.899A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET g 136 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU g 141 " --> pdb=" O ARG g 137 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU g 142 " --> pdb=" O THR g 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS g 143 " --> pdb=" O ARG g 139 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN g 146 " --> pdb=" O GLU g 142 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.551A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 removed outlier: 4.020A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY g 180 " --> pdb=" O ALA g 176 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.706A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL g 221 " --> pdb=" O VAL g 217 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.719A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 3.532A pdb=" N VAL h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.179A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY h 78 " --> pdb=" O GLY h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.696A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG h 88 " --> pdb=" O VAL h 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE h 94 " --> pdb=" O VAL h 90 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY h 96 " --> pdb=" O ALA h 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 3.542A pdb=" N ALA h 117 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER h 122 " --> pdb=" O ASP h 118 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN h 123 " --> pdb=" O SER h 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG h 126 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.784A pdb=" N LYS h 135 " --> pdb=" O ARG h 131 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET h 142 " --> pdb=" O VAL h 138 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG h 143 " --> pdb=" O GLN h 139 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.240A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG i 14 " --> pdb=" O LYS i 10 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.534A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR i 65 " --> pdb=" O VAL i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.557A pdb=" N TYR i 76 " --> pdb=" O PHE i 72 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG i 81 " --> pdb=" O LYS i 77 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.751A pdb=" N LEU i 91 " --> pdb=" O GLY i 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.616A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.666A pdb=" N VAL i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.398A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA i 157 " --> pdb=" O SER i 153 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.526A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.141A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.729A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG j 68 " --> pdb=" O MET j 64 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.204A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU j 115 " --> pdb=" O MET j 111 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA j 118 " --> pdb=" O VAL j 114 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.677A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 3.594A pdb=" N VAL j 153 " --> pdb=" O SER j 149 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA j 154 " --> pdb=" O PRO j 150 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG j 157 " --> pdb=" O VAL j 153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY j 158 " --> pdb=" O ALA j 154 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.693A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 33 removed outlier: 4.132A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix removed outlier: 3.523A pdb=" N GLU k 23 " --> pdb=" O PRO k 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA k 27 " --> pdb=" O GLU k 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 82 removed outlier: 3.543A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU k 74 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE k 80 " --> pdb=" O THR k 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.370A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL l 27 " --> pdb=" O LEU l 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE l 29 " --> pdb=" O LYS l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.738A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER l 41 " --> pdb=" O SER l 37 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE l 42 " --> pdb=" O THR l 38 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU l 48 " --> pdb=" O TYR l 44 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG l 53 " --> pdb=" O THR l 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.948A pdb=" N PHE l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU l 67 " --> pdb=" O GLU l 63 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.929A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA l 100 " --> pdb=" O ARG l 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA l 108 " --> pdb=" O ILE l 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.980A pdb=" N ARG l 119 " --> pdb=" O SER l 115 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER l 125 " --> pdb=" O ALA l 121 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP l 126 " --> pdb=" O ASN l 122 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA l 128 " --> pdb=" O LEU l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 4.238A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET l 144 " --> pdb=" O ASP l 140 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.506A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET m 10 " --> pdb=" O PRO m 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA m 19 " --> pdb=" O ARG m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.532A pdb=" N VAL m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 3.743A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.819A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 removed outlier: 4.323A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN n 50 " --> pdb=" O MET n 46 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.754A pdb=" N LEU n 54 " --> pdb=" O GLN n 50 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.528A pdb=" N HIS n 81 " --> pdb=" O GLY n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 4.052A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA o 23 " --> pdb=" O ASP o 19 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 91 removed outlier: 4.312A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.599A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.608A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.672A pdb=" N GLN p 64 " --> pdb=" O PRO p 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL p 65 " --> pdb=" O PHE p 61 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA p 66 " --> pdb=" O ALA p 62 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA p 67 " --> pdb=" O ALA p 63 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 5.525A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA p 99 " --> pdb=" O SER p 95 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU p 100 " --> pdb=" O THR p 96 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA p 102 " --> pdb=" O ARG p 98 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA p 103 " --> pdb=" O ALA p 99 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 removed outlier: 3.595A pdb=" N VAL q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.973A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 22 removed outlier: 3.567A pdb=" N LEU r 19 " --> pdb=" O ALA r 15 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 15 through 22' Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.556A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA r 36 " --> pdb=" O ALA r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.552A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP r 54 " --> pdb=" O GLU r 50 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR r 55 " --> pdb=" O GLY r 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU r 56 " --> pdb=" O GLN r 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG r 57 " --> pdb=" O ILE r 53 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.614A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU r 72 " --> pdb=" O ASP r 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE r 73 " --> pdb=" O LEU r 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER r 74 " --> pdb=" O ARG r 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS r 78 " --> pdb=" O SER r 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP r 82 " --> pdb=" O LYS r 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU r 83 " --> pdb=" O ARG r 79 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.526A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 removed outlier: 3.586A pdb=" N LYS r 110 " --> pdb=" O ALA r 106 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY r 111 " --> pdb=" O ARG r 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 106 through 111' Processing helix chain 's' and resid 3 through 21 removed outlier: 3.826A pdb=" N ARG s 9 " --> pdb=" O SER s 5 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS s 12 " --> pdb=" O ALA s 8 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG s 13 " --> pdb=" O ARG s 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.524A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU s 27 " --> pdb=" O LYS s 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 4.730A pdb=" N ASN s 43 " --> pdb=" O GLU s 39 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL s 45 " --> pdb=" O ARG s 41 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU s 46 " --> pdb=" O TRP s 42 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.734A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.722A pdb=" N LYS t 10 " --> pdb=" O GLU t 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER t 13 " --> pdb=" O ALA t 9 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU t 14 " --> pdb=" O LYS t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 44 removed outlier: 3.519A pdb=" N ALA t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 3.631A pdb=" N ARG t 54 " --> pdb=" O HIS t 50 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET t 59 " --> pdb=" O GLY t 55 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU t 66 " --> pdb=" O GLN t 62 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.507A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.647A pdb=" N HIS u 59 " --> pdb=" O ASP u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.699A pdb=" N ALA u 73 " --> pdb=" O ASP u 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA u 82 " --> pdb=" O VAL u 78 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 3.732A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.379A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.526A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.543A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.617A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 8 through 42 removed outlier: 3.760A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS y 19 " --> pdb=" O GLU y 15 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG y 24 " --> pdb=" O HIS y 20 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.513A pdb=" N LYS y 49 " --> pdb=" O ALA y 45 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.721A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.694A pdb=" N LEU y 79 " --> pdb=" O HIS y 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.598A pdb=" N ALA z 15 " --> pdb=" O PRO z 11 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG z 18 " --> pdb=" O VAL z 14 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS z 23 " --> pdb=" O PHE z 19 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLU z 24 " --> pdb=" O LYS z 20 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA z 26 " --> pdb=" O SER z 22 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY z 27 " --> pdb=" O CYS z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.624A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.620A pdb=" N ARG z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS z 49 " --> pdb=" O ARG z 45 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA z 52 " --> pdb=" O ALA z 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA z 61 " --> pdb=" O ALA z 57 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.462A pdb=" N ALA B 2 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.563A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.022A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 163 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.526A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.124A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.731A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.298A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.520A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 1 through 5 removed outlier: 3.913A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 12 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 42 through 46 removed outlier: 8.115A pdb=" N GLY D 42 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP D 91 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG D 44 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA D 87 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.682A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.757A pdb=" N ARG E 30 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR E 157 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 33 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 127 through 133 removed outlier: 3.692A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 16, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 17, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.941A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS F 86 " --> pdb=" O ALA F 165 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 90 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 2 through 6 removed outlier: 5.844A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 7 through 10 removed outlier: 5.330A pdb=" N ASP G 7 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER G 14 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL G 9 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 82 removed outlier: 7.009A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 82 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.172A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.473A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.659A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG K 64 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.732A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.815A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 103 through 106 removed outlier: 3.888A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 33 through 36 removed outlier: 6.745A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.884A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 38 through 44 removed outlier: 6.565A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.820A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.883A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 18 through 21 removed outlier: 4.659A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 57 through 60 removed outlier: 3.622A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 65 through 74 removed outlier: 3.849A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS R 73 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN R 87 " --> pdb=" O LYS R 73 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 37, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.515A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 40 through 46 removed outlier: 4.929A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 83 through 86 removed outlier: 3.833A pdb=" N ARG U 86 " --> pdb=" O VAL U 93 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 2 through 5 Processing sheet with id= 41, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.642A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 67 through 71 Processing sheet with id= 43, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.849A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 34 through 41 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'Z' and resid 34 through 39 removed outlier: 4.473A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 11 through 16 removed outlier: 4.079A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.493A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 8 through 13 removed outlier: 5.521A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.235A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.433A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 1 through 5 removed outlier: 5.681A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.903A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 90 through 93 removed outlier: 3.647A pdb=" N GLY g 71 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU g 68 " --> pdb=" O ALA g 160 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.586A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR h 70 " --> pdb=" O ALA h 104 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 164 through 170 removed outlier: 5.919A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL h 198 " --> pdb=" O SER h 187 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL h 200 " --> pdb=" O ASN h 185 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS h 204 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 141 through 145 removed outlier: 4.044A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.663A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.589A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 33 through 40 removed outlier: 4.117A pdb=" N GLY j 49 " --> pdb=" O THR j 37 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 38 through 43 removed outlier: 3.704A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL k 7 " --> pdb=" O MET k 88 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.274A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 73 through 79 removed outlier: 6.283A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.279A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER m 29 " --> pdb=" O PRO m 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.624A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.591A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS n 68 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.651A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP o 63 " --> pdb=" O VAL o 51 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU o 10 " --> pdb=" O ARG o 72 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS o 11 " --> pdb=" O ASP o 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 29 through 36 removed outlier: 3.521A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.269A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 51 through 57 removed outlier: 5.039A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.372A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 37 through 48 removed outlier: 6.813A pdb=" N VAL v 22 " --> pdb=" O VAL v 13 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU v 26 " --> pdb=" O GLN v 9 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN v 9 " --> pdb=" O GLU v 26 " (cutoff:3.500A) removed outlier: 13.163A pdb=" N PHE v 28 " --> pdb=" O THR v 7 " (cutoff:3.500A) removed outlier: 17.217A pdb=" N THR v 7 " --> pdb=" O PHE v 28 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 34 removed outlier: 3.588A pdb=" N VAL x 58 " --> pdb=" O VAL x 51 " (cutoff:3.500A) 1548 hydrogen bonds defined for protein. 4578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2994 hydrogen bonds 4642 hydrogen bond angles 0 basepair planarities 1241 basepair parallelities 2564 stacking parallelities Total time for adding SS restraints: 473.46 Time building geometry restraints manager: 58.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12258 1.29 - 1.43: 70042 1.43 - 1.56: 65418 1.56 - 1.69: 9141 1.69 - 1.83: 282 Bond restraints: 157141 Sorted by residual: bond pdb=" C4 5MU 13445 " pdb=" C5 5MU 13445 " ideal model delta sigma weight residual 1.802 1.416 0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" C4 5MU 12253 " pdb=" C5 5MU 12253 " ideal model delta sigma weight residual 1.802 1.417 0.385 2.00e-02 2.50e+03 3.71e+02 bond pdb=" N1 5MU 13445 " pdb=" C6 5MU 13445 " ideal model delta sigma weight residual 1.635 1.317 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" N1 5MU 12253 " pdb=" C6 5MU 12253 " ideal model delta sigma weight residual 1.635 1.321 0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C5 5MU 13445 " pdb=" C6 5MU 13445 " ideal model delta sigma weight residual 1.155 1.399 -0.244 2.00e-02 2.50e+03 1.49e+02 ... (remaining 157136 not shown) Histogram of bond angle deviations from ideal: 95.84 - 104.17: 17047 104.17 - 112.51: 92539 112.51 - 120.85: 76635 120.85 - 129.18: 44876 129.18 - 137.52: 3688 Bond angle restraints: 234785 Sorted by residual: angle pdb=" C4' 6MZ 13536 " pdb=" C3' 6MZ 13536 " pdb=" O3' 6MZ 13536 " ideal model delta sigma weight residual 109.40 125.33 -15.93 1.50e+00 4.44e-01 1.13e+02 angle pdb=" O4' 1MG 12251 " pdb=" C1' 1MG 12251 " pdb=" N9 1MG 12251 " ideal model delta sigma weight residual 108.20 122.78 -14.58 1.50e+00 4.44e-01 9.45e+01 angle pdb=" C4' 1MG 12251 " pdb=" C3' 1MG 12251 " pdb=" O3' 1MG 12251 " ideal model delta sigma weight residual 109.40 123.29 -13.89 1.50e+00 4.44e-01 8.57e+01 angle pdb=" C1' OMG 13757 " pdb=" N9 OMG 13757 " pdb=" C4 OMG 13757 " ideal model delta sigma weight residual 108.29 133.73 -25.44 3.00e+00 1.11e-01 7.19e+01 angle pdb=" C ILE l 12 " pdb=" N LEU l 13 " pdb=" CA LEU l 13 " ideal model delta sigma weight residual 120.83 132.90 -12.07 1.43e+00 4.89e-01 7.13e+01 ... (remaining 234780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 89331 35.96 - 71.93: 9921 71.93 - 107.89: 1160 107.89 - 143.85: 20 143.85 - 179.82: 56 Dihedral angle restraints: 100488 sinusoidal: 83479 harmonic: 17009 Sorted by residual: dihedral pdb=" C5* PSU 1 516 " pdb=" C4* PSU 1 516 " pdb=" C3* PSU 1 516 " pdb=" O3* PSU 1 516 " ideal model delta sinusoidal sigma weight residual 82.00 -79.43 161.43 1 8.00e+00 1.56e-02 2.92e+02 dihedral pdb=" C5* PSU 13423 " pdb=" C4* PSU 13423 " pdb=" C3* PSU 13423 " pdb=" O3* PSU 13423 " ideal model delta sinusoidal sigma weight residual 82.00 -77.76 159.76 1 8.00e+00 1.56e-02 2.91e+02 dihedral pdb=" C5* PSU 14010 " pdb=" C4* PSU 14010 " pdb=" C3* PSU 14010 " pdb=" O3* PSU 14010 " ideal model delta sinusoidal sigma weight residual 82.00 -72.86 154.86 1 8.00e+00 1.56e-02 2.86e+02 ... (remaining 100485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.119: 29850 1.119 - 2.238: 3 2.238 - 3.358: 0 3.358 - 4.477: 4 4.477 - 5.596: 27 Chirality restraints: 29884 Sorted by residual: chirality pdb=" C3' 4OC 11402 " pdb=" C4' 4OC 11402 " pdb=" O3' 4OC 11402 " pdb=" C2' 4OC 11402 " both_signs ideal model delta sigma weight residual False -2.74 2.85 -5.60 2.00e-01 2.50e+01 7.83e+02 chirality pdb=" C2' G7M 13575 " pdb=" C3' G7M 13575 " pdb=" O2' G7M 13575 " pdb=" C1' G7M 13575 " both_signs ideal model delta sigma weight residual False -2.75 2.67 -5.43 2.00e-01 2.50e+01 7.36e+02 chirality pdb=" C2' OMU 14058 " pdb=" C3' OMU 14058 " pdb=" O2' OMU 14058 " pdb=" C1' OMU 14058 " both_signs ideal model delta sigma weight residual False -2.75 2.61 -5.36 2.00e-01 2.50e+01 7.19e+02 ... (remaining 29881 not shown) Planarity restraints: 12775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 14432 " -0.079 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 2MG 14432 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG 14432 " -0.604 2.00e-02 2.50e+03 pdb=" C3' 2MG 14432 " 0.604 2.00e-02 2.50e+03 pdb=" O3' 2MG 14432 " 0.679 2.00e-02 2.50e+03 pdb=" C2' 2MG 14432 " 0.150 2.00e-02 2.50e+03 pdb=" O2' 2MG 14432 " -1.029 2.00e-02 2.50e+03 pdb=" C1' 2MG 14432 " -0.223 2.00e-02 2.50e+03 pdb=" N9 2MG 14432 " 0.931 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 11407 " -0.075 2.00e-02 2.50e+03 6.10e-01 8.36e+03 pdb=" C4' 5MC 11407 " -0.447 2.00e-02 2.50e+03 pdb=" O4' 5MC 11407 " -0.594 2.00e-02 2.50e+03 pdb=" C3' 5MC 11407 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 5MC 11407 " 0.694 2.00e-02 2.50e+03 pdb=" C2' 5MC 11407 " 0.158 2.00e-02 2.50e+03 pdb=" O2' 5MC 11407 " -1.028 2.00e-02 2.50e+03 pdb=" C1' 5MC 11407 " -0.210 2.00e-02 2.50e+03 pdb=" N1 5MC 11407 " 0.909 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 14004 " 0.417 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' OMC 14004 " -0.156 2.00e-02 2.50e+03 pdb=" O4' OMC 14004 " 0.664 2.00e-02 2.50e+03 pdb=" C3' OMC 14004 " -0.697 2.00e-02 2.50e+03 pdb=" O3' OMC 14004 " -0.604 2.00e-02 2.50e+03 pdb=" C2' OMC 14004 " -0.118 2.00e-02 2.50e+03 pdb=" O2' OMC 14004 " 1.029 2.00e-02 2.50e+03 pdb=" C1' OMC 14004 " 0.277 2.00e-02 2.50e+03 pdb=" N1 OMC 14004 " -0.812 2.00e-02 2.50e+03 ... (remaining 12772 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2827 2.60 - 3.18: 101337 3.18 - 3.75: 270735 3.75 - 4.33: 400712 4.33 - 4.90: 528621 Nonbonded interactions: 1304232 Sorted by model distance: nonbonded pdb=" OP1 C 12454 " pdb="MG MG 14525 " model vdw 2.029 2.170 nonbonded pdb=" OP1 U 12332 " pdb="MG MG 14652 " model vdw 2.030 2.170 nonbonded pdb=" O6 G 12076 " pdb="MG MG 14586 " model vdw 2.034 2.170 nonbonded pdb=" OP2 U 12505 " pdb="MG MG 14526 " model vdw 2.034 2.170 nonbonded pdb=" OP1 U 11199 " pdb="MG MG 14807 " model vdw 2.041 2.170 ... (remaining 1304227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 15.390 Check model and map are aligned: 1.550 Set scattering table: 0.980 Process input model: 769.090 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 803.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.010 0.386 157141 Z= 0.586 Angle : 1.021 25.441 234785 Z= 0.509 Chirality : 0.166 5.596 29884 Planarity : 0.019 0.613 12775 Dihedral : 22.745 179.816 89511 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 0.49 % Allowed : 3.76 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.09 % 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: -4.48 (0.08), residues: 5867 helix: -4.36 (0.06), residues: 1761 sheet: -2.08 (0.14), residues: 1069 loop : -2.37 (0.09), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP D 78 HIS 0.028 0.004 HIS p 118 PHE 0.039 0.004 PHE C 127 TYR 0.052 0.004 TYR c 49 ARG 0.023 0.002 ARG W 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1066 time to evaluate : 5.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8330 (mtm) cc_final: 0.7947 (mtm) REVERT: D 100 MET cc_start: 0.8042 (mtp) cc_final: 0.7616 (mtp) REVERT: D 139 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8045 (tptt) REVERT: E 132 VAL cc_start: 0.7371 (m) cc_final: 0.7052 (p) REVERT: F 29 LYS cc_start: 0.6441 (pttp) cc_final: 0.5845 (mmtt) REVERT: F 138 LYS cc_start: 0.8654 (tttt) cc_final: 0.8445 (tttp) REVERT: G 41 LYS cc_start: 0.3119 (OUTLIER) cc_final: 0.2501 (pmmt) REVERT: I 135 MET cc_start: 0.1441 (mtt) cc_final: 0.0151 (ptt) REVERT: K 20 MET cc_start: 0.9292 (ttp) cc_final: 0.9073 (ttm) REVERT: K 108 ARG cc_start: 0.7351 (ptm160) cc_final: 0.6819 (ptp-170) REVERT: L 123 ARG cc_start: 0.7372 (ttm170) cc_final: 0.7157 (ttp-170) REVERT: M 18 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7741 (ptm160) REVERT: M 24 THR cc_start: 0.8493 (m) cc_final: 0.8151 (p) REVERT: M 127 LYS cc_start: 0.7754 (ttmp) cc_final: 0.7195 (tptp) REVERT: N 110 MET cc_start: 0.8483 (mmm) cc_final: 0.8216 (mmm) REVERT: P 83 SER cc_start: 0.8242 (t) cc_final: 0.7961 (p) REVERT: P 113 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7914 (ttp80) REVERT: Q 78 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8181 (mmtt) REVERT: Q 97 ASP cc_start: 0.8677 (t70) cc_final: 0.8362 (t0) REVERT: U 47 LYS cc_start: 0.6816 (ttmt) cc_final: 0.6564 (tptt) REVERT: V 84 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: W 30 SER cc_start: 0.8851 (p) cc_final: 0.8438 (m) REVERT: W 70 GLU cc_start: 0.7970 (pt0) cc_final: 0.7738 (pt0) REVERT: Y 40 SER cc_start: 0.7628 (m) cc_final: 0.7400 (p) REVERT: Z 19 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7863 (ttpp) REVERT: b 6 ASN cc_start: 0.9241 (m110) cc_final: 0.8898 (m110) REVERT: c 37 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8564 (ttmt) REVERT: d 1 MET cc_start: 0.8285 (mtp) cc_final: 0.7689 (mtm) REVERT: g 113 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7086 (tpt170) REVERT: h 38 LYS cc_start: 0.6688 (mmtt) cc_final: 0.6249 (tptp) REVERT: h 200 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7627 (t) REVERT: i 57 GLU cc_start: 0.7057 (tp30) cc_final: 0.6807 (tp30) REVERT: j 54 ARG cc_start: 0.7841 (mmt90) cc_final: 0.7632 (mmt-90) REVERT: j 126 LYS cc_start: 0.7825 (tptt) cc_final: 0.7540 (tppt) REVERT: l 27 VAL cc_start: 0.5159 (m) cc_final: 0.4866 (t) REVERT: n 41 ARG cc_start: 0.5216 (ttt90) cc_final: 0.4712 (tpt90) REVERT: n 119 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6134 (ttt180) REVERT: q 120 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6481 (ptmm) REVERT: r 93 ARG cc_start: 0.6015 (mmp-170) cc_final: 0.5709 (mmt90) REVERT: s 47 LYS cc_start: 0.6486 (tptt) cc_final: 0.6083 (tppp) REVERT: v 62 ARG cc_start: 0.8105 (ptt90) cc_final: 0.7828 (ptt90) REVERT: y 48 GLN cc_start: 0.7476 (tp40) cc_final: 0.7177 (tp-100) REVERT: y 54 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7103 (ttp) outliers start: 24 outliers final: 7 residues processed: 1083 average time/residue: 2.4315 time to fit residues: 3682.6700 Evaluate side-chains 759 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 749 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain y residue 54 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 869 optimal weight: 8.9990 chunk 780 optimal weight: 0.9980 chunk 433 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 526 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 807 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 490 optimal weight: 0.9980 chunk 600 optimal weight: 0.7980 chunk 935 optimal weight: 7.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 134 ASN B 260 ASN C 49 GLN C 67 HIS C 136 ASN C 150 GLN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 22 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS F 88 GLN F 104 ASN G 43 ASN I 110 GLN J 80 HIS J 131 ASN K 3 GLN N 31 HIS N 62 ASN O 38 GLN O 61 GLN O 100 HIS P 75 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN S 15 GLN S 61 ASN T 48 GLN X 34 HIS Y 25 GLN Y 45 GLN Z 20 HIS a 20 ASN b 42 HIS c 26 ASN g 39 HIS g 103 ASN h 3 GLN ** i 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 12 GLN j 19 ASN j 73 ASN j 89 HIS j 132 ASN k 63 ASN l 28 ASN l 97 ASN l 130 ASN l 148 ASN m 4 GLN n 81 HIS p 22 HIS q 112 GLN s 43 ASN t 20 ASN t 40 GLN x 57 HIS y 48 GLN y 52 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 157141 Z= 0.193 Angle : 0.672 14.586 234785 Z= 0.362 Chirality : 0.045 3.972 29884 Planarity : 0.007 0.128 12775 Dihedral : 23.408 178.670 77812 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.76 % Rotamer: Outliers : 3.35 % Allowed : 11.89 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.09), residues: 5867 helix: -2.50 (0.10), residues: 1826 sheet: -1.40 (0.14), residues: 1090 loop : -1.89 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 96 HIS 0.013 0.001 HIS M 13 PHE 0.018 0.002 PHE k 8 TYR 0.016 0.002 TYR I 7 ARG 0.007 0.001 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 803 time to evaluate : 6.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8345 (mtm) cc_final: 0.7793 (mtm) REVERT: D 100 MET cc_start: 0.7843 (mtp) cc_final: 0.7491 (mtp) REVERT: D 139 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7799 (tptt) REVERT: G 41 LYS cc_start: 0.3063 (OUTLIER) cc_final: 0.2400 (mmmt) REVERT: I 78 LEU cc_start: 0.2765 (OUTLIER) cc_final: 0.1562 (mp) REVERT: I 126 ARG cc_start: 0.3107 (OUTLIER) cc_final: 0.1424 (ptp90) REVERT: I 135 MET cc_start: 0.1335 (mtt) cc_final: 0.0515 (mmp) REVERT: J 95 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6437 (ttm170) REVERT: J 138 GLN cc_start: 0.7553 (mt0) cc_final: 0.7150 (mp10) REVERT: K 108 ARG cc_start: 0.7186 (ptm160) cc_final: 0.6761 (ptp-170) REVERT: K 113 MET cc_start: 0.7059 (tpp) cc_final: 0.6777 (tpp) REVERT: L 123 ARG cc_start: 0.7343 (ttm170) cc_final: 0.7059 (ttp-170) REVERT: M 18 ARG cc_start: 0.7938 (ptm-80) cc_final: 0.7726 (ptm160) REVERT: M 127 LYS cc_start: 0.7626 (ttmp) cc_final: 0.7164 (tptp) REVERT: N 1 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8264 (mtm) REVERT: O 13 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7206 (ttt180) REVERT: P 83 SER cc_start: 0.8126 (t) cc_final: 0.7776 (p) REVERT: P 89 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7579 (ptp90) REVERT: P 113 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7833 (ttp80) REVERT: Q 78 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8124 (mmtt) REVERT: R 1 MET cc_start: 0.7228 (ttm) cc_final: 0.6974 (ttp) REVERT: R 6 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: R 43 ASN cc_start: 0.7387 (t0) cc_final: 0.6550 (t0) REVERT: S 86 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7365 (ttm) REVERT: U 5 ILE cc_start: 0.8150 (mm) cc_final: 0.7901 (mm) REVERT: V 84 PRO cc_start: 0.8601 (Cg_endo) cc_final: 0.8277 (Cg_exo) REVERT: W 30 SER cc_start: 0.8821 (p) cc_final: 0.8501 (m) REVERT: Y 27 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.7064 (m110) REVERT: b 6 ASN cc_start: 0.9142 (m110) cc_final: 0.8823 (m110) REVERT: b 15 MET cc_start: 0.8980 (mtt) cc_final: 0.8490 (mtt) REVERT: c 45 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7469 (mt0) REVERT: d 1 MET cc_start: 0.8190 (mtp) cc_final: 0.7609 (mtm) REVERT: g 113 ARG cc_start: 0.7236 (tpt170) cc_final: 0.7015 (tpt170) REVERT: h 38 LYS cc_start: 0.6611 (mmtt) cc_final: 0.6119 (tptp) REVERT: h 200 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7667 (t) REVERT: i 57 GLU cc_start: 0.6869 (tp30) cc_final: 0.6486 (tp30) REVERT: j 15 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7515 (tt) REVERT: k 87 SER cc_start: 0.8087 (p) cc_final: 0.7852 (p) REVERT: l 23 LEU cc_start: 0.3655 (OUTLIER) cc_final: 0.3039 (tm) REVERT: l 50 LEU cc_start: 0.5741 (OUTLIER) cc_final: 0.5441 (tm) REVERT: m 83 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8386 (tp) REVERT: n 33 ARG cc_start: 0.4024 (mtm180) cc_final: 0.3726 (mtp180) REVERT: n 41 ARG cc_start: 0.4972 (ttt90) cc_final: 0.4650 (ttt90) REVERT: n 61 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6018 (pp) REVERT: n 119 ARG cc_start: 0.6831 (mtp180) cc_final: 0.6237 (ttt180) REVERT: o 60 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: o 88 MET cc_start: 0.5691 (mtt) cc_final: 0.5297 (mmm) REVERT: q 20 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7331 (p0) REVERT: q 120 LYS cc_start: 0.6779 (mmtt) cc_final: 0.6380 (ptmm) REVERT: r 93 ARG cc_start: 0.6025 (mmp-170) cc_final: 0.5816 (mmt90) REVERT: t 58 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: v 22 VAL cc_start: 0.8113 (p) cc_final: 0.7795 (t) REVERT: v 62 ARG cc_start: 0.8107 (ptt90) cc_final: 0.7814 (ptt90) REVERT: y 54 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7241 (ttp) outliers start: 163 outliers final: 54 residues processed: 884 average time/residue: 2.2947 time to fit residues: 2907.7496 Evaluate side-chains 781 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 707 time to evaluate : 6.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 126 ARG Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 89 ARG Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 519 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 778 optimal weight: 5.9990 chunk 636 optimal weight: 7.9990 chunk 258 optimal weight: 40.0000 chunk 937 optimal weight: 9.9990 chunk 1012 optimal weight: 0.9980 chunk 834 optimal weight: 9.9990 chunk 929 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 751 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 116 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN Y 25 GLN Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 71 GLN i 89 ASN i 100 ASN j 12 GLN j 19 ASN j 61 GLN j 73 ASN j 82 GLN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN q 112 GLN t 40 GLN y 52 ASN y 82 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 157141 Z= 0.401 Angle : 0.800 13.894 234785 Z= 0.414 Chirality : 0.046 0.464 29884 Planarity : 0.008 0.147 12775 Dihedral : 23.378 179.216 77811 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 5.01 % Allowed : 13.22 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.10), residues: 5867 helix: -1.78 (0.11), residues: 1855 sheet: -1.25 (0.15), residues: 1102 loop : -1.81 (0.10), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 96 HIS 0.014 0.002 HIS w 74 PHE 0.023 0.003 PHE R 77 TYR 0.018 0.003 TYR G 25 ARG 0.010 0.001 ARG k 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 713 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8787 (mp) REVERT: C 105 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7761 (mttp) REVERT: D 100 MET cc_start: 0.7980 (mtp) cc_final: 0.7574 (mtp) REVERT: D 139 LYS cc_start: 0.8290 (ttpt) cc_final: 0.7845 (tptt) REVERT: E 32 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6067 (tp30) REVERT: E 69 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7069 (mtmm) REVERT: E 142 ASP cc_start: 0.5973 (t0) cc_final: 0.5748 (t70) REVERT: E 161 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6995 (mtmm) REVERT: G 41 LYS cc_start: 0.3113 (OUTLIER) cc_final: 0.2563 (mtmt) REVERT: I 78 LEU cc_start: 0.3236 (OUTLIER) cc_final: 0.2007 (mp) REVERT: I 126 ARG cc_start: 0.3535 (OUTLIER) cc_final: 0.1457 (ptp90) REVERT: I 135 MET cc_start: 0.1723 (mtt) cc_final: 0.0693 (mmp) REVERT: J 138 GLN cc_start: 0.7722 (mt0) cc_final: 0.7222 (mp10) REVERT: K 108 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6907 (ptp-170) REVERT: L 123 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7144 (ttp-170) REVERT: M 18 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.7712 (ptm160) REVERT: M 127 LYS cc_start: 0.7627 (ttmp) cc_final: 0.7102 (tptp) REVERT: M 133 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7802 (tttt) REVERT: N 110 MET cc_start: 0.8376 (mmm) cc_final: 0.7896 (mmm) REVERT: P 83 SER cc_start: 0.8369 (t) cc_final: 0.7984 (p) REVERT: P 89 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7739 (ptp90) REVERT: P 113 ARG cc_start: 0.8040 (ttp-110) cc_final: 0.7804 (ttp80) REVERT: Q 70 ARG cc_start: 0.8875 (mtt-85) cc_final: 0.8567 (mtt90) REVERT: Q 78 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8139 (mmtt) REVERT: R 1 MET cc_start: 0.7519 (ttm) cc_final: 0.7174 (ttp) REVERT: R 6 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: S 92 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7222 (ttm-80) REVERT: T 1 MET cc_start: 0.6097 (tmt) cc_final: 0.5753 (tmm) REVERT: V 84 PRO cc_start: 0.8632 (Cg_endo) cc_final: 0.8313 (Cg_exo) REVERT: W 30 SER cc_start: 0.8809 (p) cc_final: 0.8461 (m) REVERT: W 66 LYS cc_start: 0.8570 (mttt) cc_final: 0.8219 (mttm) REVERT: W 68 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8060 (tmtt) REVERT: W 70 GLU cc_start: 0.7886 (tt0) cc_final: 0.7636 (tt0) REVERT: X 54 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8301 (tptm) REVERT: Z 19 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7734 (ttpp) REVERT: c 37 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8291 (ttpt) REVERT: d 1 MET cc_start: 0.8241 (mtp) cc_final: 0.7628 (mtm) REVERT: g 113 ARG cc_start: 0.7270 (tpt170) cc_final: 0.6998 (tpt170) REVERT: h 38 LYS cc_start: 0.6608 (mmtt) cc_final: 0.6136 (tptp) REVERT: h 86 LYS cc_start: 0.5313 (tptt) cc_final: 0.4904 (ttpt) REVERT: h 127 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7549 (mtp180) REVERT: h 164 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.4681 (pmt170) REVERT: i 95 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: i 177 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5430 (mttm) REVERT: j 15 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7590 (tt) REVERT: j 62 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6967 (mttt) REVERT: j 66 LYS cc_start: 0.7057 (mttt) cc_final: 0.6433 (ptmt) REVERT: j 68 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7819 (mmt180) REVERT: j 115 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7417 (mt) REVERT: k 1 MET cc_start: 0.6047 (mmm) cc_final: 0.5634 (mmm) REVERT: k 87 SER cc_start: 0.8372 (p) cc_final: 0.8083 (p) REVERT: l 23 LEU cc_start: 0.3323 (OUTLIER) cc_final: 0.2911 (tm) REVERT: m 69 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7089 (ptpt) REVERT: n 33 ARG cc_start: 0.4177 (mtm180) cc_final: 0.3845 (mtp180) REVERT: n 41 ARG cc_start: 0.5058 (ttt90) cc_final: 0.4848 (ttt90) REVERT: n 113 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6103 (ptt90) REVERT: n 119 ARG cc_start: 0.6822 (mtp180) cc_final: 0.6183 (ttt180) REVERT: n 124 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6664 (mtt90) REVERT: o 60 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: p 82 LEU cc_start: 0.6999 (tp) cc_final: 0.6722 (tp) REVERT: q 20 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7386 (p0) REVERT: q 86 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.5343 (ppp80) REVERT: q 120 LYS cc_start: 0.6792 (mmtt) cc_final: 0.6413 (ptmm) REVERT: r 7 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5668 (pt) REVERT: r 93 ARG cc_start: 0.6125 (mmp-170) cc_final: 0.5924 (mmt90) REVERT: v 22 VAL cc_start: 0.8260 (p) cc_final: 0.7942 (t) REVERT: v 79 VAL cc_start: 0.6715 (OUTLIER) cc_final: 0.6419 (p) REVERT: x 66 MET cc_start: 0.4440 (OUTLIER) cc_final: 0.3392 (mpt) REVERT: y 54 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7317 (ttp) outliers start: 244 outliers final: 124 residues processed: 852 average time/residue: 2.2836 time to fit residues: 2789.2002 Evaluate side-chains 843 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 686 time to evaluate : 5.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 126 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain P residue 89 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 177 LYS Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 124 ARG Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain x residue 66 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 925 optimal weight: 0.7980 chunk 704 optimal weight: 4.9990 chunk 486 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 447 optimal weight: 10.0000 chunk 629 optimal weight: 0.9990 chunk 940 optimal weight: 5.9990 chunk 995 optimal weight: 4.9990 chunk 491 optimal weight: 10.0000 chunk 891 optimal weight: 20.0000 chunk 268 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN i 89 ASN i 100 ASN j 12 GLN j 61 GLN j 73 ASN j 132 ASN q 112 GLN t 40 GLN y 52 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 157141 Z= 0.214 Angle : 0.647 13.029 234785 Z= 0.348 Chirality : 0.038 0.408 29884 Planarity : 0.006 0.134 12775 Dihedral : 23.211 179.549 77810 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.77 % Rotamer: Outliers : 4.37 % Allowed : 14.72 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 5867 helix: -1.11 (0.11), residues: 1853 sheet: -0.95 (0.15), residues: 1089 loop : -1.59 (0.10), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 96 HIS 0.008 0.001 HIS w 74 PHE 0.017 0.002 PHE g 90 TYR 0.015 0.002 TYR S 38 ARG 0.006 0.000 ARG g 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 715 time to evaluate : 6.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 MET cc_start: 0.7987 (mtp) cc_final: 0.7589 (mtp) REVERT: D 139 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7846 (tptt) REVERT: E 32 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6083 (tp30) REVERT: E 69 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7063 (mtmm) REVERT: E 161 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6944 (mtmm) REVERT: G 41 LYS cc_start: 0.2968 (OUTLIER) cc_final: 0.2472 (mtmt) REVERT: H 109 LYS cc_start: 0.3166 (OUTLIER) cc_final: 0.1997 (pttt) REVERT: I 78 LEU cc_start: 0.3047 (OUTLIER) cc_final: 0.1924 (mp) REVERT: I 135 MET cc_start: 0.1141 (mtt) cc_final: 0.0160 (mmp) REVERT: J 95 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6548 (ttm170) REVERT: K 45 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: K 113 MET cc_start: 0.7055 (tpp) cc_final: 0.6726 (tpp) REVERT: L 106 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7463 (mp0) REVERT: L 123 ARG cc_start: 0.7363 (ttm170) cc_final: 0.7117 (ttp-170) REVERT: M 18 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.7681 (ptm160) REVERT: M 127 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7069 (tptp) REVERT: N 1 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8219 (mtm) REVERT: N 110 MET cc_start: 0.8351 (mmm) cc_final: 0.7916 (mmm) REVERT: O 13 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7268 (ttt180) REVERT: P 13 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: P 68 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6709 (tp30) REVERT: P 83 SER cc_start: 0.8237 (t) cc_final: 0.7866 (p) REVERT: P 113 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7797 (ttp80) REVERT: P 114 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5628 (mp) REVERT: Q 78 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8103 (mmtt) REVERT: R 1 MET cc_start: 0.7433 (ttm) cc_final: 0.7158 (ttp) REVERT: R 6 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: S 69 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8573 (mp) REVERT: S 92 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7205 (ttm-80) REVERT: T 1 MET cc_start: 0.6050 (tmt) cc_final: 0.5715 (tmm) REVERT: U 5 ILE cc_start: 0.8212 (mm) cc_final: 0.7966 (mm) REVERT: U 67 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8162 (m) REVERT: V 84 PRO cc_start: 0.8633 (Cg_endo) cc_final: 0.8299 (Cg_exo) REVERT: W 30 SER cc_start: 0.8751 (p) cc_final: 0.8478 (m) REVERT: W 66 LYS cc_start: 0.8552 (mttt) cc_final: 0.8195 (mttm) REVERT: X 54 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8261 (tptm) REVERT: Z 45 ARG cc_start: 0.8507 (mmt180) cc_final: 0.8255 (mmt180) REVERT: c 37 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: d 1 MET cc_start: 0.8238 (mtp) cc_final: 0.7628 (mtm) REVERT: g 100 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6592 (ttm) REVERT: g 113 ARG cc_start: 0.7265 (tpt170) cc_final: 0.6981 (tpt170) REVERT: h 25 ASN cc_start: 0.7147 (m-40) cc_final: 0.6929 (m110) REVERT: h 38 LYS cc_start: 0.6586 (mmtt) cc_final: 0.6146 (tptp) REVERT: h 127 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7328 (mtp180) REVERT: h 147 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.7012 (mptm) REVERT: h 164 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7083 (ptt-90) REVERT: h 177 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7268 (p) REVERT: i 95 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: i 104 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6867 (mmt90) REVERT: i 177 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5258 (mttm) REVERT: j 71 MET cc_start: 0.6973 (mtp) cc_final: 0.6652 (mtp) REVERT: k 1 MET cc_start: 0.6025 (mmm) cc_final: 0.5614 (mmm) REVERT: l 23 LEU cc_start: 0.3286 (OUTLIER) cc_final: 0.2882 (tm) REVERT: l 50 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5497 (tm) REVERT: n 33 ARG cc_start: 0.4312 (mtm180) cc_final: 0.4078 (mtp180) REVERT: n 41 ARG cc_start: 0.5021 (ttt90) cc_final: 0.4812 (ttt90) REVERT: n 119 ARG cc_start: 0.6732 (mtp180) cc_final: 0.6205 (ttt180) REVERT: o 60 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: o 88 MET cc_start: 0.5385 (mtt) cc_final: 0.5048 (mmm) REVERT: p 82 LEU cc_start: 0.7060 (tp) cc_final: 0.6733 (tp) REVERT: p 106 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6759 (ttp-110) REVERT: q 20 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7409 (p0) REVERT: q 86 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.5402 (ppp80) REVERT: q 120 LYS cc_start: 0.6843 (mmtt) cc_final: 0.6438 (ptmm) REVERT: s 23 LYS cc_start: 0.6873 (mtmt) cc_final: 0.6620 (mtmt) REVERT: v 16 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7052 (mmmt) REVERT: v 22 VAL cc_start: 0.8390 (p) cc_final: 0.8019 (t) REVERT: v 62 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7817 (ptt90) REVERT: v 79 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6444 (p) REVERT: y 54 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7248 (ttp) outliers start: 213 outliers final: 111 residues processed: 831 average time/residue: 2.2517 time to fit residues: 2689.6131 Evaluate side-chains 841 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 694 time to evaluate : 5.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 177 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 829 optimal weight: 6.9990 chunk 565 optimal weight: 0.4980 chunk 14 optimal weight: 20.0000 chunk 741 optimal weight: 10.0000 chunk 410 optimal weight: 7.9990 chunk 849 optimal weight: 9.9990 chunk 688 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 508 optimal weight: 7.9990 chunk 893 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN E 27 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN i 89 ASN j 12 GLN j 61 GLN j 73 ASN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN n 50 GLN p 118 HIS q 112 GLN t 40 GLN z 56 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 157141 Z= 0.418 Angle : 0.800 13.594 234785 Z= 0.413 Chirality : 0.047 0.439 29884 Planarity : 0.008 0.146 12775 Dihedral : 23.311 178.424 77810 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.20 % Rotamer: Outliers : 5.67 % Allowed : 14.93 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.10), residues: 5867 helix: -1.15 (0.11), residues: 1855 sheet: -0.99 (0.15), residues: 1095 loop : -1.63 (0.10), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 96 HIS 0.014 0.002 HIS w 74 PHE 0.022 0.002 PHE R 77 TYR 0.017 0.003 TYR S 38 ARG 0.008 0.001 ARG Q 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 688 time to evaluate : 6.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7764 (mttp) REVERT: D 100 MET cc_start: 0.7972 (mtp) cc_final: 0.7618 (mtp) REVERT: D 139 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7889 (tptt) REVERT: E 32 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: E 69 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7052 (mtmm) REVERT: E 161 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6950 (mtmm) REVERT: G 15 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7281 (tp) REVERT: G 41 LYS cc_start: 0.3029 (OUTLIER) cc_final: 0.2520 (mtmt) REVERT: H 109 LYS cc_start: 0.3406 (OUTLIER) cc_final: 0.2049 (pttt) REVERT: I 78 LEU cc_start: 0.3279 (OUTLIER) cc_final: 0.2081 (mp) REVERT: I 135 MET cc_start: 0.1272 (mtt) cc_final: 0.0126 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6640 (ttm170) REVERT: K 45 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: L 123 ARG cc_start: 0.7399 (ttm170) cc_final: 0.7134 (ttp-170) REVERT: M 18 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7686 (ptm160) REVERT: M 127 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7108 (tptp) REVERT: N 110 MET cc_start: 0.8482 (mmm) cc_final: 0.8083 (mmm) REVERT: O 13 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7361 (ttt180) REVERT: P 13 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: P 68 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: P 83 SER cc_start: 0.8442 (t) cc_final: 0.8038 (p) REVERT: P 113 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7783 (ttm170) REVERT: P 114 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5708 (mt) REVERT: Q 78 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8162 (mmtt) REVERT: R 1 MET cc_start: 0.7445 (ttm) cc_final: 0.7156 (ttp) REVERT: R 6 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: S 86 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8200 (tpt) REVERT: S 92 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7193 (ttm-80) REVERT: T 1 MET cc_start: 0.6196 (tmt) cc_final: 0.5835 (tmm) REVERT: V 84 PRO cc_start: 0.8642 (Cg_endo) cc_final: 0.8314 (Cg_exo) REVERT: W 30 SER cc_start: 0.8765 (p) cc_final: 0.8417 (m) REVERT: W 66 LYS cc_start: 0.8576 (mttt) cc_final: 0.8230 (mttm) REVERT: W 68 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: X 54 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8200 (tptm) REVERT: c 37 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8275 (ttpt) REVERT: g 113 ARG cc_start: 0.7252 (tpt170) cc_final: 0.7011 (tpt170) REVERT: h 38 LYS cc_start: 0.6599 (mmtt) cc_final: 0.6161 (tptp) REVERT: h 86 LYS cc_start: 0.5580 (tptt) cc_final: 0.5079 (tmtt) REVERT: h 127 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7477 (mtp180) REVERT: h 131 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6423 (mtt-85) REVERT: h 147 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6936 (mptm) REVERT: h 164 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7209 (ptt-90) REVERT: h 177 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7386 (p) REVERT: i 35 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: i 95 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: i 104 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6888 (mmt90) REVERT: i 177 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5438 (mttm) REVERT: j 62 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6912 (mttt) REVERT: j 66 LYS cc_start: 0.7287 (mttt) cc_final: 0.6553 (ptmt) REVERT: j 71 MET cc_start: 0.7054 (mtp) cc_final: 0.6688 (mtp) REVERT: j 115 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7505 (mt) REVERT: k 1 MET cc_start: 0.6067 (mmm) cc_final: 0.5633 (mmm) REVERT: l 23 LEU cc_start: 0.3312 (OUTLIER) cc_final: 0.2913 (tm) REVERT: l 67 GLU cc_start: 0.5809 (tp30) cc_final: 0.5555 (tp30) REVERT: n 41 ARG cc_start: 0.5165 (ttt90) cc_final: 0.4663 (ttt90) REVERT: n 119 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6172 (ttt180) REVERT: o 60 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: o 88 MET cc_start: 0.5503 (mtt) cc_final: 0.5095 (mmm) REVERT: p 82 LEU cc_start: 0.7064 (tp) cc_final: 0.6783 (tp) REVERT: p 97 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7094 (pt) REVERT: q 20 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7388 (p0) REVERT: q 86 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.5431 (ppp80) REVERT: q 120 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6399 (ptmm) REVERT: t 58 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: u 1 MET cc_start: 0.7306 (ptt) cc_final: 0.6831 (ptm) REVERT: v 22 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.7963 (t) REVERT: v 79 VAL cc_start: 0.6698 (OUTLIER) cc_final: 0.6416 (p) REVERT: w 44 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8101 (mp) REVERT: y 54 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7293 (ttp) outliers start: 276 outliers final: 158 residues processed: 861 average time/residue: 2.2849 time to fit residues: 2830.4742 Evaluate side-chains 871 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 672 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain g residue 212 LEU Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 43 LEU Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 173 VAL Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 177 LYS Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 96 MET Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain r residue 108 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 334 optimal weight: 6.9990 chunk 896 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 584 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 996 optimal weight: 8.9990 chunk 827 optimal weight: 5.9990 chunk 461 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN O 38 GLN O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Y 39 GLN Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN i 89 ASN j 73 ASN j 132 ASN k 37 HIS k 55 HIS ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 ASN n 31 ASN q 112 GLN t 40 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 157141 Z= 0.310 Angle : 0.715 13.314 234785 Z= 0.377 Chirality : 0.042 0.434 29884 Planarity : 0.007 0.140 12775 Dihedral : 23.257 179.062 77810 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.84 % Rotamer: Outliers : 5.50 % Allowed : 15.71 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 5867 helix: -0.90 (0.11), residues: 1850 sheet: -0.90 (0.15), residues: 1104 loop : -1.55 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 96 HIS 0.010 0.002 HIS w 74 PHE 0.018 0.002 PHE g 90 TYR 0.016 0.002 TYR q 38 ARG 0.007 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 685 time to evaluate : 6.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8034 (t0) cc_final: 0.7760 (t0) REVERT: C 2 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7369 (pt) REVERT: C 105 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7773 (mttp) REVERT: D 44 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7242 (ppt-90) REVERT: D 100 MET cc_start: 0.8022 (mtp) cc_final: 0.7641 (mtp) REVERT: D 139 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7875 (tptt) REVERT: E 32 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: E 34 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7717 (pt) REVERT: E 69 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7067 (mtmm) REVERT: E 161 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6949 (mtmm) REVERT: I 78 LEU cc_start: 0.3198 (OUTLIER) cc_final: 0.2051 (mp) REVERT: I 135 MET cc_start: 0.1097 (mtt) cc_final: 0.0099 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6594 (ttm170) REVERT: K 45 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: L 106 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7511 (mp0) REVERT: L 123 ARG cc_start: 0.7435 (ttm170) cc_final: 0.7090 (mtp180) REVERT: M 18 ARG cc_start: 0.8054 (ptm-80) cc_final: 0.7664 (ptm160) REVERT: M 127 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7131 (tptp) REVERT: N 110 MET cc_start: 0.8438 (mmm) cc_final: 0.8053 (mmm) REVERT: O 13 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7305 (ttt180) REVERT: P 13 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: P 68 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: P 83 SER cc_start: 0.8425 (t) cc_final: 0.8030 (p) REVERT: P 102 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7212 (pt0) REVERT: P 114 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5729 (mp) REVERT: Q 78 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8158 (mmtt) REVERT: R 1 MET cc_start: 0.7415 (ttm) cc_final: 0.7093 (ttp) REVERT: R 6 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: R 43 ASN cc_start: 0.7474 (t0) cc_final: 0.6708 (t0) REVERT: R 60 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7968 (mmmt) REVERT: S 92 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7062 (ttm-80) REVERT: T 1 MET cc_start: 0.6307 (tmt) cc_final: 0.5872 (tmm) REVERT: U 5 ILE cc_start: 0.8263 (mm) cc_final: 0.8021 (mm) REVERT: V 84 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8303 (Cg_exo) REVERT: W 30 SER cc_start: 0.8793 (p) cc_final: 0.8449 (m) REVERT: W 68 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8070 (tttt) REVERT: W 70 GLU cc_start: 0.7892 (tt0) cc_final: 0.7659 (tt0) REVERT: X 54 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8223 (tptm) REVERT: Z 45 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8170 (mmt180) REVERT: c 37 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8604 (ttmm) REVERT: g 100 MET cc_start: 0.7293 (ttm) cc_final: 0.6891 (mtp) REVERT: g 113 ARG cc_start: 0.7220 (tpt170) cc_final: 0.6993 (tpt170) REVERT: h 38 LYS cc_start: 0.6594 (mmtt) cc_final: 0.6176 (tptp) REVERT: h 86 LYS cc_start: 0.5422 (tptt) cc_final: 0.4946 (ttpt) REVERT: h 127 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: h 131 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6277 (mtt-85) REVERT: h 147 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6900 (mptm) REVERT: h 164 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7164 (ptt-90) REVERT: h 177 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7398 (p) REVERT: i 35 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5524 (mp0) REVERT: i 57 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6731 (tp30) REVERT: i 58 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6791 (ttmm) REVERT: i 95 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: i 104 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6912 (mmt90) REVERT: j 62 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6891 (mttt) REVERT: j 66 LYS cc_start: 0.7229 (mttt) cc_final: 0.6487 (ptmt) REVERT: j 115 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7565 (mt) REVERT: k 1 MET cc_start: 0.6084 (mmm) cc_final: 0.5629 (mmm) REVERT: l 23 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.3051 (tm) REVERT: l 47 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5726 (mp) REVERT: l 50 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5757 (tm) REVERT: n 41 ARG cc_start: 0.5168 (ttt90) cc_final: 0.4651 (ttt90) REVERT: n 61 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6230 (pp) REVERT: n 119 ARG cc_start: 0.6818 (mtp180) cc_final: 0.6123 (ttt180) REVERT: o 60 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: p 82 LEU cc_start: 0.7037 (tp) cc_final: 0.6733 (tp) REVERT: p 97 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7092 (pt) REVERT: p 106 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6657 (ttp-110) REVERT: q 20 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7437 (p0) REVERT: q 86 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.5446 (ppp80) REVERT: q 120 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6337 (ptmm) REVERT: t 58 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7643 (ttt180) REVERT: u 1 MET cc_start: 0.7082 (ptt) cc_final: 0.6834 (ptm) REVERT: v 22 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8069 (t) REVERT: v 62 ARG cc_start: 0.8069 (ptt-90) cc_final: 0.7822 (ptt90) REVERT: v 79 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6431 (p) REVERT: w 44 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8088 (mp) REVERT: y 54 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7255 (ttp) outliers start: 268 outliers final: 166 residues processed: 848 average time/residue: 2.2376 time to fit residues: 2739.5826 Evaluate side-chains 878 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 666 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 173 VAL Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 58 LYS Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 102 MET Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 114 ARG Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 960 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 567 optimal weight: 9.9990 chunk 727 optimal weight: 8.9990 chunk 563 optimal weight: 30.0000 chunk 838 optimal weight: 7.9990 chunk 556 optimal weight: 0.5980 chunk 992 optimal weight: 0.7980 chunk 621 optimal weight: 10.0000 chunk 605 optimal weight: 5.9990 chunk 458 optimal weight: 7.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN i 89 ASN j 132 ASN k 37 HIS k 55 HIS ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN t 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157141 Z= 0.311 Angle : 0.713 13.288 234785 Z= 0.376 Chirality : 0.042 0.422 29884 Planarity : 0.007 0.141 12775 Dihedral : 23.232 179.116 77806 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.44 % Favored : 94.55 % Rotamer: Outliers : 5.85 % Allowed : 15.81 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 5867 helix: -0.77 (0.12), residues: 1856 sheet: -0.86 (0.15), residues: 1105 loop : -1.50 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP g 96 HIS 0.009 0.001 HIS w 74 PHE 0.019 0.002 PHE g 90 TYR 0.017 0.002 TYR q 38 ARG 0.009 0.001 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 681 time to evaluate : 6.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.7973 (t0) cc_final: 0.7716 (t0) REVERT: C 2 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7339 (pt) REVERT: C 105 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7798 (mttp) REVERT: D 44 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7258 (ppt-90) REVERT: D 100 MET cc_start: 0.7950 (mtp) cc_final: 0.7537 (mtp) REVERT: D 139 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7902 (tptt) REVERT: E 32 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: E 69 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7077 (mtmm) REVERT: E 161 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6945 (mtmm) REVERT: F 89 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7576 (mt) REVERT: I 78 LEU cc_start: 0.3031 (OUTLIER) cc_final: 0.1950 (mp) REVERT: I 135 MET cc_start: 0.1245 (mtt) cc_final: 0.0189 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6609 (ttm170) REVERT: K 45 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: K 108 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7272 (ptp-170) REVERT: K 116 ILE cc_start: 0.8124 (pp) cc_final: 0.7838 (pt) REVERT: L 106 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7504 (mp0) REVERT: L 123 ARG cc_start: 0.7372 (ttm170) cc_final: 0.7143 (ttp-170) REVERT: M 127 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7138 (tptp) REVERT: N 1 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8136 (mtm) REVERT: N 110 MET cc_start: 0.8443 (mmm) cc_final: 0.8062 (mmm) REVERT: O 13 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7302 (ttt180) REVERT: P 13 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8406 (mtm) REVERT: P 68 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: P 83 SER cc_start: 0.8390 (t) cc_final: 0.7984 (p) REVERT: Q 78 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8120 (mmtt) REVERT: R 1 MET cc_start: 0.7452 (ttm) cc_final: 0.7139 (ttp) REVERT: R 6 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: R 43 ASN cc_start: 0.7581 (t0) cc_final: 0.6819 (t0) REVERT: R 60 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7996 (mmmt) REVERT: S 82 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8373 (ptt) REVERT: S 92 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7178 (ttm-80) REVERT: T 1 MET cc_start: 0.6305 (tmt) cc_final: 0.5831 (tmm) REVERT: U 5 ILE cc_start: 0.8285 (mm) cc_final: 0.8079 (mm) REVERT: V 84 PRO cc_start: 0.8692 (Cg_endo) cc_final: 0.8302 (Cg_exo) REVERT: W 30 SER cc_start: 0.8773 (p) cc_final: 0.8436 (m) REVERT: W 68 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8068 (tttt) REVERT: X 54 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8227 (tptm) REVERT: Z 45 ARG cc_start: 0.8498 (mmt180) cc_final: 0.8177 (mmt180) REVERT: b 15 MET cc_start: 0.8844 (mtt) cc_final: 0.8595 (mtt) REVERT: c 37 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8598 (ttmm) REVERT: g 8 ASP cc_start: 0.3997 (OUTLIER) cc_final: 0.2510 (m-30) REVERT: g 100 MET cc_start: 0.7161 (ttm) cc_final: 0.6714 (mtp) REVERT: g 113 ARG cc_start: 0.7227 (tpt170) cc_final: 0.6985 (tpt170) REVERT: h 38 LYS cc_start: 0.6588 (mmtt) cc_final: 0.6123 (tppt) REVERT: h 86 LYS cc_start: 0.5280 (tptt) cc_final: 0.4925 (ttpt) REVERT: h 127 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: h 131 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6254 (mtt-85) REVERT: h 147 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6894 (mptm) REVERT: h 164 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7168 (ptt-90) REVERT: h 177 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7416 (p) REVERT: i 29 ASP cc_start: 0.5470 (OUTLIER) cc_final: 0.5177 (p0) REVERT: i 35 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5665 (mp0) REVERT: i 95 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: i 104 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6888 (mmt90) REVERT: j 62 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6808 (mttt) REVERT: j 66 LYS cc_start: 0.7140 (mttt) cc_final: 0.6489 (ptmt) REVERT: j 115 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7569 (mt) REVERT: j 132 ASN cc_start: 0.7842 (t0) cc_final: 0.7573 (t0) REVERT: j 152 MET cc_start: 0.6799 (mtp) cc_final: 0.6576 (mtm) REVERT: k 1 MET cc_start: 0.5991 (mmm) cc_final: 0.5505 (mmm) REVERT: l 23 LEU cc_start: 0.3461 (OUTLIER) cc_final: 0.3126 (tm) REVERT: l 47 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5578 (mp) REVERT: l 50 LEU cc_start: 0.6030 (OUTLIER) cc_final: 0.5719 (tm) REVERT: n 41 ARG cc_start: 0.5201 (ttt90) cc_final: 0.4679 (ttt90) REVERT: n 61 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6165 (pp) REVERT: n 119 ARG cc_start: 0.6933 (mtp180) cc_final: 0.6181 (ttt180) REVERT: o 60 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: o 88 MET cc_start: 0.5249 (mtt) cc_final: 0.4815 (mmm) REVERT: p 82 LEU cc_start: 0.7055 (tp) cc_final: 0.6749 (tp) REVERT: p 97 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7099 (pt) REVERT: p 106 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6637 (ttp-110) REVERT: q 20 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7175 (p0) REVERT: q 86 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.5419 (ppp80) REVERT: q 120 LYS cc_start: 0.6755 (mmtt) cc_final: 0.6366 (ptmm) REVERT: s 6 MET cc_start: 0.8130 (mpt) cc_final: 0.5955 (mpt) REVERT: s 23 LYS cc_start: 0.6752 (mtmt) cc_final: 0.6452 (mtmt) REVERT: t 58 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7643 (ttt180) REVERT: v 22 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.7941 (t) REVERT: v 62 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7814 (ptt90) REVERT: v 79 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6363 (p) REVERT: w 44 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8051 (mp) REVERT: y 54 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7269 (ttp) outliers start: 285 outliers final: 180 residues processed: 858 average time/residue: 2.2055 time to fit residues: 2734.3247 Evaluate side-chains 895 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 668 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 89 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 62 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 8 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain g residue 212 LEU Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 75 ILE Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 108 LYS Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 123 GLN Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 173 VAL Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 114 ARG Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 69 ARG Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 22 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 42 THR Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 614 optimal weight: 0.0570 chunk 396 optimal weight: 7.9990 chunk 592 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 631 optimal weight: 6.9990 chunk 676 optimal weight: 0.1980 chunk 490 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 780 optimal weight: 5.9990 overall best weight: 2.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN h 25 ASN i 136 GLN k 37 HIS ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN q 112 GLN t 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 157141 Z= 0.210 Angle : 0.658 13.054 234785 Z= 0.354 Chirality : 0.038 0.407 29884 Planarity : 0.006 0.137 12775 Dihedral : 23.233 179.388 77806 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.92 % Rotamer: Outliers : 5.11 % Allowed : 16.71 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 5867 helix: -0.62 (0.12), residues: 1853 sheet: -0.83 (0.15), residues: 1109 loop : -1.43 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 96 HIS 0.009 0.001 HIS x 52 PHE 0.017 0.002 PHE g 90 TYR 0.028 0.002 TYR H 84 ARG 0.015 0.001 ARG X 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 676 time to evaluate : 6.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8037 (t0) cc_final: 0.7784 (t0) REVERT: C 2 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7305 (pt) REVERT: C 74 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: D 100 MET cc_start: 0.7956 (mtp) cc_final: 0.7579 (mtp) REVERT: D 139 LYS cc_start: 0.8377 (ttpt) cc_final: 0.7889 (tptt) REVERT: E 32 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6038 (tp30) REVERT: E 69 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7074 (mtmm) REVERT: E 117 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.5884 (mm) REVERT: E 161 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6959 (mtmm) REVERT: I 78 LEU cc_start: 0.3036 (OUTLIER) cc_final: 0.1987 (mp) REVERT: I 135 MET cc_start: 0.1223 (mtt) cc_final: 0.0187 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6590 (ttm170) REVERT: K 45 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: K 116 ILE cc_start: 0.8085 (pp) cc_final: 0.7820 (pt) REVERT: L 106 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7489 (mp0) REVERT: L 123 ARG cc_start: 0.7348 (ttm170) cc_final: 0.7141 (ttp-170) REVERT: M 127 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7118 (tptp) REVERT: N 1 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: N 110 MET cc_start: 0.8414 (mmm) cc_final: 0.8042 (mmm) REVERT: O 13 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6323 (tpt170) REVERT: P 13 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: P 68 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: P 83 SER cc_start: 0.8373 (t) cc_final: 0.7967 (p) REVERT: Q 78 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8112 (mmtt) REVERT: R 1 MET cc_start: 0.7423 (ttm) cc_final: 0.7128 (ttp) REVERT: R 6 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: R 43 ASN cc_start: 0.7494 (t0) cc_final: 0.6705 (t0) REVERT: R 60 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7988 (mmmt) REVERT: S 82 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8411 (ptt) REVERT: S 92 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7103 (ttm-80) REVERT: S 98 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8225 (mmtt) REVERT: T 1 MET cc_start: 0.6280 (tmt) cc_final: 0.5780 (tmm) REVERT: V 84 PRO cc_start: 0.8635 (Cg_endo) cc_final: 0.8300 (Cg_exo) REVERT: W 30 SER cc_start: 0.8752 (p) cc_final: 0.8448 (m) REVERT: W 66 LYS cc_start: 0.8554 (mttt) cc_final: 0.8204 (mttm) REVERT: W 68 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8083 (tttt) REVERT: X 54 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8216 (tptm) REVERT: Z 45 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8133 (mmt180) REVERT: b 15 MET cc_start: 0.8855 (mtt) cc_final: 0.8629 (mtt) REVERT: c 37 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8587 (ttmm) REVERT: c 49 TYR cc_start: 0.8900 (m-80) cc_final: 0.8645 (m-10) REVERT: g 8 ASP cc_start: 0.3946 (OUTLIER) cc_final: 0.2513 (m-30) REVERT: g 100 MET cc_start: 0.7099 (ttm) cc_final: 0.6700 (mtp) REVERT: g 113 ARG cc_start: 0.7195 (tpt170) cc_final: 0.6966 (tpt170) REVERT: h 38 LYS cc_start: 0.6563 (mmtt) cc_final: 0.6100 (tppt) REVERT: h 86 LYS cc_start: 0.5184 (tptt) cc_final: 0.4869 (ttpt) REVERT: h 127 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7375 (mtp180) REVERT: h 131 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6259 (mtt-85) REVERT: h 147 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6885 (mptm) REVERT: h 164 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7127 (ptt-90) REVERT: h 177 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7438 (p) REVERT: i 29 ASP cc_start: 0.5457 (OUTLIER) cc_final: 0.5163 (p0) REVERT: i 35 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5595 (mp0) REVERT: i 95 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: i 104 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: j 62 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6834 (mttm) REVERT: j 66 LYS cc_start: 0.7123 (mttt) cc_final: 0.6627 (tttt) REVERT: j 115 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7580 (mt) REVERT: k 1 MET cc_start: 0.5965 (mmm) cc_final: 0.5479 (mmm) REVERT: k 21 MET cc_start: 0.7303 (mtt) cc_final: 0.7102 (mtt) REVERT: l 23 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.3091 (tp) REVERT: l 47 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5543 (mp) REVERT: l 50 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5682 (tm) REVERT: n 41 ARG cc_start: 0.5119 (ttt90) cc_final: 0.4588 (ttt90) REVERT: n 61 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6152 (pp) REVERT: n 119 ARG cc_start: 0.6930 (mtp180) cc_final: 0.6263 (ttt180) REVERT: o 60 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: o 88 MET cc_start: 0.5156 (mtt) cc_final: 0.4828 (mmm) REVERT: p 82 LEU cc_start: 0.7053 (tp) cc_final: 0.6744 (tp) REVERT: p 97 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7078 (pt) REVERT: p 106 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6628 (ttp-110) REVERT: q 20 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7144 (p0) REVERT: q 86 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.5432 (ppp80) REVERT: q 120 LYS cc_start: 0.6729 (mmtt) cc_final: 0.6347 (ptmm) REVERT: t 58 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7606 (ttt180) REVERT: v 22 VAL cc_start: 0.8393 (p) cc_final: 0.8049 (t) REVERT: v 62 ARG cc_start: 0.8060 (ptt-90) cc_final: 0.7804 (ptt90) REVERT: v 79 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6267 (p) REVERT: w 44 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8038 (mp) REVERT: y 54 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7243 (ttp) outliers start: 249 outliers final: 167 residues processed: 832 average time/residue: 2.1801 time to fit residues: 2619.9957 Evaluate side-chains 880 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 667 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 4 LYS Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 89 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 8 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 108 LYS Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 123 GLN Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 114 ARG Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 903 optimal weight: 5.9990 chunk 951 optimal weight: 6.9990 chunk 867 optimal weight: 1.9990 chunk 925 optimal weight: 7.9990 chunk 950 optimal weight: 10.0000 chunk 556 optimal weight: 6.9990 chunk 403 optimal weight: 10.0000 chunk 726 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 835 optimal weight: 0.9990 chunk 874 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN h 25 ASN i 136 GLN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN q 112 GLN t 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 157141 Z= 0.231 Angle : 0.653 13.117 234785 Z= 0.351 Chirality : 0.039 0.408 29884 Planarity : 0.006 0.135 12775 Dihedral : 23.186 179.741 77806 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.23 % Rotamer: Outliers : 4.89 % Allowed : 16.98 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 5867 helix: -0.47 (0.12), residues: 1853 sheet: -0.79 (0.15), residues: 1102 loop : -1.37 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 96 HIS 0.008 0.001 HIS x 52 PHE 0.017 0.002 PHE g 90 TYR 0.017 0.002 TYR q 38 ARG 0.014 0.001 ARG X 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 676 time to evaluate : 6.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7307 (pt) REVERT: C 74 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: D 44 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7297 (ppt-90) REVERT: D 100 MET cc_start: 0.8087 (mtp) cc_final: 0.7696 (mtp) REVERT: D 139 LYS cc_start: 0.8379 (ttpt) cc_final: 0.7874 (tptt) REVERT: E 32 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6049 (tp30) REVERT: E 69 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7065 (mtmm) REVERT: E 161 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6974 (mtmm) REVERT: I 78 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2107 (mp) REVERT: I 135 MET cc_start: 0.1207 (mtt) cc_final: 0.0186 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6584 (ttm170) REVERT: K 45 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: K 116 ILE cc_start: 0.8106 (pp) cc_final: 0.7835 (pt) REVERT: L 123 ARG cc_start: 0.7360 (ttm170) cc_final: 0.7151 (ttp-170) REVERT: M 127 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7121 (tptp) REVERT: N 1 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: N 110 MET cc_start: 0.8416 (mmm) cc_final: 0.8046 (mmm) REVERT: O 13 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7265 (ttt180) REVERT: P 13 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: P 68 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6746 (tp30) REVERT: P 83 SER cc_start: 0.8361 (t) cc_final: 0.7961 (p) REVERT: Q 78 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8136 (mmtt) REVERT: R 1 MET cc_start: 0.7426 (ttm) cc_final: 0.7087 (ttp) REVERT: R 6 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: R 43 ASN cc_start: 0.7386 (t0) cc_final: 0.6620 (t0) REVERT: R 60 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (mmmt) REVERT: S 69 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (mp) REVERT: S 82 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8412 (ptt) REVERT: S 92 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7078 (ttm-80) REVERT: S 98 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (mmtt) REVERT: T 1 MET cc_start: 0.6282 (tmt) cc_final: 0.5780 (tmm) REVERT: V 84 PRO cc_start: 0.8694 (Cg_endo) cc_final: 0.8299 (Cg_exo) REVERT: W 30 SER cc_start: 0.8757 (p) cc_final: 0.8480 (m) REVERT: W 66 LYS cc_start: 0.8555 (mttt) cc_final: 0.8202 (mttm) REVERT: W 68 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: X 54 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8331 (tptm) REVERT: Z 45 ARG cc_start: 0.8480 (mmt180) cc_final: 0.8168 (mmt180) REVERT: b 15 MET cc_start: 0.8844 (mtt) cc_final: 0.8606 (mtt) REVERT: c 37 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8595 (ttmm) REVERT: c 49 TYR cc_start: 0.8900 (m-80) cc_final: 0.8621 (m-80) REVERT: g 8 ASP cc_start: 0.3939 (OUTLIER) cc_final: 0.2517 (m-30) REVERT: g 100 MET cc_start: 0.7045 (ttm) cc_final: 0.6639 (mtp) REVERT: g 113 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6967 (tpt170) REVERT: h 38 LYS cc_start: 0.6560 (mmtt) cc_final: 0.6099 (tppt) REVERT: h 86 LYS cc_start: 0.5037 (tptt) cc_final: 0.4762 (ttpt) REVERT: h 127 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7319 (mtp180) REVERT: h 131 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6236 (mtt-85) REVERT: h 147 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6852 (mptm) REVERT: h 164 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7145 (ptt-90) REVERT: h 177 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7492 (p) REVERT: i 29 ASP cc_start: 0.5513 (OUTLIER) cc_final: 0.5170 (p0) REVERT: i 35 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: i 95 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: i 104 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6821 (mmt90) REVERT: j 15 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7577 (tp) REVERT: j 62 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6779 (mttt) REVERT: j 66 LYS cc_start: 0.7122 (mttt) cc_final: 0.6632 (tttt) REVERT: j 115 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7577 (mt) REVERT: j 132 ASN cc_start: 0.7714 (t0) cc_final: 0.7482 (t0) REVERT: k 1 MET cc_start: 0.5958 (mmm) cc_final: 0.5477 (mmm) REVERT: k 21 MET cc_start: 0.7281 (mtt) cc_final: 0.7077 (mtt) REVERT: l 23 LEU cc_start: 0.3441 (OUTLIER) cc_final: 0.3101 (tm) REVERT: l 47 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5525 (mp) REVERT: l 50 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5665 (tm) REVERT: n 41 ARG cc_start: 0.5114 (ttt90) cc_final: 0.4583 (ttt90) REVERT: n 61 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6090 (pp) REVERT: n 119 ARG cc_start: 0.6927 (mtp180) cc_final: 0.6271 (ttt180) REVERT: o 60 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: o 88 MET cc_start: 0.5239 (mtt) cc_final: 0.4883 (mmm) REVERT: p 82 LEU cc_start: 0.7020 (tp) cc_final: 0.6710 (tp) REVERT: p 97 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7022 (pt) REVERT: p 106 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6625 (ttp-110) REVERT: q 20 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7131 (p0) REVERT: q 86 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.5457 (ppp80) REVERT: q 120 LYS cc_start: 0.6757 (mmtt) cc_final: 0.6367 (ptmm) REVERT: t 58 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7749 (ttm170) REVERT: v 22 VAL cc_start: 0.8391 (p) cc_final: 0.8042 (t) REVERT: v 62 ARG cc_start: 0.8051 (ptt-90) cc_final: 0.7778 (ptt90) REVERT: w 44 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8053 (mp) REVERT: y 54 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7208 (ttp) outliers start: 238 outliers final: 164 residues processed: 819 average time/residue: 2.2232 time to fit residues: 2632.4145 Evaluate side-chains 879 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 668 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 8 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 177 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 114 ARG Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 86 VAL Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 44 ILE Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 921 optimal weight: 6.9990 chunk 607 optimal weight: 0.0770 chunk 978 optimal weight: 20.0000 chunk 597 optimal weight: 30.0000 chunk 464 optimal weight: 1.9990 chunk 680 optimal weight: 7.9990 chunk 1026 optimal weight: 5.9990 chunk 944 optimal weight: 1.9990 chunk 817 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 631 optimal weight: 0.6980 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Y 45 GLN Z 20 HIS ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN h 25 ASN i 136 GLN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN t 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 157141 Z= 0.172 Angle : 0.628 12.923 234785 Z= 0.341 Chirality : 0.037 0.401 29884 Planarity : 0.006 0.133 12775 Dihedral : 23.185 179.892 77806 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.23 % Rotamer: Outliers : 4.64 % Allowed : 17.20 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.10), residues: 5867 helix: -0.39 (0.12), residues: 1857 sheet: -0.74 (0.15), residues: 1095 loop : -1.35 (0.11), residues: 2915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 96 HIS 0.009 0.001 HIS x 52 PHE 0.021 0.001 PHE U 96 TYR 0.015 0.002 TYR q 38 ARG 0.010 0.000 ARG B 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11734 Ramachandran restraints generated. 5867 Oldfield, 0 Emsley, 5867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 672 time to evaluate : 6.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7282 (pt) REVERT: C 183 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: D 100 MET cc_start: 0.8080 (mtp) cc_final: 0.7685 (mtp) REVERT: D 139 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7870 (tptt) REVERT: E 32 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6044 (tp30) REVERT: E 69 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7058 (mtmm) REVERT: E 161 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6971 (mtmm) REVERT: I 78 LEU cc_start: 0.3079 (OUTLIER) cc_final: 0.2084 (mp) REVERT: I 135 MET cc_start: 0.1083 (mtt) cc_final: 0.0102 (OUTLIER) REVERT: J 95 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6571 (ttm170) REVERT: K 45 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: K 116 ILE cc_start: 0.8057 (pp) cc_final: 0.7789 (pt) REVERT: L 123 ARG cc_start: 0.7333 (ttm170) cc_final: 0.7121 (ttp-170) REVERT: M 127 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7110 (tptp) REVERT: N 1 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8211 (mtm) REVERT: N 110 MET cc_start: 0.8385 (mmm) cc_final: 0.8013 (mmm) REVERT: O 13 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7233 (ttt180) REVERT: P 13 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8425 (mtm) REVERT: P 68 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: P 83 SER cc_start: 0.8260 (t) cc_final: 0.7880 (p) REVERT: Q 78 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8115 (mmtt) REVERT: R 1 MET cc_start: 0.7409 (ttm) cc_final: 0.7077 (ttp) REVERT: R 6 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: R 43 ASN cc_start: 0.7338 (t0) cc_final: 0.6577 (t0) REVERT: R 60 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7976 (mmmt) REVERT: S 69 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8684 (mp) REVERT: S 82 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8398 (ptt) REVERT: S 92 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7035 (ttm-80) REVERT: S 98 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8201 (mmtt) REVERT: T 1 MET cc_start: 0.6274 (tmt) cc_final: 0.5785 (tmm) REVERT: V 84 PRO cc_start: 0.8635 (Cg_endo) cc_final: 0.8295 (Cg_exo) REVERT: W 30 SER cc_start: 0.8735 (p) cc_final: 0.8474 (m) REVERT: W 66 LYS cc_start: 0.8548 (mttt) cc_final: 0.8196 (mttm) REVERT: W 68 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8079 (tttt) REVERT: X 54 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8309 (tptm) REVERT: Z 45 ARG cc_start: 0.8444 (mmt180) cc_final: 0.8130 (mmt180) REVERT: b 15 MET cc_start: 0.8849 (mtt) cc_final: 0.8617 (mtt) REVERT: c 37 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8584 (ttmm) REVERT: c 49 TYR cc_start: 0.8894 (m-80) cc_final: 0.8635 (m-10) REVERT: g 8 ASP cc_start: 0.3910 (OUTLIER) cc_final: 0.2512 (m-30) REVERT: g 100 MET cc_start: 0.7036 (ttm) cc_final: 0.6629 (mtp) REVERT: g 113 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6978 (tpt170) REVERT: h 38 LYS cc_start: 0.6543 (mmtt) cc_final: 0.6087 (tppt) REVERT: h 86 LYS cc_start: 0.5017 (tptt) cc_final: 0.4769 (ttpt) REVERT: h 127 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: h 131 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6207 (mtt-85) REVERT: h 147 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6834 (mptm) REVERT: h 164 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7141 (ptt-90) REVERT: i 29 ASP cc_start: 0.5494 (OUTLIER) cc_final: 0.5160 (p0) REVERT: i 35 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: i 95 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: i 104 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6794 (mmt90) REVERT: j 15 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7576 (tp) REVERT: j 62 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6786 (mttt) REVERT: j 66 LYS cc_start: 0.7107 (mttt) cc_final: 0.6616 (tttt) REVERT: j 82 GLN cc_start: 0.6771 (mt0) cc_final: 0.6108 (tp-100) REVERT: j 115 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7557 (mt) REVERT: k 1 MET cc_start: 0.5949 (mmm) cc_final: 0.5468 (mmm) REVERT: k 21 MET cc_start: 0.7245 (mtt) cc_final: 0.7038 (mtt) REVERT: l 23 LEU cc_start: 0.3417 (OUTLIER) cc_final: 0.3091 (tp) REVERT: l 47 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5537 (mp) REVERT: l 50 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5515 (tm) REVERT: n 41 ARG cc_start: 0.5107 (ttt90) cc_final: 0.4578 (ttt90) REVERT: n 61 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6078 (pp) REVERT: n 119 ARG cc_start: 0.6924 (mtp180) cc_final: 0.6265 (ttt180) REVERT: o 60 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: o 88 MET cc_start: 0.5298 (mtt) cc_final: 0.4954 (mmm) REVERT: p 82 LEU cc_start: 0.7004 (tp) cc_final: 0.6699 (tp) REVERT: p 97 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7001 (pt) REVERT: p 106 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6623 (ttp-110) REVERT: q 20 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7122 (p0) REVERT: q 86 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.5451 (ppp80) REVERT: q 120 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6359 (ptmm) REVERT: t 58 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: v 22 VAL cc_start: 0.8379 (p) cc_final: 0.8033 (t) REVERT: v 62 ARG cc_start: 0.8042 (ptt-90) cc_final: 0.7801 (ptt90) REVERT: y 54 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7168 (ttp) outliers start: 226 outliers final: 157 residues processed: 808 average time/residue: 2.2276 time to fit residues: 2604.8161 Evaluate side-chains 869 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 668 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 69 ARG Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 95 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 127 LYS Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain P residue 13 MET Chi-restraints excluded: chain P residue 68 GLU Chi-restraints excluded: chain P residue 89 ARG Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 100 SER Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 54 LYS Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain c residue 22 THR Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 43 THR Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain g residue 8 ASP Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 54 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain g residue 106 THR Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 197 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 70 THR Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 110 GLU Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 127 ARG Chi-restraints excluded: chain h residue 128 VAL Chi-restraints excluded: chain h residue 131 ARG Chi-restraints excluded: chain h residue 147 LYS Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 164 ARG Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 29 ASP Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 104 ARG Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 144 SER Chi-restraints excluded: chain i residue 159 LEU Chi-restraints excluded: chain i residue 160 GLU Chi-restraints excluded: chain i residue 205 SER Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 94 VAL Chi-restraints excluded: chain j residue 115 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 148 ASN Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 50 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 GLU Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 124 LEU Chi-restraints excluded: chain m residue 69 LYS Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 114 ARG Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 55 SER Chi-restraints excluded: chain p residue 64 GLN Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 106 ARG Chi-restraints excluded: chain q residue 20 ASN Chi-restraints excluded: chain q residue 21 VAL Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 86 ARG Chi-restraints excluded: chain q residue 87 VAL Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 68 ASP Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain t residue 5 THR Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 58 ARG Chi-restraints excluded: chain u residue 19 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 52 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 33 ILE Chi-restraints excluded: chain v residue 43 LYS Chi-restraints excluded: chain v residue 79 VAL Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 44 MET Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 23 SER Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 501 optimal weight: 10.0000 chunk 649 optimal weight: 1.9990 chunk 870 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 753 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 818 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 840 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** g 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 178 ASN h 25 ASN i 136 GLN j 132 ASN ** k 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN t 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.171691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.137076 restraints weight = 154480.937| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.88 r_work: 0.3089 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 157141 Z= 0.331 Angle : 0.725 13.295 234785 Z= 0.380 Chirality : 0.042 0.420 29884 Planarity : 0.007 0.142 12775 Dihedral : 23.209 178.840 77806 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 4.99 % Allowed : 17.04 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 5867 helix: -0.52 (0.12), residues: 1860 sheet: -0.80 (0.15), residues: 1096 loop : -1.41 (0.11), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 62 HIS 0.009 0.002 HIS x 52 PHE 0.018 0.002 PHE g 90 TYR 0.019 0.002 TYR q 38 ARG 0.011 0.001 ARG B 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41359.18 seconds wall clock time: 719 minutes 31.03 seconds (43171.03 seconds total)