Starting phenix.real_space_refine on Fri Mar 15 21:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s05_10071/03_2024/6s05_10071.pdb" } resolution = 3.9 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= 0.003 sd= 0.021 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 3419 5.49 5 S 128 5.16 5 C 68103 2.51 5 N 23766 2.21 5 O 33720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "P GLU 128": "OE1" <-> "OE2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "P ARG 140": "NH1" <-> "NH2" Residue "P ARG 158": "NH1" <-> "NH2" Residue "P GLU 177": "OE1" <-> "OE2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P GLU 257": "OE1" <-> "OE2" Residue "P GLU 263": "OE1" <-> "OE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 148": "OE1" <-> "OE2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 18": "NH1" <-> "NH2" Residue "U GLU 31": "OE1" <-> "OE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 96": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 16": "NH1" <-> "NH2" Residue "g GLU 97": "OE1" <-> "OE2" Residue "h ARG 99": "NH1" <-> "NH2" Residue "i ARG 63": "NH1" <-> "NH2" Residue "j GLU 13": "OE1" <-> "OE2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n GLU 12": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n GLU 41": "OE1" <-> "OE2" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n GLU 124": "OE1" <-> "OE2" Residue "n GLU 136": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "z GLU 405": "OE1" <-> "OE2" Residue "z ARG 419": "NH1" <-> "NH2" Residue "z ARG 427": "NH1" <-> "NH2" Residue "w ARG 51": "NH1" <-> "NH2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "w ARG 73": "NH1" <-> "NH2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w ARG 79": "NH1" <-> "NH2" Residue "w GLU 80": "OE1" <-> "OE2" Residue "w ARG 87": "NH1" <-> "NH2" Residue "w ARG 88": "NH1" <-> "NH2" Residue "w ARG 96": "NH1" <-> "NH2" Residue "w ARG 111": "NH1" <-> "NH2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 247": "OE1" <-> "OE2" Residue "w ARG 303": "NH1" <-> "NH2" Residue "w ARG 330": "NH1" <-> "NH2" Residue "w ARG 333": "NH1" <-> "NH2" Residue "w ARG 342": "NH1" <-> "NH2" Residue "w ARG 404": "NH1" <-> "NH2" Residue "v GLU 4": "OE1" <-> "OE2" Residue "v ASP 6": "OD1" <-> "OD2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "o ARG 153": "NH1" <-> "NH2" Residue "o GLU 157": "OE1" <-> "OE2" Residue "o GLU 161": "OE1" <-> "OE2" Residue "o ARG 197": "NH1" <-> "NH2" Residue "o ARG 208": "NH1" <-> "NH2" Residue "o ARG 214": "NH1" <-> "NH2" Residue "o ARG 220": "NH1" <-> "NH2" Residue "o GLU 224": "OE1" <-> "OE2" Residue "o ARG 228": "NH1" <-> "NH2" Residue "o ARG 246": "NH1" <-> "NH2" Residue "o ARG 267": "NH1" <-> "NH2" Residue "o PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 402": "OE1" <-> "OE2" Residue "o ARG 427": "NH1" <-> "NH2" Residue "o GLU 434": "OE1" <-> "OE2" Residue "o ARG 446": "NH1" <-> "NH2" Residue "o GLU 448": "OE1" <-> "OE2" Residue "o ARG 466": "NH1" <-> "NH2" Residue "o ARG 468": "NH1" <-> "NH2" Residue "o ARG 482": "NH1" <-> "NH2" Residue "o ARG 485": "NH1" <-> "NH2" Residue "s GLU 254": "OE1" <-> "OE2" Residue "s GLU 294": "OE1" <-> "OE2" Residue "s GLU 300": "OE1" <-> "OE2" 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: 129144 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 67292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3146, 67292 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "'] Classifications: {'RNA': 3146} Modifications used: {'5*END': 2, 'rna2p_pur': 320, 'rna2p_pyr': 205, 'rna3p_pur': 1428, 'rna3p_pyr': 1193} Link IDs: {'rna2p': 525, 'rna3p': 2620} Chain breaks: 3 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1878 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain: "C" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3039 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 14, 'TRANS': 366} Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1399 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1742 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "J" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1486 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1002 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1045 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "N" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1719 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2176 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "Q" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1440 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1275 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1222 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "V" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 786 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Y" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 963 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 415 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "b" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1760 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 741 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 849 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 812 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "h" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 763 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "j" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 435 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "l" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 756 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "m" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 680 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "n" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "z" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 491 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "w" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3076 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 14, 'TRANS': 374} Chain: "v" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 500 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2593 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 17, 'TRANS': 304} Chain breaks: 2 Chain: "p" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "s" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 119} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "x" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2576 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "y" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3310 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 126} Chain: "g" 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A06JQ SG CYS g 44 132.856 120.328 199.766 1.00 48.89 S ATOM A06K8 SG CYS g 47 128.741 118.594 201.227 1.00 57.46 S ATOM A06RT SG CYS g 84 132.842 117.296 201.839 1.00 53.89 S ATOM A07LJ SG CYS i 19 155.119 136.436 149.523 1.00 28.45 S ATOM A07M8 SG CYS i 22 155.221 138.415 145.721 1.00 30.71 S ATOM A07P0 SG CYS i 34 153.267 134.903 146.745 1.00 27.46 S ATOM A07PI SG CYS i 37 156.997 134.629 146.053 1.00 26.44 S ATOM A08VS SG CYS l 12 151.377 64.765 86.411 1.00 47.25 S ATOM A08WR SG CYS l 17 153.802 61.378 84.480 1.00 61.46 S ATOM A099N SG CYS l 74 150.761 60.666 86.760 1.00 47.08 S ATOM A09A9 SG CYS l 77 154.399 62.873 87.769 1.00 50.07 S ATOM A09MW SG CYS m 39 116.865 107.780 197.216 1.00 43.31 S ATOM A09QK SG CYS m 57 117.558 111.683 196.349 1.00 36.82 S ATOM A0BUH SG CYS w 58 73.912 99.016 111.725 1.00138.37 S ATOM A0BV6 SG CYS w 61 78.342 99.223 113.999 1.00155.87 S ATOM A0CDY SG CYS w 143 76.494 102.857 110.852 1.00137.10 S ATOM A0CEJ SG CYS w 146 79.375 100.696 111.132 1.00137.96 S ATOM A0BML SG CYS w 19 31.948 126.208 129.496 1.00111.11 S ATOM A0BN5 SG CYS w 22 28.735 124.412 127.343 1.00107.71 S ATOM A0BQ7 SG CYS w 38 33.046 123.945 125.665 1.00121.18 S ATOM A0H8L SG CYS s 235 21.855 145.219 116.152 1.00123.78 S ATOM A0HOM SG CYS s 307 22.180 145.103 112.124 1.00142.86 S ATOM A0HS1 SG CYS s 324 24.916 124.228 103.640 1.00143.61 S Time building chain proxies: 46.96, per 1000 atoms: 0.36 Number of scatterers: 129144 At special positions: 0 Unit cell: (239.625, 231.105, 249.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 128 16.00 P 3419 15.00 O 33720 8.00 N 23766 7.00 C 68103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 47.05 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 22 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 19 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 37 " pdb=" ZN l 201 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 12 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 17 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 74 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 77 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 57 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 39 " pdb=" ZN s 401 " pdb="ZN ZN s 401 " - pdb=" SG CYS s 235 " pdb="ZN ZN s 401 " - pdb=" SG CYS s 307 " pdb=" ZN s 402 " pdb="ZN ZN s 402 " - pdb=" SG CYS s 324 " pdb=" ZN w 601 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 58 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 143 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 146 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 61 " pdb=" ZN w 602 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 19 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 22 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 38 " Number of angles added : 18 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13320 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 75 sheets defined 31.9% alpha, 13.2% beta 761 base pairs and 1525 stacking pairs defined. Time for finding SS restraints: 35.21 Creating SS restraints... Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.552A pdb=" N HIS B 38 " --> pdb=" O TYR B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.728A pdb=" N ALA B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.800A pdb=" N TYR C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 138' Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.580A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 3.926A pdb=" N ASP C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.602A pdb=" N TRP C 233 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 removed outlier: 3.733A pdb=" N HIS C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 31 through 43 removed outlier: 3.724A pdb=" N VAL D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.966A pdb=" N ALA D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.650A pdb=" N VAL D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 139 " --> pdb=" O VAL D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.679A pdb=" N LEU D 156 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 158 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.746A pdb=" N ALA D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 removed outlier: 3.801A pdb=" N LEU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 195 removed outlier: 4.204A pdb=" N GLY D 192 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR D 194 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 220 Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.650A pdb=" N TRP D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.757A pdb=" N ASN D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 320 through 328 removed outlier: 3.577A pdb=" N LEU D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.610A pdb=" N GLU D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 342 removed outlier: 4.027A pdb=" N LYS D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 360 removed outlier: 3.545A pdb=" N GLU D 357 " --> pdb=" O ALA D 353 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.927A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.018A pdb=" N ALA E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.659A pdb=" N GLY E 113 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.698A pdb=" N PHE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN E 165 " --> pdb=" O SER E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 84 removed outlier: 3.765A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 75 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL F 82 " --> pdb=" O MET F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.896A pdb=" N GLY F 119 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 155 Processing helix chain 'F' and resid 155 through 164 removed outlier: 3.853A pdb=" N ILE F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.556A pdb=" N PHE G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA G 107 " --> pdb=" O GLU G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 131 through 150 removed outlier: 4.039A pdb=" N GLN G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'H' and resid 53 through 58 Processing helix chain 'H' and resid 58 through 69 removed outlier: 4.070A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE H 64 " --> pdb=" O ARG H 60 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 removed outlier: 3.855A pdb=" N GLN H 77 " --> pdb=" O PRO H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 95 removed outlier: 3.863A pdb=" N GLU H 89 " --> pdb=" O ASN H 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 114 removed outlier: 3.856A pdb=" N GLU H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.806A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 165 through 174 Processing helix chain 'H' and resid 182 through 191 removed outlier: 3.879A pdb=" N LEU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.662A pdb=" N LEU H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR H 217 " --> pdb=" O LYS H 213 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 228 removed outlier: 4.246A pdb=" N ASP H 227 " --> pdb=" O ASP H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 247 removed outlier: 3.644A pdb=" N MET H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 24 removed outlier: 3.709A pdb=" N THR J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.521A pdb=" N ASN J 49 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU J 51 " --> pdb=" O PHE J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 85 removed outlier: 4.047A pdb=" N LEU J 79 " --> pdb=" O PRO J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 99 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.810A pdb=" N ASP J 112 " --> pdb=" O PRO J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 122 removed outlier: 3.703A pdb=" N ALA J 122 " --> pdb=" O VAL J 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 119 through 122' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.766A pdb=" N SER J 143 " --> pdb=" O LYS J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 181 removed outlier: 3.736A pdb=" N ARG J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG J 162 " --> pdb=" O LYS J 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU J 165 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS J 175 " --> pdb=" O ARG J 171 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 192 Processing helix chain 'K' and resid 26 through 30 removed outlier: 4.482A pdb=" N ALA K 29 " --> pdb=" O PHE K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 removed outlier: 4.313A pdb=" N ALA K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 105 through 121 removed outlier: 3.965A pdb=" N PHE K 109 " --> pdb=" O ASN K 105 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU K 118 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 removed outlier: 3.945A pdb=" N THR K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 184 removed outlier: 3.552A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS K 178 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY K 181 " --> pdb=" O LYS K 177 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE K 182 " --> pdb=" O LYS K 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 126 Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 removed outlier: 4.033A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 110 removed outlier: 3.858A pdb=" N ALA M 110 " --> pdb=" O ARG M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 124 Processing helix chain 'M' and resid 126 through 132 Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.505A pdb=" N MET N 45 " --> pdb=" O HIS N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.030A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 77 through 82' Processing helix chain 'N' and resid 87 through 92 Processing helix chain 'N' and resid 105 through 108 Processing helix chain 'N' and resid 131 through 141 removed outlier: 4.164A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA N 141 " --> pdb=" O LYS N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 16 through 33 removed outlier: 3.515A pdb=" N PHE O 21 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 51 removed outlier: 3.708A pdb=" N ARG O 50 " --> pdb=" O ASP O 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU O 51 " --> pdb=" O LYS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.756A pdb=" N GLN O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 110 removed outlier: 3.666A pdb=" N GLU O 103 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL O 106 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 148 through 153 removed outlier: 3.938A pdb=" N ILE O 151 " --> pdb=" O TYR O 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP O 153 " --> pdb=" O TRP O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 173 removed outlier: 3.771A pdb=" N LYS O 170 " --> pdb=" O ALA O 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER O 171 " --> pdb=" O THR O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 195 Processing helix chain 'P' and resid 10 through 15 removed outlier: 3.771A pdb=" N ARG P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 29 through 38 Processing helix chain 'P' and resid 94 through 114 removed outlier: 3.631A pdb=" N ARG P 107 " --> pdb=" O LEU P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 170 removed outlier: 3.852A pdb=" N LEU P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 180 removed outlier: 4.268A pdb=" N ARG P 179 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 199 removed outlier: 3.833A pdb=" N SER P 197 " --> pdb=" O GLU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 213 removed outlier: 3.512A pdb=" N GLU P 210 " --> pdb=" O GLN P 206 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 223 Processing helix chain 'P' and resid 223 through 228 removed outlier: 3.642A pdb=" N LEU P 227 " --> pdb=" O PHE P 223 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 223 through 228' Processing helix chain 'P' and resid 232 through 234 No H-bonds generated for 'chain 'P' and resid 232 through 234' Processing helix chain 'P' and resid 235 through 250 removed outlier: 3.981A pdb=" N ALA P 243 " --> pdb=" O ILE P 239 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU P 245 " --> pdb=" O THR P 241 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG P 248 " --> pdb=" O HIS P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 273 removed outlier: 4.687A pdb=" N LYS P 271 " --> pdb=" O ALA P 267 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR P 272 " --> pdb=" O GLU P 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 37 removed outlier: 4.247A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.722A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 109 through 114 Processing helix chain 'Q' and resid 125 through 131 Processing helix chain 'Q' and resid 149 through 153 removed outlier: 3.809A pdb=" N HIS Q 152 " --> pdb=" O ALA Q 149 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE Q 153 " --> pdb=" O VAL Q 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 149 through 153' Processing helix chain 'R' and resid 6 through 14 removed outlier: 4.096A pdb=" N ALA R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER R 13 " --> pdb=" O ARG R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 33 removed outlier: 3.668A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 40 removed outlier: 3.852A pdb=" N ALA R 40 " --> pdb=" O SER R 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 37 through 40' Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.725A pdb=" N LYS R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 84 through 89 removed outlier: 3.562A pdb=" N LEU R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 103 removed outlier: 4.220A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU R 102 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.854A pdb=" N ARG R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.780A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY R 129 " --> pdb=" O LYS R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 removed outlier: 4.290A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA R 147 " --> pdb=" O ILE R 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 45 removed outlier: 3.706A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 48 No H-bonds generated for 'chain 'S' and resid 46 through 48' Processing helix chain 'S' and resid 52 through 54 No H-bonds generated for 'chain 'S' and resid 52 through 54' Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.550A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU S 104 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR S 105 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.584A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 11 through 16' Processing helix chain 'T' and resid 27 through 32 removed outlier: 3.864A pdb=" N LEU T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS T 32 " --> pdb=" O SER T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 27 through 32' Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.739A pdb=" N GLN T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 96 No H-bonds generated for 'chain 'T' and resid 94 through 96' Processing helix chain 'T' and resid 99 through 123 removed outlier: 4.183A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE T 105 " --> pdb=" O CYS T 101 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU T 107 " --> pdb=" O GLN T 103 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA T 114 " --> pdb=" O LYS T 110 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU T 118 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 36 removed outlier: 3.650A pdb=" N ILE U 36 " --> pdb=" O THR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'U' and resid 70 through 77 removed outlier: 3.937A pdb=" N GLY U 73 " --> pdb=" O THR U 70 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU U 75 " --> pdb=" O GLN U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 103 removed outlier: 3.700A pdb=" N LYS U 89 " --> pdb=" O ALA U 85 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY U 93 " --> pdb=" O LYS U 89 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU U 94 " --> pdb=" O PHE U 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 24 removed outlier: 3.640A pdb=" N THR V 23 " --> pdb=" O VAL V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 39 Processing helix chain 'V' and resid 72 through 87 removed outlier: 3.569A pdb=" N LEU V 76 " --> pdb=" O SER V 72 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS V 81 " --> pdb=" O LYS V 77 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR V 83 " --> pdb=" O LEU V 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 62 removed outlier: 3.787A pdb=" N VAL W 62 " --> pdb=" O ASP W 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 58 through 62' Processing helix chain 'W' and resid 73 through 79 removed outlier: 4.289A pdb=" N GLU W 77 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP W 78 " --> pdb=" O LYS W 74 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY W 79 " --> pdb=" O LYS W 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 79' Processing helix chain 'W' and resid 93 through 99 Processing helix chain 'W' and resid 131 through 139 removed outlier: 3.574A pdb=" N ILE W 135 " --> pdb=" O ASP W 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 21 removed outlier: 3.893A pdb=" N ALA X 18 " --> pdb=" O LYS X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 31 removed outlier: 3.526A pdb=" N LEU X 30 " --> pdb=" O GLN X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 43 removed outlier: 3.742A pdb=" N ALA X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 117 through 123 removed outlier: 3.523A pdb=" N LYS X 122 " --> pdb=" O LEU X 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 65 Processing helix chain 'Y' and resid 78 through 80 No H-bonds generated for 'chain 'Y' and resid 78 through 80' Processing helix chain 'Y' and resid 103 through 124 removed outlier: 4.252A pdb=" N GLU Y 109 " --> pdb=" O SER Y 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL Y 114 " --> pdb=" O ALA Y 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU Y 119 " --> pdb=" O LYS Y 115 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Y 120 " --> pdb=" O LYS Y 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 10 Processing helix chain 'Z' and resid 14 through 34 removed outlier: 3.686A pdb=" N ASP Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 38 removed outlier: 3.717A pdb=" N ARG Z 38 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 35 through 38' Processing helix chain 'Z' and resid 41 through 43 No H-bonds generated for 'chain 'Z' and resid 41 through 43' Processing helix chain 'Z' and resid 44 through 70 removed outlier: 3.592A pdb=" N SER Z 50 " --> pdb=" O THR Z 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL Z 57 " --> pdb=" O CYS Z 53 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Z 64 " --> pdb=" O GLU Z 60 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 91 removed outlier: 3.971A pdb=" N ARG Z 89 " --> pdb=" O THR Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 111 Processing helix chain 'a' and resid 11 through 19 removed outlier: 4.173A pdb=" N ASN a 19 " --> pdb=" O LYS a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 54 removed outlier: 3.663A pdb=" N ASN a 42 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS a 52 " --> pdb=" O HIS a 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 72 removed outlier: 4.209A pdb=" N ALA b 42 " --> pdb=" O LYS b 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN b 61 " --> pdb=" O THR b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 107 removed outlier: 3.681A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 128 removed outlier: 4.512A pdb=" N LEU b 126 " --> pdb=" O ALA b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 133 Processing helix chain 'b' and resid 141 through 151 removed outlier: 3.663A pdb=" N GLN b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 159 removed outlier: 4.070A pdb=" N LYS b 158 " --> pdb=" O LYS b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 174 removed outlier: 4.273A pdb=" N ILE b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 177 No H-bonds generated for 'chain 'b' and resid 175 through 177' Processing helix chain 'b' and resid 180 through 190 Processing helix chain 'b' and resid 194 through 200 Processing helix chain 'b' and resid 235 through 243 removed outlier: 3.826A pdb=" N LYS b 241 " --> pdb=" O ASN b 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 21 removed outlier: 4.038A pdb=" N ALA c 15 " --> pdb=" O ASN c 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER c 20 " --> pdb=" O LEU c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 35 removed outlier: 4.301A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 removed outlier: 3.743A pdb=" N ALA c 60 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU c 62 " --> pdb=" O TYR c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 27 through 40 removed outlier: 3.589A pdb=" N ALA d 32 " --> pdb=" O ARG d 28 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS d 38 " --> pdb=" O LYS d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 63 removed outlier: 4.336A pdb=" N ARG d 62 " --> pdb=" O ILE d 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 removed outlier: 4.024A pdb=" N LYS e 64 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 88 removed outlier: 4.284A pdb=" N MET e 87 " --> pdb=" O THR e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.859A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.584A pdb=" N LEU f 45 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 64 removed outlier: 3.771A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 removed outlier: 3.523A pdb=" N HIS g 69 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.503A pdb=" N LYS g 86 " --> pdb=" O ALA g 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN g 98 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 removed outlier: 3.992A pdb=" N LYS h 29 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 46 removed outlier: 3.580A pdb=" N LYS h 38 " --> pdb=" O SER h 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 62 removed outlier: 3.842A pdb=" N ARG h 62 " --> pdb=" O ILE h 58 " (cutoff:3.500A) Processing helix chain 'h' and resid 68 through 78 removed outlier: 3.536A pdb=" N ALA h 73 " --> pdb=" O ALA h 69 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS h 74 " --> pdb=" O ARG h 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 98 removed outlier: 3.672A pdb=" N ALA h 85 " --> pdb=" O THR h 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE h 93 " --> pdb=" O GLU h 89 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA h 95 " --> pdb=" O ASN h 91 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG h 98 " --> pdb=" O ILE h 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 8 Processing helix chain 'i' and resid 50 through 56 removed outlier: 3.937A pdb=" N ARG i 55 " --> pdb=" O ALA i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 76 removed outlier: 3.881A pdb=" N LYS i 75 " --> pdb=" O SER i 71 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN i 76 " --> pdb=" O ARG i 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 15 removed outlier: 3.798A pdb=" N PHE j 11 " --> pdb=" O ASP j 7 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU j 12 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU j 13 " --> pdb=" O LYS j 9 " (cutoff:3.500A) Processing helix chain 'j' and resid 59 through 68 removed outlier: 4.011A pdb=" N GLN j 67 " --> pdb=" O LYS j 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER j 68 " --> pdb=" O LYS j 64 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 19 removed outlier: 3.939A pdb=" N LYS k 10 " --> pdb=" O SER k 6 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS k 12 " --> pdb=" O ARG k 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA k 14 " --> pdb=" O LYS k 10 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS k 15 " --> pdb=" O GLN k 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 47 removed outlier: 3.574A pdb=" N ARG l 45 " --> pdb=" O ARG l 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 15 removed outlier: 3.582A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY m 15 " --> pdb=" O GLY m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 34 removed outlier: 4.205A pdb=" N GLN m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 90 removed outlier: 3.568A pdb=" N VAL m 90 " --> pdb=" O LEU m 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 16 removed outlier: 4.372A pdb=" N PHE n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 12 through 16' Processing helix chain 'n' and resid 31 through 42 removed outlier: 3.808A pdb=" N TYR n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA n 37 " --> pdb=" O ASN n 33 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE n 38 " --> pdb=" O PHE n 34 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU n 41 " --> pdb=" O ALA n 37 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 56 removed outlier: 4.071A pdb=" N GLY n 55 " --> pdb=" O THR n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 88 removed outlier: 3.761A pdb=" N GLN n 82 " --> pdb=" O ASP n 78 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N HIS n 83 " --> pdb=" O GLN n 79 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 107 Processing helix chain 'n' and resid 127 through 132 removed outlier: 3.670A pdb=" N VAL n 132 " --> pdb=" O LEU n 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 147 through 150 Processing helix chain 'n' and resid 166 through 178 Processing helix chain 'n' and resid 211 through 222 removed outlier: 3.671A pdb=" N LEU n 215 " --> pdb=" O THR n 211 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER n 220 " --> pdb=" O SER n 216 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 385 removed outlier: 4.348A pdb=" N ARG z 384 " --> pdb=" O ALA z 380 " (cutoff:3.500A) Processing helix chain 'z' and resid 390 through 417 removed outlier: 3.592A pdb=" N LYS z 395 " --> pdb=" O GLU z 391 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS z 400 " --> pdb=" O LYS z 396 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR z 411 " --> pdb=" O ASN z 407 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN z 412 " --> pdb=" O ALA z 408 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE z 413 " --> pdb=" O ILE z 409 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG z 415 " --> pdb=" O THR z 411 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE z 417 " --> pdb=" O ILE z 413 " (cutoff:3.500A) Processing helix chain 'w' and resid 35 through 42 Processing helix chain 'w' and resid 80 through 88 Processing helix chain 'w' and resid 144 through 149 Processing helix chain 'w' and resid 169 through 175 removed outlier: 3.966A pdb=" N GLU w 175 " --> pdb=" O PHE w 171 " (cutoff:3.500A) Processing helix chain 'w' and resid 177 through 182 Processing helix chain 'w' and resid 203 through 215 removed outlier: 3.588A pdb=" N ALA w 207 " --> pdb=" O GLN w 203 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 265 Processing helix chain 'w' and resid 300 through 304 removed outlier: 3.594A pdb=" N ARG w 303 " --> pdb=" O VAL w 300 " (cutoff:3.500A) Processing helix chain 'w' and resid 311 through 315 removed outlier: 3.757A pdb=" N LEU w 315 " --> pdb=" O VAL w 312 " (cutoff:3.500A) Processing helix chain 'w' and resid 388 through 392 removed outlier: 3.789A pdb=" N VAL w 392 " --> pdb=" O ILE w 389 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 42 Processing helix chain 'v' and resid 52 through 59 Processing helix chain 'o' and resid 148 through 173 removed outlier: 3.894A pdb=" N GLU o 155 " --> pdb=" O LEU o 151 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU o 169 " --> pdb=" O LYS o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 187 through 191 Processing helix chain 'o' and resid 242 through 254 removed outlier: 4.401A pdb=" N ILE o 247 " --> pdb=" O LYS o 243 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA o 248 " --> pdb=" O LYS o 244 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP o 249 " --> pdb=" O GLN o 245 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR o 252 " --> pdb=" O ALA o 248 " (cutoff:3.500A) Processing helix chain 'o' and resid 351 through 358 removed outlier: 4.048A pdb=" N VAL o 357 " --> pdb=" O ILE o 353 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY o 358 " --> pdb=" O ASN o 354 " (cutoff:3.500A) Processing helix chain 'o' and resid 403 through 407 removed outlier: 3.655A pdb=" N GLY o 407 " --> pdb=" O VAL o 404 " (cutoff:3.500A) Processing helix chain 'o' and resid 418 through 427 removed outlier: 3.948A pdb=" N LEU o 423 " --> pdb=" O GLY o 419 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL o 424 " --> pdb=" O PRO o 420 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA o 425 " --> pdb=" O ALA o 421 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG o 427 " --> pdb=" O LEU o 423 " (cutoff:3.500A) Processing helix chain 'o' and resid 429 through 436 removed outlier: 3.507A pdb=" N ILE o 433 " --> pdb=" O PRO o 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 460 through 466 Processing helix chain 'o' and resid 480 through 492 removed outlier: 4.811A pdb=" N TYR o 486 " --> pdb=" O ARG o 482 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS o 489 " --> pdb=" O ARG o 485 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP o 490 " --> pdb=" O TYR o 486 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 8 removed outlier: 3.581A pdb=" N UNK p 7 " --> pdb=" O UNK p 4 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N UNK p 8 " --> pdb=" O UNK p 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 4 through 8' Processing helix chain 'p' and resid 80 through 85 removed outlier: 3.804A pdb=" N UNK p 84 " --> pdb=" O UNK p 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 97 Processing helix chain 's' and resid 291 through 297 Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 6.790A pdb=" N LYS B 60 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG B 64 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 42 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'B' and resid 135 through 139 removed outlier: 5.941A pdb=" N ILE B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG B 149 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 72 current: chain 'C' and resid 321 through 325 removed outlier: 6.313A pdb=" N PHE C 321 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 285 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET C 323 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 281 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR C 276 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA C 219 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 278 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 217 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C 55 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE C 359 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 57 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 106 removed outlier: 7.004A pdb=" N GLY C 91 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 104 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 89 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP C 106 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 87 " --> pdb=" O TRP C 106 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 157 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 106 removed outlier: 7.004A pdb=" N GLY C 91 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 104 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 89 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TRP C 106 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL C 87 " --> pdb=" O TRP C 106 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 86 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 201 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 227 removed outlier: 3.927A pdb=" N GLY C 225 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.850A pdb=" N VAL D 8 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASN D 18 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 186 through 187 Processing sheet with id=AB1, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 48 removed outlier: 3.700A pdb=" N VAL E 46 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 11 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 28 Processing sheet with id=AB6, first strand: chain 'F' and resid 133 through 136 removed outlier: 3.722A pdb=" N TYR F 86 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS F 87 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS F 184 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS F 89 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AB8, first strand: chain 'G' and resid 51 through 53 removed outlier: 4.945A pdb=" N VAL G 39 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 63 through 66 Processing sheet with id=AC1, first strand: chain 'H' and resid 177 through 180 Processing sheet with id=AC2, first strand: chain 'J' and resid 101 through 103 removed outlier: 6.065A pdb=" N VAL J 6 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL J 35 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE J 8 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC4, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.522A pdb=" N LEU O 199 " --> pdb=" O LYS K 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC6, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AC7, first strand: chain 'L' and resid 22 through 25 removed outlier: 6.518A pdb=" N ALA L 99 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE L 102 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 85 through 86 removed outlier: 6.436A pdb=" N PHE L 92 " --> pdb=" O LEU v 20 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL v 22 " --> pdb=" O PHE L 92 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR L 94 " --> pdb=" O VAL v 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.096A pdb=" N SER L 133 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLY L 116 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL L 135 " --> pdb=" O GLY L 116 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 56 through 59 removed outlier: 7.809A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 101 through 103 removed outlier: 6.174A pdb=" N VAL N 125 " --> pdb=" O GLU N 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 36 through 39 removed outlier: 4.373A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR O 127 " --> pdb=" O ASP O 124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP O 124 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU O 131 " --> pdb=" O TRP O 120 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP O 120 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE O 133 " --> pdb=" O SER O 118 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER O 118 " --> pdb=" O ILE O 133 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL O 135 " --> pdb=" O LEU O 116 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU O 116 " --> pdb=" O VAL O 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 74 through 79 removed outlier: 3.691A pdb=" N ALA P 76 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL P 53 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AD6, first strand: chain 'Q' and resid 121 through 122 removed outlier: 6.474A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 22 through 23 Processing sheet with id=AD8, first strand: chain 'S' and resid 56 through 63 removed outlier: 5.470A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA S 31 " --> pdb=" O LYS S 5 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 87 through 91 removed outlier: 4.611A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 39 through 41 removed outlier: 8.267A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER T 71 " --> pdb=" O THR T 68 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 139 through 141 removed outlier: 3.749A pdb=" N TYR b 75 " --> pdb=" O VAL T 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 14 through 22 removed outlier: 3.751A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS U 145 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL U 119 " --> pdb=" O HIS U 145 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU U 147 " --> pdb=" O ILE U 117 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE U 117 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL U 149 " --> pdb=" O SER U 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'U' and resid 125 through 131 removed outlier: 3.680A pdb=" N GLN U 125 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG U 135 " --> pdb=" O ARG U 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 54 through 58 removed outlier: 7.815A pdb=" N TYR V 103 " --> pdb=" O THR V 14 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR V 16 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU V 105 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP V 18 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.912A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN W 111 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS W 109 " --> pdb=" O ARG W 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AE9, first strand: chain 'X' and resid 94 through 99 removed outlier: 6.423A pdb=" N VAL X 85 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N LEU X 99 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N ASP X 83 " --> pdb=" O LEU X 99 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA X 79 " --> pdb=" O VAL X 73 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL X 73 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL X 85 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N GLU X 67 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU X 55 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 70 through 76 removed outlier: 6.507A pdb=" N ALA Y 44 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE Y 25 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE Y 46 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL Y 23 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N TYR Y 85 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N VAL Y 12 " --> pdb=" O THR Y 83 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR Y 83 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 83 through 87 Processing sheet with id=AF3, first strand: chain 'b' and resid 135 through 136 Processing sheet with id=AF4, first strand: chain 'b' and resid 153 through 154 Processing sheet with id=AF5, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.767A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 49 through 50 Processing sheet with id=AF7, first strand: chain 'd' and resid 14 through 15 removed outlier: 3.647A pdb=" N ILE d 14 " --> pdb=" O LEU d 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU d 71 " --> pdb=" O ILE d 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'e' and resid 72 through 76 Processing sheet with id=AF9, first strand: chain 'f' and resid 9 through 18 removed outlier: 5.398A pdb=" N HIS f 13 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS f 31 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL f 27 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA f 83 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA f 55 " --> pdb=" O LYS f 63 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AG2, first strand: chain 'i' and resid 16 through 18 Processing sheet with id=AG3, first strand: chain 'j' and resid 3 through 4 removed outlier: 4.908A pdb=" N THR j 22 " --> pdb=" O ARG j 46 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA j 23 " --> pdb=" O LYS j 74 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'l' and resid 3 through 4 Processing sheet with id=AG5, first strand: chain 'l' and resid 7 through 10 removed outlier: 3.524A pdb=" N THR l 10 " --> pdb=" O THR l 21 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL l 68 " --> pdb=" O LEU l 85 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'm' and resid 47 through 49 Processing sheet with id=AG7, first strand: chain 'n' and resid 3 through 5 removed outlier: 5.846A pdb=" N THR n 3 " --> pdb=" O THR n 206 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL n 198 " --> pdb=" O VAL n 205 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'n' and resid 17 through 19 Processing sheet with id=AG9, first strand: chain 'n' and resid 64 through 65 removed outlier: 3.570A pdb=" N ALA n 64 " --> pdb=" O LEU n 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU n 70 " --> pdb=" O GLN n 95 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 108 through 110 removed outlier: 6.407A pdb=" N ALA n 115 " --> pdb=" O PHE n 138 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'n' and resid 152 through 154 Processing sheet with id=AH3, first strand: chain 'w' and resid 52 through 57 removed outlier: 5.737A pdb=" N ALA w 53 " --> pdb=" O ILE w 137 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE w 139 " --> pdb=" O ALA w 53 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE w 55 " --> pdb=" O ILE w 139 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN w 130 " --> pdb=" O VAL w 118 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL w 118 " --> pdb=" O GLN w 130 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE w 132 " --> pdb=" O LEU w 116 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG w 113 " --> pdb=" O ILE w 103 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'w' and resid 189 through 192 removed outlier: 3.545A pdb=" N THR w 158 " --> pdb=" O PHE w 242 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'w' and resid 220 through 222 Processing sheet with id=AH6, first strand: chain 'w' and resid 256 through 257 removed outlier: 7.197A pdb=" N GLN w 284 " --> pdb=" O SER w 277 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'w' and resid 353 through 354 removed outlier: 3.809A pdb=" N ALA w 341 " --> pdb=" O ILE w 319 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'w' and resid 329 through 330 removed outlier: 3.602A pdb=" N ARG w 333 " --> pdb=" O ARG w 330 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'v' and resid 4 through 5 removed outlier: 4.132A pdb=" N GLU v 4 " --> pdb=" O ILE v 13 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'o' and resid 201 through 203 Processing sheet with id=AI2, first strand: chain 'p' and resid 59 through 60 removed outlier: 5.416A pdb=" N UNK p 102 " --> pdb=" O UNK p 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 's' and resid 240 through 241 1475 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1883 hydrogen bonds 3132 hydrogen bond angles 0 basepair planarities 761 basepair parallelities 1525 stacking parallelities Total time for adding SS restraints: 152.32 Time building geometry restraints manager: 51.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16264 1.32 - 1.44: 56165 1.44 - 1.57: 59405 1.57 - 1.69: 6836 1.69 - 1.82: 198 Bond restraints: 138868 Sorted by residual: bond pdb=" N PRO w 25 " pdb=" CA PRO w 25 " ideal model delta sigma weight residual 1.469 1.702 -0.233 1.28e-02 6.10e+03 3.32e+02 bond pdb=" N PRO w 298 " pdb=" CA PRO w 298 " ideal model delta sigma weight residual 1.469 1.687 -0.218 1.25e-02 6.40e+03 3.04e+02 bond pdb=" C CYS s 307 " pdb=" N PRO s 308 " ideal model delta sigma weight residual 1.335 1.506 -0.170 1.36e-02 5.41e+03 1.57e+02 bond pdb=" C SER w 297 " pdb=" N PRO w 298 " ideal model delta sigma weight residual 1.337 1.448 -0.111 1.06e-02 8.90e+03 1.11e+02 bond pdb=" C CYS w 143 " pdb=" N PRO w 144 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.35e+01 ... (remaining 138863 not shown) Histogram of bond angle deviations from ideal: 83.63 - 95.35: 3 95.35 - 107.08: 24270 107.08 - 118.80: 108600 118.80 - 130.52: 69863 130.52 - 142.25: 1589 Bond angle restraints: 204325 Sorted by residual: angle pdb=" C SER w 297 " pdb=" N PRO w 298 " pdb=" CA PRO w 298 " ideal model delta sigma weight residual 120.04 140.09 -20.05 1.08e+00 8.57e-01 3.45e+02 angle pdb=" N ALA s 247 " pdb=" CA ALA s 247 " pdb=" C ALA s 247 " ideal model delta sigma weight residual 108.73 83.63 25.10 1.63e+00 3.76e-01 2.37e+02 angle pdb=" C THR o 367 " pdb=" N PRO o 368 " pdb=" CA PRO o 368 " ideal model delta sigma weight residual 119.84 137.47 -17.63 1.25e+00 6.40e-01 1.99e+02 angle pdb=" C LEU o 409 " pdb=" N PRO o 410 " pdb=" CA PRO o 410 " ideal model delta sigma weight residual 120.79 139.02 -18.23 1.30e+00 5.92e-01 1.97e+02 angle pdb=" C THR w 24 " pdb=" N PRO w 25 " pdb=" CA PRO w 25 " ideal model delta sigma weight residual 119.84 136.75 -16.91 1.25e+00 6.40e-01 1.83e+02 ... (remaining 204320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 78643 35.94 - 71.89: 8343 71.89 - 107.83: 855 107.83 - 143.78: 19 143.78 - 179.72: 42 Dihedral angle restraints: 87902 sinusoidal: 67262 harmonic: 20640 Sorted by residual: dihedral pdb=" C ALA s 247 " pdb=" N ALA s 247 " pdb=" CA ALA s 247 " pdb=" CB ALA s 247 " ideal model delta harmonic sigma weight residual -122.60 -89.27 -33.33 0 2.50e+00 1.60e-01 1.78e+02 dihedral pdb=" N HIS s 248 " pdb=" C HIS s 248 " pdb=" CA HIS s 248 " pdb=" CB HIS s 248 " ideal model delta harmonic sigma weight residual 122.80 97.90 24.90 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" C4' U A1288 " pdb=" C3' U A1288 " pdb=" C2' U A1288 " pdb=" C1' U A1288 " ideal model delta sinusoidal sigma weight residual -35.00 31.31 -66.31 1 8.00e+00 1.56e-02 8.97e+01 ... (remaining 87899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 25097 0.137 - 0.275: 514 0.275 - 0.412: 34 0.412 - 0.549: 3 0.549 - 0.687: 3 Chirality restraints: 25651 Sorted by residual: chirality pdb=" CA ALA s 247 " pdb=" N ALA s 247 " pdb=" C ALA s 247 " pdb=" CB ALA s 247 " both_signs ideal model delta sigma weight residual False 2.48 3.17 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB THR o 179 " pdb=" CA THR o 179 " pdb=" OG1 THR o 179 " pdb=" CG2 THR o 179 " both_signs ideal model delta sigma weight residual False 2.55 1.88 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA HIS s 248 " pdb=" N HIS s 248 " pdb=" C HIS s 248 " pdb=" CB HIS s 248 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.04e+00 ... (remaining 25648 not shown) Planarity restraints: 13188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU W 126 " -0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C LEU W 126 " 0.087 2.00e-02 2.50e+03 pdb=" O LEU W 126 " -0.033 2.00e-02 2.50e+03 pdb=" N THR W 127 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 945 " 0.007 2.00e-02 2.50e+03 3.25e-02 2.38e+01 pdb=" N1 C A 945 " -0.007 2.00e-02 2.50e+03 pdb=" C2 C A 945 " -0.082 2.00e-02 2.50e+03 pdb=" O2 C A 945 " 0.049 2.00e-02 2.50e+03 pdb=" N3 C A 945 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C A 945 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C A 945 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C A 945 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C A 945 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER s 306 " -0.024 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C SER s 306 " 0.083 2.00e-02 2.50e+03 pdb=" O SER s 306 " -0.030 2.00e-02 2.50e+03 pdb=" N CYS s 307 " -0.028 2.00e-02 2.50e+03 ... (remaining 13185 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.70: 9 1.70 - 2.50: 1045 2.50 - 3.30: 136699 3.30 - 4.10: 386561 4.10 - 4.90: 597266 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1121580 Sorted by model distance: nonbonded pdb=" NH1 ARG n 4 " pdb=" CE LYS s 233 " model vdw 0.906 3.520 nonbonded pdb=" O LYS o 430 " pdb=" OE1 GLU o 434 " model vdw 0.946 3.040 nonbonded pdb=" OE2 GLU o 402 " pdb=" CG1 VAL o 404 " model vdw 1.416 3.460 nonbonded pdb=" CE1 PHE s 305 " pdb=" O GLY s 315 " model vdw 1.541 3.340 nonbonded pdb=" CG2 ILE b 89 " pdb=" CZ PHE b 229 " model vdw 1.569 3.760 ... (remaining 1121575 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 group one per residue 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: 1.710 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: 0.070 Extract box with map and model: 13.800 Check model and map are aligned: 1.340 Set scattering table: 0.830 Process input model: 385.350 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 408.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.233 138868 Z= 0.510 Angle : 1.034 25.101 204325 Z= 0.536 Chirality : 0.054 0.687 25651 Planarity : 0.007 0.109 13188 Dihedral : 22.892 179.720 74582 Min Nonbonded Distance : 0.906 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.36 % Favored : 90.41 % Rotamer: Outliers : 1.92 % Allowed : 13.97 % Favored : 84.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.08), residues: 6829 helix: -3.83 (0.07), residues: 2022 sheet: -2.61 (0.15), residues: 945 loop : -2.93 (0.08), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP P 95 HIS 0.026 0.002 HIS C 273 PHE 0.032 0.003 PHE M 115 TYR 0.050 0.003 TYR N 52 ARG 0.016 0.001 ARG b 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1244 time to evaluate : 5.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.8417 (m-80) cc_final: 0.8192 (m-80) REVERT: B 204 MET cc_start: 0.8705 (mtt) cc_final: 0.8296 (mtt) REVERT: C 7 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6086 (tt0) REVERT: C 29 VAL cc_start: 0.9133 (t) cc_final: 0.8862 (m) REVERT: C 62 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7508 (ptm160) REVERT: C 332 ARG cc_start: 0.7703 (pmt170) cc_final: 0.7434 (ptp-110) REVERT: C 358 TRP cc_start: 0.9003 (t60) cc_final: 0.8722 (t60) REVERT: C 360 ASP cc_start: 0.7726 (t0) cc_final: 0.7164 (t0) REVERT: C 371 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8335 (mm-40) REVERT: E 11 ASP cc_start: 0.7092 (p0) cc_final: 0.6602 (p0) REVERT: F 8 GLN cc_start: 0.7923 (mm110) cc_final: 0.6873 (mm-40) REVERT: F 63 LYS cc_start: 0.4645 (pttp) cc_final: 0.4403 (mtpt) REVERT: F 78 MET cc_start: 0.7479 (ttp) cc_final: 0.7247 (tmm) REVERT: F 153 ASP cc_start: 0.7956 (m-30) cc_final: 0.7606 (m-30) REVERT: H 43 LYS cc_start: 0.7422 (mttm) cc_final: 0.5838 (pttp) REVERT: K 11 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8053 (mttp) REVERT: L 23 MET cc_start: 0.8584 (ptt) cc_final: 0.8366 (ptt) REVERT: L 49 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8634 (pp) REVERT: L 70 ARG cc_start: 0.7584 (ptm-80) cc_final: 0.7341 (ptt-90) REVERT: M 47 ASP cc_start: 0.8193 (t0) cc_final: 0.7942 (t0) REVERT: M 121 MET cc_start: 0.7905 (tmm) cc_final: 0.7395 (tmm) REVERT: O 8 GLU cc_start: 0.8176 (pt0) cc_final: 0.7942 (pt0) REVERT: O 24 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7503 (ttt90) REVERT: P 151 GLN cc_start: 0.7544 (tp40) cc_final: 0.7291 (mm110) REVERT: P 183 TRP cc_start: 0.8281 (t60) cc_final: 0.8027 (t-100) REVERT: Q 78 ASN cc_start: 0.7987 (m-40) cc_final: 0.7513 (t0) REVERT: Q 182 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8467 (mmmt) REVERT: R 31 GLU cc_start: 0.8519 (tp30) cc_final: 0.8218 (tp30) REVERT: S 129 ILE cc_start: 0.8236 (mt) cc_final: 0.7782 (mt) REVERT: S 166 LYS cc_start: 0.8344 (ptpt) cc_final: 0.8085 (pttt) REVERT: U 34 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8861 (mm-40) REVERT: U 55 GLN cc_start: 0.8091 (mp10) cc_final: 0.7764 (mp10) REVERT: U 64 ASN cc_start: 0.9086 (p0) cc_final: 0.8547 (p0) REVERT: U 155 GLU cc_start: 0.5026 (mm-30) cc_final: 0.4705 (mm-30) REVERT: V 13 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7448 (mmmt) REVERT: V 89 LEU cc_start: 0.8715 (mp) cc_final: 0.8348 (mp) REVERT: V 101 ASN cc_start: 0.8776 (m110) cc_final: 0.8499 (m-40) REVERT: W 106 ASP cc_start: 0.8067 (p0) cc_final: 0.7832 (p0) REVERT: X 17 LYS cc_start: 0.8668 (tttp) cc_final: 0.8239 (tttt) REVERT: X 38 GLU cc_start: 0.7752 (mp0) cc_final: 0.7480 (mp0) REVERT: Y 102 GLU cc_start: 0.6893 (mp0) cc_final: 0.6618 (mm-30) REVERT: Y 126 LYS cc_start: 0.6073 (mmtt) cc_final: 0.5166 (tppt) REVERT: Z 51 ILE cc_start: 0.9168 (mt) cc_final: 0.8940 (tt) REVERT: a 22 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8061 (mttt) REVERT: a 41 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8320 (mtm-85) REVERT: b 138 TYR cc_start: 0.8837 (m-80) cc_final: 0.8302 (m-10) REVERT: c 47 ASN cc_start: 0.9032 (p0) cc_final: 0.8802 (p0) REVERT: c 57 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7285 (mt-10) REVERT: d 35 GLU cc_start: 0.8323 (tp30) cc_final: 0.7814 (tp30) REVERT: d 57 GLN cc_start: 0.8235 (pt0) cc_final: 0.7515 (tm-30) REVERT: d 75 ILE cc_start: 0.9129 (mp) cc_final: 0.8827 (tt) REVERT: e 83 GLU cc_start: 0.8027 (pp20) cc_final: 0.7747 (pp20) REVERT: f 23 ASN cc_start: 0.9309 (p0) cc_final: 0.9043 (p0) REVERT: f 44 TYR cc_start: 0.8640 (m-80) cc_final: 0.8213 (m-80) REVERT: f 53 TYR cc_start: 0.9261 (p90) cc_final: 0.8979 (p90) REVERT: f 63 LYS cc_start: 0.8946 (tppp) cc_final: 0.8495 (tptt) REVERT: h 43 LEU cc_start: 0.9471 (tp) cc_final: 0.9132 (tp) REVERT: i 13 ASN cc_start: 0.8997 (p0) cc_final: 0.8399 (p0) REVERT: j 3 ARG cc_start: 0.8464 (ptp-170) cc_final: 0.8211 (mtp-110) REVERT: j 27 ILE cc_start: 0.9113 (tp) cc_final: 0.8898 (tt) REVERT: j 46 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7744 (tpt170) REVERT: k 40 LYS cc_start: 0.8933 (mttt) cc_final: 0.8485 (mttp) REVERT: l 45 ARG cc_start: 0.8868 (tpt-90) cc_final: 0.8551 (tpt170) REVERT: m 18 TYR cc_start: 0.9033 (m-80) cc_final: 0.8806 (m-80) REVERT: n 1 MET cc_start: 0.3622 (mmt) cc_final: 0.3037 (mmt) REVERT: n 9 ASN cc_start: 0.8279 (t0) cc_final: 0.7811 (t0) REVERT: n 16 PHE cc_start: 0.7951 (m-80) cc_final: 0.7734 (m-80) REVERT: n 62 MET cc_start: 0.8435 (mmm) cc_final: 0.7591 (mmm) REVERT: n 104 LEU cc_start: 0.8448 (mt) cc_final: 0.8120 (mm) REVERT: z 385 MET cc_start: 0.6840 (ptm) cc_final: 0.6496 (ptt) REVERT: w 114 ILE cc_start: 0.7665 (mm) cc_final: 0.7204 (tt) REVERT: w 162 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6556 (mmt90) REVERT: w 206 HIS cc_start: 0.6512 (m170) cc_final: 0.6190 (m170) REVERT: v 14 TYR cc_start: 0.8570 (m-80) cc_final: 0.8285 (m-80) REVERT: o 171 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.4017 (pp20) REVERT: o 263 TYR cc_start: 0.1406 (t80) cc_final: 0.0975 (p90) REVERT: s 231 ARG cc_start: 0.0807 (OUTLIER) cc_final: -0.0601 (ttp-170) outliers start: 112 outliers final: 60 residues processed: 1324 average time/residue: 1.1875 time to fit residues: 2665.6800 Evaluate side-chains 1008 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 944 time to evaluate : 6.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 PRO Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain W residue 127 THR Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 41 PHE Chi-restraints excluded: chain m residue 42 CYS Chi-restraints excluded: chain m residue 60 CYS Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 86 ASN Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain w residue 65 LEU Chi-restraints excluded: chain w residue 162 ARG Chi-restraints excluded: chain w residue 221 LYS Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 249 VAL Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 171 GLU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 213 PHE Chi-restraints excluded: chain o residue 304 LYS Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 409 LEU Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 500 ASN Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 233 LYS Chi-restraints excluded: chain s residue 296 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 870 optimal weight: 7.9990 chunk 781 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 527 optimal weight: 1.9990 chunk 417 optimal weight: 7.9990 chunk 808 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 491 optimal weight: 3.9990 chunk 601 optimal weight: 3.9990 chunk 936 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN C 313 HIS D 48 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN O 86 ASN R 75 HIS R 141 HIS S 46 GLN V 87 ASN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN Y 36 HIS Y 40 HIS b 64 GLN ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 ASN b 172 ASN ** b 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 GLN e 98 HIS f 5 HIS f 88 ASN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 40 GLN j 57 ASN k 19 GLN k 38 ASN l 82 GLN ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 86 ASN ** n 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 402 GLN w 60 ASN ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 170 GLN o 395 ASN s 277 GLN s 282 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 138868 Z= 0.197 Angle : 0.620 16.992 204325 Z= 0.321 Chirality : 0.037 0.266 25651 Planarity : 0.005 0.149 13188 Dihedral : 23.419 179.951 60920 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.85 % Favored : 93.09 % Rotamer: Outliers : 3.55 % Allowed : 19.66 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.09), residues: 6829 helix: -2.68 (0.09), residues: 2036 sheet: -2.21 (0.15), residues: 944 loop : -2.55 (0.09), residues: 3849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 233 HIS 0.009 0.001 HIS w 222 PHE 0.022 0.001 PHE v 8 TYR 0.028 0.002 TYR J 167 ARG 0.029 0.000 ARG n 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1070 time to evaluate : 6.407 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6140 (tt0) REVERT: C 123 TYR cc_start: 0.9033 (p90) cc_final: 0.8691 (p90) REVERT: C 261 MET cc_start: 0.6903 (mtm) cc_final: 0.6629 (mtm) REVERT: C 332 ARG cc_start: 0.7859 (pmt170) cc_final: 0.7469 (ptp-110) REVERT: C 360 ASP cc_start: 0.7590 (t0) cc_final: 0.7274 (t0) REVERT: E 9 MET cc_start: 0.7817 (mtm) cc_final: 0.7338 (ptp) REVERT: E 11 ASP cc_start: 0.6897 (p0) cc_final: 0.6476 (p0) REVERT: E 57 PHE cc_start: 0.2766 (m-10) cc_final: 0.1729 (m-10) REVERT: F 63 LYS cc_start: 0.4468 (pttp) cc_final: 0.4267 (mtpt) REVERT: F 78 MET cc_start: 0.7169 (ttp) cc_final: 0.6715 (tmm) REVERT: F 153 ASP cc_start: 0.7965 (m-30) cc_final: 0.7643 (m-30) REVERT: G 46 ARG cc_start: 0.8197 (tmt170) cc_final: 0.7475 (ttp-110) REVERT: K 9 ILE cc_start: 0.8648 (tp) cc_final: 0.8329 (tp) REVERT: K 11 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8058 (mttm) REVERT: L 49 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8570 (pp) REVERT: M 14 LEU cc_start: 0.8050 (mt) cc_final: 0.7829 (mm) REVERT: M 47 ASP cc_start: 0.8411 (t0) cc_final: 0.8135 (t0) REVERT: M 121 MET cc_start: 0.7951 (tmm) cc_final: 0.7437 (tmm) REVERT: N 45 MET cc_start: 0.8879 (mmm) cc_final: 0.8645 (mmt) REVERT: O 24 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7373 (ttt90) REVERT: O 77 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7547 (tttt) REVERT: P 151 GLN cc_start: 0.7450 (tp40) cc_final: 0.7239 (mm110) REVERT: P 183 TRP cc_start: 0.8321 (t60) cc_final: 0.8014 (t-100) REVERT: Q 78 ASN cc_start: 0.7958 (m-40) cc_final: 0.7456 (t0) REVERT: R 31 GLU cc_start: 0.8545 (tp30) cc_final: 0.8212 (tp30) REVERT: S 166 LYS cc_start: 0.8250 (ptpt) cc_final: 0.8020 (pttt) REVERT: U 34 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9024 (mm-40) REVERT: U 64 ASN cc_start: 0.9001 (p0) cc_final: 0.8499 (p0) REVERT: U 155 GLU cc_start: 0.5038 (mm-30) cc_final: 0.4729 (mm-30) REVERT: V 89 LEU cc_start: 0.8507 (mp) cc_final: 0.8272 (mp) REVERT: X 17 LYS cc_start: 0.8538 (tttp) cc_final: 0.8010 (tttt) REVERT: X 38 GLU cc_start: 0.7652 (mp0) cc_final: 0.7360 (mp0) REVERT: Y 126 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5092 (tppt) REVERT: a 22 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8142 (mttt) REVERT: c 58 TYR cc_start: 0.8353 (t80) cc_final: 0.8131 (t80) REVERT: d 25 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: d 35 GLU cc_start: 0.8250 (tp30) cc_final: 0.7802 (tp30) REVERT: d 57 GLN cc_start: 0.8077 (pt0) cc_final: 0.7448 (tm-30) REVERT: d 75 ILE cc_start: 0.9136 (mp) cc_final: 0.8767 (tt) REVERT: e 30 GLU cc_start: 0.8181 (tp30) cc_final: 0.7686 (tp30) REVERT: e 83 GLU cc_start: 0.7995 (pp20) cc_final: 0.7710 (pp20) REVERT: f 8 TYR cc_start: 0.8838 (p90) cc_final: 0.8588 (p90) REVERT: f 44 TYR cc_start: 0.8586 (m-80) cc_final: 0.8279 (m-80) REVERT: f 53 TYR cc_start: 0.9340 (p90) cc_final: 0.9107 (p90) REVERT: f 63 LYS cc_start: 0.8886 (tppp) cc_final: 0.8565 (tptm) REVERT: h 43 LEU cc_start: 0.9526 (tp) cc_final: 0.9093 (tp) REVERT: h 68 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7717 (mmm160) REVERT: i 13 ASN cc_start: 0.8835 (p0) cc_final: 0.8406 (p0) REVERT: j 51 LEU cc_start: 0.9408 (tp) cc_final: 0.9154 (tt) REVERT: k 40 LYS cc_start: 0.8939 (mttt) cc_final: 0.8481 (mttp) REVERT: k 50 ASN cc_start: 0.8039 (m-40) cc_final: 0.7832 (m-40) REVERT: l 45 ARG cc_start: 0.8835 (tpt-90) cc_final: 0.8579 (tpt170) REVERT: m 5 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8148 (p) REVERT: m 14 TYR cc_start: 0.9011 (m-80) cc_final: 0.8355 (m-80) REVERT: m 18 TYR cc_start: 0.8981 (m-80) cc_final: 0.8604 (m-80) REVERT: n 9 ASN cc_start: 0.8312 (t0) cc_final: 0.7788 (t0) REVERT: n 19 LEU cc_start: 0.8285 (tp) cc_final: 0.7753 (tt) REVERT: n 62 MET cc_start: 0.8085 (mmm) cc_final: 0.7359 (mmm) REVERT: z 385 MET cc_start: 0.6779 (ptm) cc_final: 0.6443 (ptt) REVERT: w 114 ILE cc_start: 0.7637 (mm) cc_final: 0.7197 (tt) REVERT: w 275 LEU cc_start: 0.8096 (mm) cc_final: 0.7743 (tp) REVERT: v 14 TYR cc_start: 0.8514 (m-80) cc_final: 0.8260 (m-80) REVERT: s 231 ARG cc_start: 0.1057 (OUTLIER) cc_final: -0.0027 (ttp-170) outliers start: 207 outliers final: 145 residues processed: 1182 average time/residue: 1.0762 time to fit residues: 2220.9773 Evaluate side-chains 1120 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 970 time to evaluate : 6.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 46 GLN Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 47 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 402 GLN Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 249 VAL Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain v residue 7 SER Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 202 VAL Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 213 PHE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 409 LEU Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain s residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 520 optimal weight: 10.0000 chunk 290 optimal weight: 30.0000 chunk 779 optimal weight: 0.0050 chunk 637 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 937 optimal weight: 8.9990 chunk 1013 optimal weight: 10.0000 chunk 835 optimal weight: 7.9990 chunk 930 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 752 optimal weight: 1.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN C 173 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN E 7 ASN G 80 ASN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN P 57 ASN P 274 GLN S 46 GLN T 98 HIS ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN Y 78 ASN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN b 80 GLN ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 HIS ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN j 40 GLN k 19 GLN n 11 ASN ** n 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 406 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 138868 Z= 0.338 Angle : 0.696 16.434 204325 Z= 0.354 Chirality : 0.040 0.427 25651 Planarity : 0.005 0.148 13188 Dihedral : 23.321 179.911 60868 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.39 % Favored : 90.57 % Rotamer: Outliers : 5.66 % Allowed : 21.15 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.09), residues: 6829 helix: -2.16 (0.10), residues: 2032 sheet: -2.15 (0.16), residues: 935 loop : -2.44 (0.09), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 85 HIS 0.011 0.001 HIS C 68 PHE 0.029 0.002 PHE S 30 TYR 0.036 0.002 TYR J 167 ARG 0.011 0.001 ARG L 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 978 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.8388 (m-80) cc_final: 0.7600 (m-10) REVERT: B 204 MET cc_start: 0.8863 (mtt) cc_final: 0.8262 (mtt) REVERT: C 7 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6125 (tt0) REVERT: C 123 TYR cc_start: 0.9131 (p90) cc_final: 0.8777 (p90) REVERT: C 261 MET cc_start: 0.7050 (mtm) cc_final: 0.6728 (mtm) REVERT: C 332 ARG cc_start: 0.7803 (pmt170) cc_final: 0.7514 (ptp-110) REVERT: D 286 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8555 (t) REVERT: F 7 GLU cc_start: 0.7674 (pp20) cc_final: 0.7415 (pp20) REVERT: F 9 GLN cc_start: 0.7162 (mp10) cc_final: 0.6650 (mp10) REVERT: F 63 LYS cc_start: 0.4490 (pttp) cc_final: 0.4164 (mtpt) REVERT: F 78 MET cc_start: 0.7073 (ttp) cc_final: 0.6850 (tmm) REVERT: F 153 ASP cc_start: 0.8057 (m-30) cc_final: 0.7740 (m-30) REVERT: G 46 ARG cc_start: 0.8268 (tmt170) cc_final: 0.7569 (ttp-110) REVERT: H 43 LYS cc_start: 0.7315 (mttm) cc_final: 0.6839 (mmtm) REVERT: H 130 TYR cc_start: 0.7922 (m-80) cc_final: 0.7622 (m-80) REVERT: K 11 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8138 (mttm) REVERT: L 49 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8538 (pp) REVERT: M 14 LEU cc_start: 0.8148 (mt) cc_final: 0.7859 (mm) REVERT: M 47 ASP cc_start: 0.8374 (t0) cc_final: 0.8092 (t0) REVERT: M 121 MET cc_start: 0.8058 (tmm) cc_final: 0.7579 (tmm) REVERT: O 24 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7487 (ttt90) REVERT: O 60 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9125 (p) REVERT: O 77 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7605 (tttt) REVERT: P 151 GLN cc_start: 0.7629 (tp40) cc_final: 0.7390 (mm110) REVERT: P 183 TRP cc_start: 0.8417 (t60) cc_final: 0.8046 (t-100) REVERT: Q 78 ASN cc_start: 0.7968 (m-40) cc_final: 0.7521 (t0) REVERT: R 31 GLU cc_start: 0.8549 (tp30) cc_final: 0.8278 (tp30) REVERT: S 91 TYR cc_start: 0.7379 (t80) cc_final: 0.7064 (t80) REVERT: S 166 LYS cc_start: 0.8306 (ptpt) cc_final: 0.8086 (pttt) REVERT: U 34 GLN cc_start: 0.9285 (mm-40) cc_final: 0.9053 (mm-40) REVERT: V 13 LYS cc_start: 0.7690 (mmtp) cc_final: 0.7312 (mmmt) REVERT: W 91 ASN cc_start: 0.8794 (p0) cc_final: 0.8449 (p0) REVERT: X 17 LYS cc_start: 0.8596 (tttp) cc_final: 0.8201 (tttt) REVERT: X 38 GLU cc_start: 0.7698 (mp0) cc_final: 0.7462 (mp0) REVERT: Y 126 LYS cc_start: 0.5952 (mmtt) cc_final: 0.5157 (tppt) REVERT: a 22 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8165 (mttt) REVERT: c 58 TYR cc_start: 0.8456 (t80) cc_final: 0.8197 (t80) REVERT: d 21 HIS cc_start: 0.8428 (t-90) cc_final: 0.7961 (t70) REVERT: d 25 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8040 (m-10) REVERT: d 57 GLN cc_start: 0.8247 (pt0) cc_final: 0.7637 (tm-30) REVERT: e 83 GLU cc_start: 0.8051 (pp20) cc_final: 0.7684 (pp20) REVERT: f 44 TYR cc_start: 0.8600 (m-80) cc_final: 0.8199 (m-80) REVERT: f 53 TYR cc_start: 0.9374 (p90) cc_final: 0.9075 (p90) REVERT: g 57 LEU cc_start: 0.9277 (mt) cc_final: 0.8967 (mt) REVERT: h 43 LEU cc_start: 0.9559 (tp) cc_final: 0.9297 (tp) REVERT: i 13 ASN cc_start: 0.8876 (p0) cc_final: 0.8446 (p0) REVERT: j 51 LEU cc_start: 0.9422 (tp) cc_final: 0.9184 (tt) REVERT: k 40 LYS cc_start: 0.8989 (mttt) cc_final: 0.8547 (mttp) REVERT: l 11 TYR cc_start: 0.8596 (t80) cc_final: 0.8332 (t80) REVERT: l 45 ARG cc_start: 0.8907 (tpt-90) cc_final: 0.8615 (tpt170) REVERT: m 18 TYR cc_start: 0.9096 (m-80) cc_final: 0.8745 (m-80) REVERT: n 9 ASN cc_start: 0.8306 (t0) cc_final: 0.7897 (t0) REVERT: n 11 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.6839 (t0) REVERT: n 62 MET cc_start: 0.8164 (mmm) cc_final: 0.7396 (mmm) REVERT: n 197 MET cc_start: 0.8634 (ppp) cc_final: 0.8225 (ptm) REVERT: z 385 MET cc_start: 0.6811 (ptm) cc_final: 0.6610 (ptt) REVERT: w 275 LEU cc_start: 0.8164 (mm) cc_final: 0.7574 (tp) REVERT: w 286 MET cc_start: 0.8029 (tmm) cc_final: 0.7430 (tmm) REVERT: v 14 TYR cc_start: 0.8560 (m-80) cc_final: 0.8199 (m-80) REVERT: s 231 ARG cc_start: 0.0780 (OUTLIER) cc_final: 0.0216 (tpp80) REVERT: s 273 ILE cc_start: -0.0827 (OUTLIER) cc_final: -0.1256 (mp) outliers start: 330 outliers final: 241 residues processed: 1186 average time/residue: 1.1358 time to fit residues: 2380.3207 Evaluate side-chains 1177 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 928 time to evaluate : 6.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 122 CYS Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 71 SER Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 144 GLU Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Z residue 51 ILE Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 81 CYS Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 18 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 47 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 167 VAL Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 ASP Chi-restraints excluded: chain w residue 249 VAL Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 195 VAL Chi-restraints excluded: chain o residue 202 VAL Chi-restraints excluded: chain o residue 204 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 213 PHE Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 392 VAL Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 409 LEU Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 273 ILE Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain s residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 926 optimal weight: 0.9990 chunk 705 optimal weight: 3.9990 chunk 486 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 447 optimal weight: 8.9990 chunk 629 optimal weight: 8.9990 chunk 941 optimal weight: 7.9990 chunk 996 optimal weight: 20.0000 chunk 491 optimal weight: 7.9990 chunk 892 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN C 173 GLN C 231 HIS C 319 ASN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS ** K 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS U 92 GLN W 65 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN n 11 ASN ** n 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 402 GLN ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 138868 Z= 0.272 Angle : 0.632 16.202 204325 Z= 0.324 Chirality : 0.038 0.395 25651 Planarity : 0.005 0.143 13188 Dihedral : 23.263 179.609 60867 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.99 % Rotamer: Outliers : 6.07 % Allowed : 22.79 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.09), residues: 6829 helix: -1.78 (0.11), residues: 2022 sheet: -2.02 (0.16), residues: 948 loop : -2.30 (0.09), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 85 HIS 0.008 0.001 HIS w 234 PHE 0.029 0.001 PHE S 30 TYR 0.048 0.002 TYR J 167 ARG 0.008 0.000 ARG Y 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 971 time to evaluate : 6.297 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8903 (mtt) cc_final: 0.8501 (mtt) REVERT: C 7 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6220 (tt0) REVERT: C 123 TYR cc_start: 0.9128 (p90) cc_final: 0.8757 (p90) REVERT: C 261 MET cc_start: 0.7053 (mtm) cc_final: 0.6752 (mtm) REVERT: C 332 ARG cc_start: 0.7958 (pmt170) cc_final: 0.7507 (ptp-110) REVERT: C 360 ASP cc_start: 0.7550 (t0) cc_final: 0.7313 (m-30) REVERT: C 369 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8051 (mtp85) REVERT: C 371 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8194 (mm-40) REVERT: E 9 MET cc_start: 0.7750 (mtm) cc_final: 0.7246 (ptp) REVERT: E 11 ASP cc_start: 0.6648 (p0) cc_final: 0.5980 (t0) REVERT: E 57 PHE cc_start: 0.2504 (m-10) cc_final: 0.1545 (m-10) REVERT: E 108 GLU cc_start: 0.7239 (tp30) cc_final: 0.6784 (tp30) REVERT: F 7 GLU cc_start: 0.7700 (pp20) cc_final: 0.7418 (pp20) REVERT: F 9 GLN cc_start: 0.7098 (mp10) cc_final: 0.6595 (mp10) REVERT: F 24 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6352 (mp) REVERT: F 63 LYS cc_start: 0.4534 (pttp) cc_final: 0.4134 (mtpt) REVERT: F 78 MET cc_start: 0.7024 (ttp) cc_final: 0.6804 (tmm) REVERT: F 153 ASP cc_start: 0.8080 (m-30) cc_final: 0.7766 (m-30) REVERT: G 46 ARG cc_start: 0.8210 (tmt170) cc_final: 0.7731 (ttp80) REVERT: H 43 LYS cc_start: 0.7350 (mttm) cc_final: 0.6887 (mmtm) REVERT: H 130 TYR cc_start: 0.7903 (m-80) cc_final: 0.7583 (m-80) REVERT: J 167 TYR cc_start: 0.8569 (t80) cc_final: 0.8295 (t80) REVERT: K 11 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8167 (mttp) REVERT: K 160 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: K 176 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7957 (tm-30) REVERT: L 15 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7837 (mm) REVERT: M 47 ASP cc_start: 0.8336 (t0) cc_final: 0.8118 (t0) REVERT: M 121 MET cc_start: 0.8090 (tmm) cc_final: 0.7575 (tmm) REVERT: N 45 MET cc_start: 0.8710 (mmm) cc_final: 0.8508 (mmt) REVERT: O 24 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7439 (ttt90) REVERT: O 77 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7681 (tttt) REVERT: P 90 HIS cc_start: 0.6920 (m90) cc_final: 0.6684 (m90) REVERT: P 151 GLN cc_start: 0.7539 (tp40) cc_final: 0.7301 (mm110) REVERT: P 183 TRP cc_start: 0.8398 (t60) cc_final: 0.8041 (t-100) REVERT: Q 78 ASN cc_start: 0.8003 (m-40) cc_final: 0.7595 (t0) REVERT: R 31 GLU cc_start: 0.8544 (tp30) cc_final: 0.8296 (tp30) REVERT: R 103 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7197 (ttm170) REVERT: S 58 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8919 (mp) REVERT: S 91 TYR cc_start: 0.7411 (t80) cc_final: 0.7140 (t80) REVERT: S 166 LYS cc_start: 0.8304 (ptpt) cc_final: 0.8051 (pttt) REVERT: T 102 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.6949 (ttm-80) REVERT: U 34 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9054 (mm-40) REVERT: V 89 LEU cc_start: 0.8631 (mp) cc_final: 0.8410 (mp) REVERT: W 91 ASN cc_start: 0.8786 (p0) cc_final: 0.8390 (p0) REVERT: X 17 LYS cc_start: 0.8591 (tttp) cc_final: 0.8099 (tttt) REVERT: Y 126 LYS cc_start: 0.5853 (mmtt) cc_final: 0.5152 (tttt) REVERT: Z 7 TYR cc_start: 0.8564 (p90) cc_final: 0.8341 (p90) REVERT: a 22 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8232 (mttt) REVERT: c 58 TYR cc_start: 0.8465 (t80) cc_final: 0.8205 (t80) REVERT: d 21 HIS cc_start: 0.8489 (t-90) cc_final: 0.7780 (t70) REVERT: d 25 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8039 (m-10) REVERT: d 57 GLN cc_start: 0.8222 (pt0) cc_final: 0.7573 (tm-30) REVERT: e 83 GLU cc_start: 0.7880 (pp20) cc_final: 0.7605 (pp20) REVERT: f 8 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8304 (p90) REVERT: f 10 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8702 (mmtt) REVERT: f 13 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8800 (t-170) REVERT: f 44 TYR cc_start: 0.8621 (m-80) cc_final: 0.8225 (m-80) REVERT: g 57 LEU cc_start: 0.9248 (mt) cc_final: 0.8969 (mt) REVERT: h 43 LEU cc_start: 0.9562 (tp) cc_final: 0.9151 (tp) REVERT: i 13 ASN cc_start: 0.8879 (p0) cc_final: 0.8440 (p0) REVERT: j 51 LEU cc_start: 0.9397 (tp) cc_final: 0.9099 (tt) REVERT: k 40 LYS cc_start: 0.9015 (mttt) cc_final: 0.8556 (mttp) REVERT: l 11 TYR cc_start: 0.8579 (t80) cc_final: 0.8279 (t80) REVERT: l 45 ARG cc_start: 0.8859 (tpt-90) cc_final: 0.8563 (tpt170) REVERT: m 5 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8166 (p) REVERT: m 14 TYR cc_start: 0.9074 (m-80) cc_final: 0.8608 (m-80) REVERT: m 18 TYR cc_start: 0.9039 (m-80) cc_final: 0.8678 (m-80) REVERT: n 9 ASN cc_start: 0.8367 (t0) cc_final: 0.8092 (t0) REVERT: n 11 ASN cc_start: 0.7657 (t0) cc_final: 0.6616 (t0) REVERT: n 35 TYR cc_start: 0.6568 (m-80) cc_final: 0.6177 (m-80) REVERT: n 62 MET cc_start: 0.8115 (mmm) cc_final: 0.7395 (mmm) REVERT: z 385 MET cc_start: 0.6852 (ptm) cc_final: 0.6635 (ptt) REVERT: w 61 CYS cc_start: 0.4720 (OUTLIER) cc_final: 0.3670 (m) REVERT: w 128 ILE cc_start: 0.4738 (tt) cc_final: 0.4499 (tp) REVERT: w 275 LEU cc_start: 0.8199 (mm) cc_final: 0.7631 (tp) REVERT: w 286 MET cc_start: 0.8098 (tmm) cc_final: 0.7845 (tmm) REVERT: w 359 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6467 (mp) REVERT: o 182 GLU cc_start: 0.1429 (OUTLIER) cc_final: 0.0979 (mm-30) REVERT: s 231 ARG cc_start: 0.0460 (OUTLIER) cc_final: -0.0069 (mtp85) outliers start: 354 outliers final: 259 residues processed: 1194 average time/residue: 1.0877 time to fit residues: 2282.0193 Evaluate side-chains 1199 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 927 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 160 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 64 GLN Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 166 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 80 GLN Chi-restraints excluded: chain b residue 81 HIS Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 8 TYR Chi-restraints excluded: chain f residue 13 HIS Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 39 GLN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain k residue 47 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 3 THR Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 167 VAL Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 202 VAL Chi-restraints excluded: chain o residue 204 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 829 optimal weight: 0.7980 chunk 565 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 742 optimal weight: 0.9980 chunk 411 optimal weight: 9.9990 chunk 850 optimal weight: 9.9990 chunk 688 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 508 optimal weight: 4.9990 chunk 894 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN C 173 GLN C 319 ASN F 157 ASN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN U 125 GLN W 65 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 194 HIS ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 215 ASN ** w 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 248 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 138868 Z= 0.291 Angle : 0.644 15.971 204325 Z= 0.328 Chirality : 0.038 0.415 25651 Planarity : 0.005 0.140 13188 Dihedral : 23.223 179.943 60862 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.42 % Favored : 90.54 % Rotamer: Outliers : 6.79 % Allowed : 23.34 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.09), residues: 6829 helix: -1.59 (0.11), residues: 2017 sheet: -1.94 (0.16), residues: 958 loop : -2.26 (0.09), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 85 HIS 0.009 0.001 HIS w 234 PHE 0.020 0.002 PHE S 30 TYR 0.035 0.002 TYR J 167 ARG 0.022 0.001 ARG Z 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 941 time to evaluate : 6.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8876 (mtt) cc_final: 0.8521 (mmt) REVERT: C 7 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6220 (tt0) REVERT: C 123 TYR cc_start: 0.9135 (p90) cc_final: 0.8764 (p90) REVERT: C 261 MET cc_start: 0.7038 (mtm) cc_final: 0.6751 (mtm) REVERT: C 332 ARG cc_start: 0.7997 (pmt170) cc_final: 0.7530 (ptp-110) REVERT: C 360 ASP cc_start: 0.7568 (t0) cc_final: 0.7256 (m-30) REVERT: C 369 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.8045 (mtp85) REVERT: E 9 MET cc_start: 0.7705 (mtm) cc_final: 0.7249 (ptp) REVERT: E 11 ASP cc_start: 0.6574 (p0) cc_final: 0.6027 (t0) REVERT: E 57 PHE cc_start: 0.2293 (m-10) cc_final: 0.1314 (m-10) REVERT: E 108 GLU cc_start: 0.7190 (tp30) cc_final: 0.6692 (tp30) REVERT: F 7 GLU cc_start: 0.7656 (pp20) cc_final: 0.7283 (pp20) REVERT: F 9 GLN cc_start: 0.7110 (mp10) cc_final: 0.6588 (mp10) REVERT: F 24 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6374 (mp) REVERT: F 63 LYS cc_start: 0.4544 (pttp) cc_final: 0.4303 (mmmt) REVERT: F 78 MET cc_start: 0.7050 (ttp) cc_final: 0.6801 (tmm) REVERT: F 153 ASP cc_start: 0.8099 (m-30) cc_final: 0.7793 (m-30) REVERT: G 46 ARG cc_start: 0.8240 (tmt170) cc_final: 0.7543 (ttp-110) REVERT: H 130 TYR cc_start: 0.7887 (m-80) cc_final: 0.7569 (m-80) REVERT: K 11 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8142 (mttp) REVERT: K 176 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8065 (tm-30) REVERT: K 183 ARG cc_start: 0.6754 (mtt90) cc_final: 0.6358 (ptp-170) REVERT: L 15 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7847 (mm) REVERT: L 87 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.6959 (tpp-160) REVERT: M 47 ASP cc_start: 0.8321 (t0) cc_final: 0.8085 (t0) REVERT: M 121 MET cc_start: 0.8075 (tmm) cc_final: 0.7559 (tmm) REVERT: N 8 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8921 (t) REVERT: O 24 ARG cc_start: 0.7871 (mtp180) cc_final: 0.7441 (ttt90) REVERT: O 77 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7620 (tttt) REVERT: P 151 GLN cc_start: 0.7511 (tp40) cc_final: 0.7273 (mm110) REVERT: P 183 TRP cc_start: 0.8389 (t60) cc_final: 0.8051 (t-100) REVERT: Q 78 ASN cc_start: 0.7996 (m-40) cc_final: 0.7625 (t0) REVERT: R 103 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7215 (ttm170) REVERT: S 91 TYR cc_start: 0.7434 (t80) cc_final: 0.7050 (t80) REVERT: S 93 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7426 (mm-30) REVERT: S 110 MET cc_start: 0.9175 (tpp) cc_final: 0.8920 (tpp) REVERT: S 166 LYS cc_start: 0.8319 (ptpt) cc_final: 0.8069 (pttt) REVERT: U 34 GLN cc_start: 0.9282 (mm-40) cc_final: 0.9079 (mm-40) REVERT: U 64 ASN cc_start: 0.8821 (p0) cc_final: 0.8247 (p0) REVERT: V 89 LEU cc_start: 0.8717 (mp) cc_final: 0.8494 (mp) REVERT: W 58 ASP cc_start: 0.8186 (p0) cc_final: 0.7839 (p0) REVERT: W 91 ASN cc_start: 0.8819 (p0) cc_final: 0.8438 (p0) REVERT: X 17 LYS cc_start: 0.8581 (tttp) cc_final: 0.8077 (tttt) REVERT: X 46 LYS cc_start: 0.8912 (mttt) cc_final: 0.8670 (mttt) REVERT: Y 126 LYS cc_start: 0.5858 (mmtt) cc_final: 0.5142 (tptt) REVERT: a 22 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8223 (mttt) REVERT: c 66 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5330 (mmtt) REVERT: d 25 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.7990 (m-10) REVERT: d 57 GLN cc_start: 0.8251 (pt0) cc_final: 0.7474 (tm-30) REVERT: e 30 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8086 (tp30) REVERT: e 83 GLU cc_start: 0.7901 (pp20) cc_final: 0.7624 (pp20) REVERT: f 8 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.8114 (p90) REVERT: f 10 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8627 (mmtt) REVERT: f 44 TYR cc_start: 0.8651 (m-80) cc_final: 0.8242 (m-80) REVERT: f 60 ARG cc_start: 0.7570 (mpt180) cc_final: 0.7242 (mpt180) REVERT: g 57 LEU cc_start: 0.9273 (mt) cc_final: 0.8990 (mt) REVERT: h 43 LEU cc_start: 0.9514 (tp) cc_final: 0.9144 (tp) REVERT: i 13 ASN cc_start: 0.8890 (p0) cc_final: 0.8445 (p0) REVERT: j 51 LEU cc_start: 0.9404 (tp) cc_final: 0.9028 (tt) REVERT: k 40 LYS cc_start: 0.9017 (mttt) cc_final: 0.8548 (mttp) REVERT: l 11 TYR cc_start: 0.8630 (t80) cc_final: 0.8363 (t80) REVERT: l 45 ARG cc_start: 0.8860 (tpt-90) cc_final: 0.8544 (tpt170) REVERT: l 53 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: l 80 ARG cc_start: 0.8080 (mpp-170) cc_final: 0.7682 (mpt180) REVERT: m 5 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8211 (p) REVERT: n 9 ASN cc_start: 0.8329 (t0) cc_final: 0.7873 (t0) REVERT: n 11 ASN cc_start: 0.7674 (t0) cc_final: 0.6802 (t0) REVERT: n 35 TYR cc_start: 0.6627 (m-80) cc_final: 0.6200 (m-80) REVERT: n 62 MET cc_start: 0.8116 (mmm) cc_final: 0.7403 (mmm) REVERT: z 385 MET cc_start: 0.6868 (ptm) cc_final: 0.6660 (ptt) REVERT: z 414 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8182 (mtm180) REVERT: w 17 LEU cc_start: 0.1710 (OUTLIER) cc_final: 0.1222 (pp) REVERT: w 275 LEU cc_start: 0.8217 (mm) cc_final: 0.7635 (tp) REVERT: w 286 MET cc_start: 0.8102 (tmm) cc_final: 0.7866 (tmm) REVERT: w 359 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6467 (mp) REVERT: o 182 GLU cc_start: 0.1534 (OUTLIER) cc_final: 0.1041 (mm-30) REVERT: s 231 ARG cc_start: 0.0437 (OUTLIER) cc_final: -0.0828 (tpp80) REVERT: s 273 ILE cc_start: -0.0279 (OUTLIER) cc_final: -0.0623 (mp) outliers start: 396 outliers final: 307 residues processed: 1207 average time/residue: 1.0797 time to fit residues: 2292.7587 Evaluate side-chains 1232 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 910 time to evaluate : 6.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 166 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 59 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 75 ARG Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 81 HIS Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 8 TYR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 39 GLN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain k residue 47 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 11 THR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 3 THR Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 167 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain z residue 414 ARG Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 ASP Chi-restraints excluded: chain w residue 222 HIS Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 315 LEU Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 204 ILE Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 505 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 273 ILE Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain s residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 335 optimal weight: 0.9990 chunk 897 optimal weight: 0.2980 chunk 196 optimal weight: 10.0000 chunk 585 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 997 optimal weight: 50.0000 chunk 828 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 523 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN K 28 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN O 156 HIS ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 ASN U 92 GLN W 65 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN ** Y 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS f 39 GLN ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 59 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 138868 Z= 0.180 Angle : 0.562 14.221 204325 Z= 0.289 Chirality : 0.035 0.434 25651 Planarity : 0.004 0.136 13188 Dihedral : 23.146 179.801 60861 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 5.40 % Allowed : 25.38 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6829 helix: -1.28 (0.11), residues: 2009 sheet: -1.70 (0.17), residues: 935 loop : -2.07 (0.09), residues: 3885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 23 HIS 0.007 0.001 HIS w 234 PHE 0.019 0.001 PHE l 58 TYR 0.058 0.001 TYR J 167 ARG 0.008 0.000 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 999 time to evaluate : 6.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8801 (mtt) cc_final: 0.8413 (mmt) REVERT: C 7 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6184 (tt0) REVERT: C 123 TYR cc_start: 0.9105 (p90) cc_final: 0.8702 (p90) REVERT: C 261 MET cc_start: 0.6832 (mtm) cc_final: 0.6579 (mtm) REVERT: C 332 ARG cc_start: 0.7959 (pmt170) cc_final: 0.7457 (ptp-110) REVERT: C 369 ARG cc_start: 0.8457 (ptp-110) cc_final: 0.8050 (mtp85) REVERT: E 9 MET cc_start: 0.7547 (mtm) cc_final: 0.7209 (ptp) REVERT: E 11 ASP cc_start: 0.6521 (p0) cc_final: 0.6085 (t0) REVERT: E 57 PHE cc_start: 0.1968 (m-10) cc_final: 0.1101 (m-10) REVERT: E 108 GLU cc_start: 0.7104 (tp30) cc_final: 0.6511 (tp30) REVERT: F 7 GLU cc_start: 0.7572 (pp20) cc_final: 0.7159 (pp20) REVERT: F 24 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6334 (mp) REVERT: F 63 LYS cc_start: 0.4544 (pttp) cc_final: 0.4240 (mtpt) REVERT: F 78 MET cc_start: 0.7074 (ttp) cc_final: 0.6806 (tmm) REVERT: F 153 ASP cc_start: 0.8092 (m-30) cc_final: 0.7778 (m-30) REVERT: G 46 ARG cc_start: 0.8180 (tmt170) cc_final: 0.7713 (ttp80) REVERT: H 130 TYR cc_start: 0.7835 (m-80) cc_final: 0.7507 (m-80) REVERT: J 167 TYR cc_start: 0.8523 (t80) cc_final: 0.8304 (t80) REVERT: K 11 LYS cc_start: 0.8391 (mtpp) cc_final: 0.8160 (mttp) REVERT: K 160 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: K 176 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8159 (tm-30) REVERT: K 183 ARG cc_start: 0.6787 (mtt90) cc_final: 0.6435 (ptp-170) REVERT: M 22 LEU cc_start: 0.9107 (tp) cc_final: 0.8835 (tt) REVERT: M 47 ASP cc_start: 0.8352 (t0) cc_final: 0.8143 (t0) REVERT: M 121 MET cc_start: 0.8117 (tmm) cc_final: 0.7607 (tmm) REVERT: O 24 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7416 (ttt90) REVERT: O 77 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7668 (tttt) REVERT: P 151 GLN cc_start: 0.7384 (tp40) cc_final: 0.7163 (mm110) REVERT: P 183 TRP cc_start: 0.8362 (t60) cc_final: 0.8038 (t-100) REVERT: Q 78 ASN cc_start: 0.8007 (m-40) cc_final: 0.7616 (t0) REVERT: R 103 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6963 (ttm170) REVERT: S 91 TYR cc_start: 0.7453 (t80) cc_final: 0.7037 (t80) REVERT: S 110 MET cc_start: 0.9104 (tpp) cc_final: 0.8869 (tpp) REVERT: S 166 LYS cc_start: 0.8280 (ptpt) cc_final: 0.8017 (pttt) REVERT: V 89 LEU cc_start: 0.8639 (mp) cc_final: 0.8412 (mp) REVERT: W 58 ASP cc_start: 0.8174 (p0) cc_final: 0.7863 (p0) REVERT: X 17 LYS cc_start: 0.8506 (tttp) cc_final: 0.7997 (tttt) REVERT: Y 126 LYS cc_start: 0.5651 (mmtt) cc_final: 0.5005 (tppt) REVERT: Y 135 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8085 (mmm-85) REVERT: a 22 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8172 (mttt) REVERT: c 66 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5356 (mmtt) REVERT: d 25 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: d 35 GLU cc_start: 0.8219 (tp30) cc_final: 0.7917 (tp30) REVERT: d 57 GLN cc_start: 0.8113 (pt0) cc_final: 0.7431 (tm-30) REVERT: e 30 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8035 (tp30) REVERT: e 78 ASN cc_start: 0.8922 (p0) cc_final: 0.8605 (p0) REVERT: f 8 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8014 (p90) REVERT: f 10 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8613 (mmtt) REVERT: f 44 TYR cc_start: 0.8624 (m-80) cc_final: 0.8303 (m-80) REVERT: f 60 ARG cc_start: 0.7570 (mpt180) cc_final: 0.7205 (mpt180) REVERT: g 57 LEU cc_start: 0.9201 (mt) cc_final: 0.8959 (mt) REVERT: h 43 LEU cc_start: 0.9473 (tp) cc_final: 0.9183 (tp) REVERT: h 68 ARG cc_start: 0.8274 (mmm160) cc_final: 0.8057 (mmm160) REVERT: i 13 ASN cc_start: 0.8762 (p0) cc_final: 0.8370 (p0) REVERT: j 51 LEU cc_start: 0.9416 (tp) cc_final: 0.9026 (tt) REVERT: k 19 GLN cc_start: 0.7979 (mt0) cc_final: 0.6749 (tm-30) REVERT: k 40 LYS cc_start: 0.9033 (mttt) cc_final: 0.8554 (mttp) REVERT: l 11 TYR cc_start: 0.8574 (t80) cc_final: 0.8243 (t80) REVERT: l 45 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.8522 (tpt170) REVERT: l 80 ARG cc_start: 0.8095 (mpp-170) cc_final: 0.7654 (mpt180) REVERT: m 5 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8116 (p) REVERT: m 14 TYR cc_start: 0.8952 (m-80) cc_final: 0.8604 (m-80) REVERT: n 9 ASN cc_start: 0.8326 (t0) cc_final: 0.7820 (t0) REVERT: n 11 ASN cc_start: 0.7477 (t0) cc_final: 0.6251 (t0) REVERT: n 35 TYR cc_start: 0.6585 (m-80) cc_final: 0.6265 (m-80) REVERT: n 62 MET cc_start: 0.7968 (mmm) cc_final: 0.7300 (mmm) REVERT: z 385 MET cc_start: 0.6786 (ptm) cc_final: 0.6500 (ptt) REVERT: w 17 LEU cc_start: 0.1588 (OUTLIER) cc_final: 0.1110 (pp) REVERT: w 275 LEU cc_start: 0.8179 (mm) cc_final: 0.7676 (tp) REVERT: w 286 MET cc_start: 0.8100 (tmm) cc_final: 0.7891 (tmm) REVERT: v 55 PHE cc_start: 0.8049 (t80) cc_final: 0.7386 (t80) REVERT: o 182 GLU cc_start: 0.1511 (OUTLIER) cc_final: 0.1181 (mm-30) REVERT: s 231 ARG cc_start: 0.0455 (OUTLIER) cc_final: -0.0815 (tpp80) REVERT: s 273 ILE cc_start: -0.0030 (OUTLIER) cc_final: -0.0297 (mp) outliers start: 315 outliers final: 241 residues processed: 1199 average time/residue: 1.1252 time to fit residues: 2373.3898 Evaluate side-chains 1188 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 936 time to evaluate : 6.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 TYR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 160 GLN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 198 TYR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 8 TYR Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 39 GLN Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 3 THR Chi-restraints excluded: chain n residue 78 ASP Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 195 VAL Chi-restraints excluded: chain o residue 202 VAL Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 382 SER Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 404 VAL Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 505 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 271 ILE Chi-restraints excluded: chain s residue 273 ILE Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Chi-restraints excluded: chain s residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 961 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 568 optimal weight: 10.0000 chunk 728 optimal weight: 2.9990 chunk 564 optimal weight: 0.6980 chunk 839 optimal weight: 3.9990 chunk 557 optimal weight: 0.0370 chunk 993 optimal weight: 10.0000 chunk 621 optimal weight: 0.9990 chunk 605 optimal weight: 10.0000 chunk 458 optimal weight: 0.5980 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 215 ASN C 173 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS G 61 ASN G 80 ASN L 132 ASN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 HIS R 66 HIS U 92 GLN W 117 ASN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 GLN f 42 GLN ** n 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 346 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 138868 Z= 0.132 Angle : 0.520 12.416 204325 Z= 0.268 Chirality : 0.032 0.482 25651 Planarity : 0.004 0.133 13188 Dihedral : 23.021 179.629 60855 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.46 % Favored : 93.50 % Rotamer: Outliers : 4.51 % Allowed : 26.89 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.10), residues: 6829 helix: -0.98 (0.12), residues: 2004 sheet: -1.49 (0.16), residues: 935 loop : -1.91 (0.10), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP w 155 HIS 0.007 0.001 HIS W 53 PHE 0.028 0.001 PHE v 55 TYR 0.042 0.001 TYR J 167 ARG 0.009 0.000 ARG Q 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1021 time to evaluate : 6.363 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8759 (mtt) cc_final: 0.8344 (mmt) REVERT: C 7 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6120 (tt0) REVERT: C 123 TYR cc_start: 0.9054 (p90) cc_final: 0.8712 (p90) REVERT: C 181 ILE cc_start: 0.9092 (mm) cc_final: 0.8874 (mm) REVERT: C 332 ARG cc_start: 0.7770 (pmt170) cc_final: 0.7200 (ptp-110) REVERT: E 11 ASP cc_start: 0.6523 (p0) cc_final: 0.6151 (t0) REVERT: E 57 PHE cc_start: 0.2176 (m-10) cc_final: 0.1532 (m-10) REVERT: F 1 MET cc_start: 0.4598 (ptm) cc_final: 0.3600 (ppp) REVERT: F 5 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7438 (tm-30) REVERT: F 7 GLU cc_start: 0.7826 (pp20) cc_final: 0.7442 (pp20) REVERT: F 45 PHE cc_start: 0.6295 (m-80) cc_final: 0.5944 (m-80) REVERT: F 78 MET cc_start: 0.7021 (ttp) cc_final: 0.6721 (tmm) REVERT: F 153 ASP cc_start: 0.8092 (m-30) cc_final: 0.7800 (m-30) REVERT: G 46 ARG cc_start: 0.8121 (tmt170) cc_final: 0.7683 (ttp80) REVERT: J 167 TYR cc_start: 0.8494 (t80) cc_final: 0.8178 (t80) REVERT: K 11 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8147 (mttp) REVERT: K 107 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: K 176 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8197 (tm-30) REVERT: K 179 PHE cc_start: 0.7818 (m-80) cc_final: 0.7217 (m-80) REVERT: K 183 ARG cc_start: 0.6665 (mtt90) cc_final: 0.6286 (ptp-170) REVERT: L 15 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7740 (mm) REVERT: M 14 LEU cc_start: 0.8073 (mt) cc_final: 0.7699 (mm) REVERT: M 22 LEU cc_start: 0.9080 (tp) cc_final: 0.8789 (tt) REVERT: M 121 MET cc_start: 0.8093 (tmm) cc_final: 0.7613 (tmm) REVERT: O 77 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7567 (tttt) REVERT: O 192 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8467 (ttpt) REVERT: P 183 TRP cc_start: 0.8334 (t60) cc_final: 0.8023 (t-100) REVERT: P 188 GLU cc_start: 0.7763 (mp0) cc_final: 0.6760 (pp20) REVERT: Q 78 ASN cc_start: 0.8124 (m-40) cc_final: 0.7614 (t0) REVERT: R 103 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6927 (ttm170) REVERT: S 91 TYR cc_start: 0.7429 (t80) cc_final: 0.7025 (t80) REVERT: T 16 GLN cc_start: 0.8460 (pt0) cc_final: 0.8210 (pt0) REVERT: V 49 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7651 (p0) REVERT: V 89 LEU cc_start: 0.8536 (mp) cc_final: 0.8318 (mp) REVERT: W 58 ASP cc_start: 0.8142 (p0) cc_final: 0.7780 (p0) REVERT: W 77 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: X 17 LYS cc_start: 0.8340 (tttp) cc_final: 0.8083 (tttt) REVERT: Y 4 PHE cc_start: 0.6693 (p90) cc_final: 0.6186 (m-80) REVERT: Y 126 LYS cc_start: 0.5466 (mmtt) cc_final: 0.5077 (tptt) REVERT: Y 135 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: Z 7 TYR cc_start: 0.8705 (p90) cc_final: 0.8428 (p90) REVERT: a 22 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8179 (mttt) REVERT: c 66 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5224 (mmtt) REVERT: d 35 GLU cc_start: 0.8126 (tp30) cc_final: 0.7881 (tm-30) REVERT: d 57 GLN cc_start: 0.8002 (pt0) cc_final: 0.7367 (tm-30) REVERT: e 78 ASN cc_start: 0.8866 (p0) cc_final: 0.8585 (p0) REVERT: f 44 TYR cc_start: 0.8559 (m-80) cc_final: 0.8341 (m-80) REVERT: f 60 ARG cc_start: 0.7596 (mpt180) cc_final: 0.7266 (mpt180) REVERT: f 88 ASN cc_start: 0.8375 (m-40) cc_final: 0.8128 (m-40) REVERT: g 11 ASN cc_start: 0.9007 (t0) cc_final: 0.8764 (t0) REVERT: g 57 LEU cc_start: 0.9142 (mt) cc_final: 0.8927 (mt) REVERT: h 43 LEU cc_start: 0.9471 (tp) cc_final: 0.9229 (tp) REVERT: i 13 ASN cc_start: 0.8563 (p0) cc_final: 0.8262 (p0) REVERT: j 51 LEU cc_start: 0.9355 (tp) cc_final: 0.9054 (tt) REVERT: k 19 GLN cc_start: 0.7890 (mt0) cc_final: 0.6662 (tm-30) REVERT: k 40 LYS cc_start: 0.9018 (mttt) cc_final: 0.8544 (mttp) REVERT: l 80 ARG cc_start: 0.8027 (mpp-170) cc_final: 0.7759 (mpt180) REVERT: m 5 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8092 (p) REVERT: m 14 TYR cc_start: 0.8900 (m-80) cc_final: 0.8441 (m-80) REVERT: n 9 ASN cc_start: 0.8151 (t0) cc_final: 0.7687 (t0) REVERT: n 11 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6485 (t0) REVERT: n 35 TYR cc_start: 0.6553 (m-80) cc_final: 0.6348 (m-80) REVERT: n 62 MET cc_start: 0.7927 (mmm) cc_final: 0.7315 (mmm) REVERT: n 188 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7345 (ttm170) REVERT: z 385 MET cc_start: 0.6695 (ptm) cc_final: 0.6436 (ptt) REVERT: w 17 LEU cc_start: 0.1468 (OUTLIER) cc_final: 0.1051 (pp) REVERT: w 275 LEU cc_start: 0.8155 (mm) cc_final: 0.7738 (tp) REVERT: s 231 ARG cc_start: 0.0658 (OUTLIER) cc_final: 0.0343 (mtp85) outliers start: 263 outliers final: 197 residues processed: 1182 average time/residue: 1.0738 time to fit residues: 2227.6164 Evaluate side-chains 1149 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 942 time to evaluate : 6.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 153 ASP Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 39 GLN Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 198 TYR Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 10 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 51 THR Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 222 HIS Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 382 SER Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 404 VAL Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 271 ILE Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 614 optimal weight: 0.9990 chunk 396 optimal weight: 0.5980 chunk 593 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 631 optimal weight: 9.9990 chunk 677 optimal weight: 0.9990 chunk 491 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 781 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 215 ASN C 68 HIS C 165 GLN C 173 GLN C 256 HIS C 319 ASN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN J 49 ASN L 132 ASN N 39 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN U 125 GLN X 4 GLN ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN ** b 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 215 ASN w 358 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 138868 Z= 0.162 Angle : 0.529 11.806 204325 Z= 0.271 Chirality : 0.033 0.488 25651 Planarity : 0.004 0.131 13188 Dihedral : 22.967 179.567 60850 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 4.83 % Allowed : 27.06 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6829 helix: -0.86 (0.12), residues: 2006 sheet: -1.42 (0.17), residues: 916 loop : -1.87 (0.10), residues: 3907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP w 155 HIS 0.023 0.001 HIS C 256 PHE 0.030 0.001 PHE R 132 TYR 0.038 0.001 TYR J 167 ARG 0.006 0.000 ARG m 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 958 time to evaluate : 6.634 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8808 (mtt) cc_final: 0.8396 (mmt) REVERT: C 7 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6130 (tt0) REVERT: C 123 TYR cc_start: 0.9069 (p90) cc_final: 0.8726 (p90) REVERT: C 181 ILE cc_start: 0.9063 (mm) cc_final: 0.8832 (mm) REVERT: C 332 ARG cc_start: 0.7815 (pmt170) cc_final: 0.7458 (ptp-110) REVERT: E 9 MET cc_start: 0.7748 (mtm) cc_final: 0.7129 (ptp) REVERT: E 11 ASP cc_start: 0.6513 (p0) cc_final: 0.6138 (t0) REVERT: E 57 PHE cc_start: 0.2006 (m-10) cc_final: 0.1422 (m-10) REVERT: E 108 GLU cc_start: 0.7108 (tp30) cc_final: 0.6586 (tp30) REVERT: F 1 MET cc_start: 0.4642 (ptm) cc_final: 0.3693 (ppp) REVERT: F 5 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7429 (tm-30) REVERT: F 7 GLU cc_start: 0.7719 (pp20) cc_final: 0.7415 (pp20) REVERT: F 24 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6348 (mp) REVERT: F 45 PHE cc_start: 0.6247 (m-80) cc_final: 0.5902 (m-80) REVERT: F 78 MET cc_start: 0.7016 (ttp) cc_final: 0.6733 (tmm) REVERT: F 153 ASP cc_start: 0.8112 (m-30) cc_final: 0.7813 (m-30) REVERT: G 46 ARG cc_start: 0.8170 (tmt170) cc_final: 0.7694 (ttp80) REVERT: H 130 TYR cc_start: 0.7662 (m-80) cc_final: 0.7316 (m-80) REVERT: J 49 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8752 (m-40) REVERT: J 167 TYR cc_start: 0.8525 (t80) cc_final: 0.8205 (t80) REVERT: K 11 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8137 (mttp) REVERT: K 160 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: K 176 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8183 (tm-30) REVERT: K 183 ARG cc_start: 0.6689 (mtt90) cc_final: 0.6327 (ptp-170) REVERT: L 15 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7759 (mm) REVERT: M 22 LEU cc_start: 0.9127 (tp) cc_final: 0.8807 (tt) REVERT: M 121 MET cc_start: 0.8065 (tmm) cc_final: 0.7599 (tmm) REVERT: O 29 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7807 (tm-30) REVERT: O 77 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7570 (tttt) REVERT: O 192 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8488 (ttpt) REVERT: P 183 TRP cc_start: 0.8333 (t60) cc_final: 0.8035 (t-100) REVERT: P 188 GLU cc_start: 0.7585 (mp0) cc_final: 0.6605 (pp20) REVERT: Q 78 ASN cc_start: 0.8199 (m-40) cc_final: 0.7743 (t0) REVERT: R 103 ARG cc_start: 0.7467 (mtt180) cc_final: 0.6983 (ttm170) REVERT: R 109 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: S 58 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8895 (mp) REVERT: S 91 TYR cc_start: 0.7216 (t80) cc_final: 0.6989 (t80) REVERT: S 110 MET cc_start: 0.8966 (tpp) cc_final: 0.8650 (tpp) REVERT: U 127 ARG cc_start: 0.9304 (ttm170) cc_final: 0.9040 (mtm-85) REVERT: V 49 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7637 (p0) REVERT: V 89 LEU cc_start: 0.8518 (mp) cc_final: 0.8298 (mp) REVERT: W 77 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: X 17 LYS cc_start: 0.8534 (tttp) cc_final: 0.8130 (tttt) REVERT: X 46 LYS cc_start: 0.8870 (mttt) cc_final: 0.8621 (mttt) REVERT: Y 126 LYS cc_start: 0.5897 (mmtt) cc_final: 0.5249 (tptt) REVERT: Y 135 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8130 (mmm-85) REVERT: Z 7 TYR cc_start: 0.8675 (p90) cc_final: 0.8404 (p90) REVERT: a 22 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8177 (mtmt) REVERT: c 66 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5231 (mmtt) REVERT: d 25 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8214 (m-10) REVERT: d 57 GLN cc_start: 0.8012 (pt0) cc_final: 0.7430 (tm-30) REVERT: e 78 ASN cc_start: 0.8878 (p0) cc_final: 0.8558 (p0) REVERT: f 44 TYR cc_start: 0.8573 (m-80) cc_final: 0.8321 (m-80) REVERT: f 60 ARG cc_start: 0.7592 (mpt180) cc_final: 0.7241 (mpt180) REVERT: f 88 ASN cc_start: 0.8394 (m-40) cc_final: 0.8144 (m-40) REVERT: h 43 LEU cc_start: 0.9461 (tp) cc_final: 0.9174 (tp) REVERT: i 13 ASN cc_start: 0.8611 (p0) cc_final: 0.8314 (p0) REVERT: j 51 LEU cc_start: 0.9374 (tp) cc_final: 0.9076 (tt) REVERT: k 40 LYS cc_start: 0.9054 (mttt) cc_final: 0.8600 (mttp) REVERT: k 42 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8034 (ppt170) REVERT: l 53 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: l 80 ARG cc_start: 0.8086 (mpp-170) cc_final: 0.7824 (mpt180) REVERT: m 5 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8091 (p) REVERT: m 14 TYR cc_start: 0.8943 (m-80) cc_final: 0.8505 (m-80) REVERT: n 9 ASN cc_start: 0.8190 (t0) cc_final: 0.7646 (t0) REVERT: n 62 MET cc_start: 0.7905 (mmm) cc_final: 0.7235 (mmm) REVERT: n 139 ARG cc_start: 0.7267 (ptm160) cc_final: 0.6804 (ptm160) REVERT: n 188 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7341 (ttm170) REVERT: z 385 MET cc_start: 0.6714 (ptm) cc_final: 0.6438 (ptt) REVERT: w 17 LEU cc_start: 0.1532 (OUTLIER) cc_final: 0.1061 (pp) REVERT: w 275 LEU cc_start: 0.8200 (mm) cc_final: 0.7757 (tp) REVERT: w 359 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6364 (mp) REVERT: w 372 TYR cc_start: 0.8469 (m-80) cc_final: 0.8148 (m-80) REVERT: s 231 ARG cc_start: 0.0694 (OUTLIER) cc_final: 0.0387 (mtp85) outliers start: 282 outliers final: 227 residues processed: 1140 average time/residue: 1.0774 time to fit residues: 2168.6251 Evaluate side-chains 1175 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 931 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 49 ASN Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 160 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 62 TYR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 198 TYR Chi-restraints excluded: chain Q residue 166 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 18 TYR Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 18 THR Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 382 SER Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 404 VAL Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 433 ILE Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 505 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 271 ILE Chi-restraints excluded: chain s residue 296 GLN Chi-restraints excluded: chain s residue 306 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 903 optimal weight: 0.0050 chunk 952 optimal weight: 30.0000 chunk 868 optimal weight: 9.9990 chunk 926 optimal weight: 4.9990 chunk 951 optimal weight: 30.0000 chunk 557 optimal weight: 10.0000 chunk 403 optimal weight: 8.9990 chunk 727 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 836 optimal weight: 2.9990 chunk 875 optimal weight: 3.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN D 45 ASN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN G 102 ASN L 132 ASN N 39 HIS ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 GLN ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 GLN ** b 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 138868 Z= 0.237 Angle : 0.575 12.715 204325 Z= 0.292 Chirality : 0.035 0.475 25651 Planarity : 0.005 0.131 13188 Dihedral : 22.939 179.755 60848 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.18 % Rotamer: Outliers : 4.92 % Allowed : 27.03 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 6829 helix: -0.85 (0.12), residues: 2013 sheet: -1.47 (0.17), residues: 909 loop : -1.90 (0.10), residues: 3907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP w 155 HIS 0.013 0.001 HIS W 53 PHE 0.032 0.002 PHE R 132 TYR 0.036 0.002 TYR J 167 ARG 0.009 0.000 ARG O 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 935 time to evaluate : 6.441 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8846 (mtt) cc_final: 0.8525 (mtt) REVERT: C 7 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6136 (tt0) REVERT: C 123 TYR cc_start: 0.9098 (p90) cc_final: 0.8712 (p90) REVERT: C 332 ARG cc_start: 0.7854 (pmt170) cc_final: 0.7353 (ptp-110) REVERT: C 369 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8020 (mtp85) REVERT: E 9 MET cc_start: 0.7758 (mtm) cc_final: 0.7169 (ptp) REVERT: E 11 ASP cc_start: 0.6436 (p0) cc_final: 0.6051 (t0) REVERT: E 57 PHE cc_start: 0.2018 (m-10) cc_final: 0.1481 (m-10) REVERT: F 5 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7451 (tm-30) REVERT: F 7 GLU cc_start: 0.7759 (pp20) cc_final: 0.7455 (pp20) REVERT: F 24 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6299 (mp) REVERT: F 45 PHE cc_start: 0.6282 (m-80) cc_final: 0.5881 (m-80) REVERT: F 78 MET cc_start: 0.7040 (ttp) cc_final: 0.6761 (tmm) REVERT: F 153 ASP cc_start: 0.8124 (m-30) cc_final: 0.7844 (m-30) REVERT: G 46 ARG cc_start: 0.8217 (tmt170) cc_final: 0.7698 (ttp80) REVERT: H 130 TYR cc_start: 0.7693 (m-80) cc_final: 0.7373 (m-80) REVERT: J 167 TYR cc_start: 0.8589 (t80) cc_final: 0.8328 (t80) REVERT: K 11 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8150 (mttp) REVERT: K 160 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: K 176 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8170 (tm-30) REVERT: K 183 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6465 (ptp-170) REVERT: L 15 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7809 (mm) REVERT: M 22 LEU cc_start: 0.9159 (tp) cc_final: 0.8891 (tt) REVERT: M 121 MET cc_start: 0.8049 (tmm) cc_final: 0.7507 (tmm) REVERT: N 8 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8865 (t) REVERT: O 77 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7548 (tttt) REVERT: P 183 TRP cc_start: 0.8374 (t60) cc_final: 0.8098 (t-100) REVERT: Q 78 ASN cc_start: 0.8187 (m-40) cc_final: 0.7771 (t0) REVERT: R 103 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7015 (ttm170) REVERT: R 109 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: S 91 TYR cc_start: 0.7283 (t80) cc_final: 0.7005 (t80) REVERT: S 93 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7045 (mm-30) REVERT: U 64 ASN cc_start: 0.8612 (p0) cc_final: 0.8272 (p0) REVERT: U 127 ARG cc_start: 0.9319 (ttm170) cc_final: 0.9029 (mtm-85) REVERT: V 49 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (p0) REVERT: V 89 LEU cc_start: 0.8638 (mp) cc_final: 0.8411 (mp) REVERT: W 77 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: X 17 LYS cc_start: 0.8556 (tttp) cc_final: 0.8108 (tttt) REVERT: X 46 LYS cc_start: 0.8887 (mttt) cc_final: 0.8634 (mttt) REVERT: Y 126 LYS cc_start: 0.5950 (mmtt) cc_final: 0.5364 (tptt) REVERT: Y 135 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8203 (mmm-85) REVERT: a 22 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8192 (mtmt) REVERT: b 197 GLN cc_start: 0.7683 (mm110) cc_final: 0.7288 (mm110) REVERT: c 66 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5202 (mmtt) REVERT: d 25 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: d 57 GLN cc_start: 0.8055 (pt0) cc_final: 0.7451 (tm-30) REVERT: e 78 ASN cc_start: 0.8899 (p0) cc_final: 0.8591 (p0) REVERT: f 8 TYR cc_start: 0.8615 (p90) cc_final: 0.8349 (p90) REVERT: f 44 TYR cc_start: 0.8594 (m-80) cc_final: 0.8328 (m-80) REVERT: f 60 ARG cc_start: 0.7626 (mpt180) cc_final: 0.7233 (mpt180) REVERT: f 88 ASN cc_start: 0.8446 (m-40) cc_final: 0.8202 (m-40) REVERT: h 43 LEU cc_start: 0.9474 (tp) cc_final: 0.9179 (tp) REVERT: i 13 ASN cc_start: 0.8701 (p0) cc_final: 0.8378 (p0) REVERT: j 51 LEU cc_start: 0.9386 (tp) cc_final: 0.9119 (tt) REVERT: k 32 ASN cc_start: 0.7517 (m110) cc_final: 0.7268 (m110) REVERT: k 40 LYS cc_start: 0.9048 (mttt) cc_final: 0.8610 (mttp) REVERT: k 42 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8158 (ppt170) REVERT: l 53 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: l 80 ARG cc_start: 0.8124 (mpp-170) cc_final: 0.7632 (mpt180) REVERT: m 5 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8126 (p) REVERT: m 14 TYR cc_start: 0.8995 (m-80) cc_final: 0.8381 (m-80) REVERT: n 9 ASN cc_start: 0.8225 (t0) cc_final: 0.7723 (t0) REVERT: n 11 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6464 (t0) REVERT: n 62 MET cc_start: 0.7959 (mmm) cc_final: 0.7222 (mmm) REVERT: n 188 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7315 (ttm170) REVERT: z 385 MET cc_start: 0.6774 (ptm) cc_final: 0.6471 (ptt) REVERT: w 17 LEU cc_start: 0.1631 (OUTLIER) cc_final: 0.1146 (pp) REVERT: w 275 LEU cc_start: 0.8309 (mm) cc_final: 0.7792 (tp) REVERT: w 359 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6426 (mp) REVERT: s 231 ARG cc_start: 0.0761 (OUTLIER) cc_final: 0.0482 (mtp85) REVERT: s 273 ILE cc_start: 0.0115 (OUTLIER) cc_final: -0.0132 (mp) outliers start: 287 outliers final: 247 residues processed: 1123 average time/residue: 1.0621 time to fit residues: 2102.2754 Evaluate side-chains 1180 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 915 time to evaluate : 6.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 165 GLN Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 160 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 198 TYR Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 166 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 105 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 65 TYR Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 14 ILE Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 56 THR Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 46 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 109 CYS Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain v residue 5 ILE Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 195 VAL Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 382 SER Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 404 VAL Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 433 ILE Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 505 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 271 ILE Chi-restraints excluded: chain s residue 273 ILE Chi-restraints excluded: chain s residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 922 optimal weight: 4.9990 chunk 608 optimal weight: 20.0000 chunk 979 optimal weight: 40.0000 chunk 597 optimal weight: 0.9990 chunk 464 optimal weight: 9.9990 chunk 680 optimal weight: 5.9990 chunk 1027 optimal weight: 10.0000 chunk 945 optimal weight: 1.9990 chunk 817 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 631 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN G 102 ASN L 132 ASN M 56 GLN N 39 HIS Q 136 ASN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 138868 Z= 0.199 Angle : 0.558 12.615 204325 Z= 0.285 Chirality : 0.034 0.488 25651 Planarity : 0.004 0.130 13188 Dihedral : 22.947 179.947 60843 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 4.63 % Allowed : 27.32 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 6829 helix: -0.82 (0.12), residues: 2016 sheet: -1.49 (0.17), residues: 907 loop : -1.87 (0.10), residues: 3906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP w 155 HIS 0.012 0.001 HIS W 53 PHE 0.024 0.001 PHE V 95 TYR 0.037 0.001 TYR J 167 ARG 0.015 0.000 ARG Z 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13658 Ramachandran restraints generated. 6829 Oldfield, 0 Emsley, 6829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 934 time to evaluate : 5.885 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE G 176 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG R 151 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.8836 (mtt) cc_final: 0.8449 (mmt) REVERT: C 123 TYR cc_start: 0.9087 (p90) cc_final: 0.8693 (p90) REVERT: C 332 ARG cc_start: 0.7855 (pmt170) cc_final: 0.7343 (ptp-110) REVERT: C 369 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8044 (mtp85) REVERT: D 110 ASN cc_start: 0.8881 (m-40) cc_final: 0.8598 (m-40) REVERT: E 9 MET cc_start: 0.7696 (mtm) cc_final: 0.7161 (ptp) REVERT: E 11 ASP cc_start: 0.6540 (p0) cc_final: 0.6149 (t0) REVERT: E 57 PHE cc_start: 0.2028 (m-10) cc_final: 0.1483 (m-10) REVERT: F 5 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 7 GLU cc_start: 0.7665 (pp20) cc_final: 0.7381 (pp20) REVERT: F 24 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6309 (mp) REVERT: F 78 MET cc_start: 0.7032 (ttp) cc_final: 0.6733 (tmm) REVERT: F 153 ASP cc_start: 0.8146 (m-30) cc_final: 0.7865 (m-30) REVERT: G 46 ARG cc_start: 0.8208 (tmt170) cc_final: 0.7707 (ttp80) REVERT: H 130 TYR cc_start: 0.7701 (m-80) cc_final: 0.7374 (m-80) REVERT: J 41 ASN cc_start: 0.8593 (m-40) cc_final: 0.8283 (m-40) REVERT: J 167 TYR cc_start: 0.8637 (t80) cc_final: 0.8329 (t80) REVERT: K 11 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8134 (mttp) REVERT: K 160 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: K 176 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8173 (tm-30) REVERT: K 183 ARG cc_start: 0.6744 (mtt90) cc_final: 0.6442 (ptp-170) REVERT: L 15 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7793 (mm) REVERT: M 22 LEU cc_start: 0.9137 (tp) cc_final: 0.8836 (tt) REVERT: M 121 MET cc_start: 0.8061 (tmm) cc_final: 0.7501 (tmm) REVERT: N 8 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8808 (t) REVERT: O 77 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7539 (tttt) REVERT: O 152 CYS cc_start: 0.7742 (t) cc_final: 0.7365 (t) REVERT: P 183 TRP cc_start: 0.8400 (t60) cc_final: 0.8114 (t-100) REVERT: Q 78 ASN cc_start: 0.8223 (m-40) cc_final: 0.7771 (t0) REVERT: R 103 ARG cc_start: 0.7350 (mtt180) cc_final: 0.7019 (ttm170) REVERT: R 109 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: S 91 TYR cc_start: 0.7354 (t80) cc_final: 0.7028 (t80) REVERT: S 93 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7066 (mm-30) REVERT: S 110 MET cc_start: 0.9065 (tpp) cc_final: 0.8720 (tpp) REVERT: U 64 ASN cc_start: 0.8570 (p0) cc_final: 0.8233 (p0) REVERT: V 49 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7632 (p0) REVERT: V 89 LEU cc_start: 0.8638 (mp) cc_final: 0.8410 (mp) REVERT: W 77 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: X 17 LYS cc_start: 0.8548 (tttp) cc_final: 0.8062 (tttt) REVERT: X 46 LYS cc_start: 0.8902 (mttt) cc_final: 0.8654 (mttt) REVERT: Y 126 LYS cc_start: 0.5910 (mmtt) cc_final: 0.5338 (tptt) REVERT: Y 135 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8227 (mmm-85) REVERT: a 22 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8185 (mtmt) REVERT: c 66 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5319 (mmtt) REVERT: d 25 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8252 (m-10) REVERT: d 57 GLN cc_start: 0.8055 (pt0) cc_final: 0.7464 (tm-30) REVERT: e 78 ASN cc_start: 0.8908 (p0) cc_final: 0.8606 (p0) REVERT: f 44 TYR cc_start: 0.8586 (m-80) cc_final: 0.8324 (m-80) REVERT: f 60 ARG cc_start: 0.7657 (mpt180) cc_final: 0.7234 (mpt180) REVERT: f 88 ASN cc_start: 0.8462 (m-40) cc_final: 0.8215 (m-40) REVERT: h 43 LEU cc_start: 0.9477 (tp) cc_final: 0.9171 (tp) REVERT: i 13 ASN cc_start: 0.8743 (p0) cc_final: 0.8373 (p0) REVERT: j 51 LEU cc_start: 0.9361 (tp) cc_final: 0.9111 (tt) REVERT: k 13 MET cc_start: 0.8385 (mmm) cc_final: 0.8159 (mmt) REVERT: k 28 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7276 (ttm110) REVERT: k 32 ASN cc_start: 0.7501 (m110) cc_final: 0.7218 (m-40) REVERT: k 40 LYS cc_start: 0.9068 (mttt) cc_final: 0.8626 (mttp) REVERT: k 42 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8137 (ppt170) REVERT: l 53 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: l 80 ARG cc_start: 0.8065 (mpp-170) cc_final: 0.7640 (mpt180) REVERT: m 5 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8118 (p) REVERT: m 14 TYR cc_start: 0.8952 (m-80) cc_final: 0.8593 (m-80) REVERT: n 9 ASN cc_start: 0.8199 (t0) cc_final: 0.7683 (t0) REVERT: n 11 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.6470 (t0) REVERT: n 62 MET cc_start: 0.7920 (mmm) cc_final: 0.7245 (mmm) REVERT: n 188 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7360 (ttm170) REVERT: z 385 MET cc_start: 0.6777 (ptm) cc_final: 0.6476 (ptt) REVERT: w 17 LEU cc_start: 0.1627 (OUTLIER) cc_final: 0.1129 (pp) REVERT: w 275 LEU cc_start: 0.8309 (mm) cc_final: 0.7847 (tp) REVERT: w 359 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6408 (mp) REVERT: o 182 GLU cc_start: 0.1511 (OUTLIER) cc_final: 0.1198 (mm-30) REVERT: s 231 ARG cc_start: 0.0481 (OUTLIER) cc_final: 0.0114 (mtp85) REVERT: s 273 ILE cc_start: 0.0114 (OUTLIER) cc_final: -0.0126 (mp) outliers start: 270 outliers final: 235 residues processed: 1112 average time/residue: 1.1330 time to fit residues: 2229.1007 Evaluate side-chains 1178 residues out of total 5837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 924 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 71 HIS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 107 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 160 GLN Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 176 LYS Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 183 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 185 PHE Chi-restraints excluded: chain P residue 198 TYR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 166 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain U residue 16 SER Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain V residue 14 THR Chi-restraints excluded: chain V residue 17 VAL Chi-restraints excluded: chain V residue 29 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 73 VAL Chi-restraints excluded: chain X residue 80 VAL Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain Z residue 85 THR Chi-restraints excluded: chain a residue 21 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 119 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 39 SER Chi-restraints excluded: chain c residue 66 LYS Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 8 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 25 PHE Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 6 HIS Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 40 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 59 VAL Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 76 TYR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain g residue 83 ASN Chi-restraints excluded: chain g residue 84 CYS Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain j residue 6 THR Chi-restraints excluded: chain j residue 20 VAL Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 42 ARG Chi-restraints excluded: chain l residue 7 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 53 GLN Chi-restraints excluded: chain l residue 65 THR Chi-restraints excluded: chain l residue 83 LEU Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 8 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 77 THR Chi-restraints excluded: chain n residue 147 LEU Chi-restraints excluded: chain n residue 205 VAL Chi-restraints excluded: chain z residue 386 VAL Chi-restraints excluded: chain w residue 16 THR Chi-restraints excluded: chain w residue 17 LEU Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 61 CYS Chi-restraints excluded: chain w residue 105 THR Chi-restraints excluded: chain w residue 123 MET Chi-restraints excluded: chain w residue 134 VAL Chi-restraints excluded: chain w residue 138 VAL Chi-restraints excluded: chain w residue 165 VAL Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 189 SER Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 242 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 290 THR Chi-restraints excluded: chain w residue 307 ASN Chi-restraints excluded: chain w residue 328 ILE Chi-restraints excluded: chain w residue 348 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain v residue 49 ILE Chi-restraints excluded: chain o residue 166 LEU Chi-restraints excluded: chain o residue 177 LEU Chi-restraints excluded: chain o residue 182 GLU Chi-restraints excluded: chain o residue 192 TRP Chi-restraints excluded: chain o residue 211 LEU Chi-restraints excluded: chain o residue 216 VAL Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 365 SER Chi-restraints excluded: chain o residue 382 SER Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 404 VAL Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 414 LEU Chi-restraints excluded: chain o residue 433 ILE Chi-restraints excluded: chain o residue 443 THR Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain o residue 485 ARG Chi-restraints excluded: chain o residue 488 LEU Chi-restraints excluded: chain o residue 505 LEU Chi-restraints excluded: chain s residue 231 ARG Chi-restraints excluded: chain s residue 271 ILE Chi-restraints excluded: chain s residue 273 ILE Chi-restraints excluded: chain s residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1031 random chunks: chunk 501 optimal weight: 6.9990 chunk 649 optimal weight: 20.0000 chunk 871 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 754 optimal weight: 9.9990 chunk 120 optimal weight: 40.0000 chunk 227 optimal weight: 40.0000 chunk 819 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 841 optimal weight: 0.2980 chunk 103 optimal weight: 20.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 ASN G 102 ASN M 56 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 65 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095168 restraints weight = 297462.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095444 restraints weight = 206197.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095864 restraints weight = 161087.232| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 138868 Z= 0.240 Angle : 0.591 59.192 204325 Z= 0.308 Chirality : 0.035 0.461 25651 Planarity : 0.005 0.130 13188 Dihedral : 22.943 179.926 60840 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.57 % Favored : 92.40 % Rotamer: Outliers : 4.68 % Allowed : 27.18 % Favored : 68.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6829 helix: -0.83 (0.12), residues: 2022 sheet: -1.48 (0.17), residues: 907 loop : -1.87 (0.10), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 358 HIS 0.011 0.001 HIS W 53 PHE 0.022 0.001 PHE V 95 TYR 0.033 0.001 TYR J 167 ARG 0.023 0.000 ARG U 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30343.64 seconds wall clock time: 532 minutes 28.44 seconds (31948.44 seconds total)