Starting phenix.real_space_refine on Sun Feb 18 04:46:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ri5_4884/02_2024/6ri5_4884.pdb" } resolution = 3.3 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= 0.002 sd= 0.017 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 7 6.06 5 P 3420 5.49 5 S 132 5.16 5 C 68732 2.51 5 N 23969 2.21 5 O 33879 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 109": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 357": "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 GLU 78": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "J PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J GLU 165": "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 GLU 155": "OE1" <-> "OE2" Residue "K ARG 157": "NH1" <-> "NH2" 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 ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 49": "NH1" <-> "NH2" 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 186": "OE1" <-> "OE2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 95": "OE1" <-> "OE2" 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 TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 21": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 56": "NH1" <-> "NH2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "W TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Z GLU 8": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d GLU 83": "OE1" <-> "OE2" 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 87": "OE1" <-> "OE2" Residue "g GLU 97": "OE1" <-> "OE2" Residue "h ARG 99": "NH1" <-> "NH2" Residue "i ARG 63": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" 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 32": "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 127": "OE1" <-> "OE2" Residue "n GLU 171": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "n GLU 214": "OE1" <-> "OE2" Residue "n GLU 219": "OE1" <-> "OE2" 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 75": "OE1" <-> "OE2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w ARG 79": "NH1" <-> "NH2" Residue "w ARG 87": "NH1" <-> "NH2" Residue "w ARG 88": "NH1" <-> "NH2" Residue "w ARG 96": "NH1" <-> "NH2" Residue "w GLU 106": "OE1" <-> "OE2" Residue "w ARG 111": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w ARG 169": "NH1" <-> "NH2" Residue "w ARG 303": "NH1" <-> "NH2" Residue "w GLU 317": "OE1" <-> "OE2" Residue "w ARG 330": "NH1" <-> "NH2" Residue "w ARG 333": "NH1" <-> "NH2" Residue "w ARG 342": "NH1" <-> "NH2" Residue "v GLU 4": "OE1" <-> "OE2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "v PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 141": "OE1" <-> "OE2" Residue "o GLU 144": "OE1" <-> "OE2" Residue "o ARG 153": "NH1" <-> "NH2" Residue "o GLU 157": "OE1" <-> "OE2" Residue "o ARG 163": "NH1" <-> "NH2" Residue "o GLU 182": "OE1" <-> "OE2" Residue "o GLU 186": "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 ARG 228": "NH1" <-> "NH2" Residue "o ARG 246": "NH1" <-> "NH2" Residue "o PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 303": "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 GLU 459": "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 "q ARG 4": "NH1" <-> "NH2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q GLU 58": "OE1" <-> "OE2" Residue "q GLU 63": "OE1" <-> "OE2" Residue "q ARG 110": "NH1" <-> "NH2" Residue "q ARG 139": "NH1" <-> "NH2" Residue "q ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 130139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 67312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3147, 67312 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "'] Classifications: {'RNA': 3147} Modifications used: {'5*END': 2, 'rna2p_pur': 319, 'rna2p_pyr': 205, 'rna3p_pur': 1429, 'rna3p_pyr': 1194} Link IDs: {'rna2p': 524, 'rna3p': 2622} 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: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2896 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain breaks: 2 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: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2569 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} 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: "q" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1754 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain: "t" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} 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': 14, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} 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: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A06KA SG CYS g 44 125.672 117.055 199.940 1.00 45.67 S ATOM A06KS SG CYS g 47 121.445 116.546 199.564 1.00 49.47 S ATOM A06SD SG CYS g 84 123.848 114.250 202.110 1.00 52.39 S ATOM A07M3 SG CYS i 19 147.842 132.968 149.535 1.00 34.33 S ATOM A07MS SG CYS i 22 147.803 135.217 145.635 1.00 36.38 S ATOM A07PK SG CYS i 34 145.690 131.929 146.550 1.00 32.61 S ATOM A07Q2 SG CYS i 37 149.552 131.553 146.286 1.00 33.82 S ATOM A08WC SG CYS l 12 144.561 61.346 85.143 1.00 57.65 S ATOM A08XB SG CYS l 17 146.336 58.522 84.613 1.00 67.00 S ATOM A09A7 SG CYS l 74 142.969 57.801 87.704 1.00 56.43 S ATOM A09AT SG CYS l 77 146.701 59.196 87.750 1.00 58.08 S ATOM A09NG SG CYS m 39 108.613 105.233 197.065 1.00 48.04 S ATOM A09R4 SG CYS m 57 109.604 108.408 196.218 1.00 47.26 S ATOM A09RM SG CYS m 60 112.608 106.661 197.584 1.00 47.73 S ATOM A0BN5 SG CYS w 19 24.140 122.907 129.117 1.00142.04 S ATOM A0BQ1 SG CYS w 35 24.776 118.226 129.107 1.00153.78 S ATOM A0II3 SG CYS t 96 55.800 129.932 79.685 1.00103.50 S ATOM A0IIT SG CYS t 99 56.075 133.225 81.489 1.00 97.77 S ATOM A0IL8 SG CYS t 110 55.986 134.370 78.245 1.00 97.58 S Time building chain proxies: 48.19, per 1000 atoms: 0.37 Number of scatterers: 130139 At special positions: 0 Unit cell: (231.105, 227.91, 248.145, 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 7 29.99 S 132 16.00 P 3420 15.00 O 33879 8.00 N 23969 7.00 C 68732 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: 50.00 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 19 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 22 " 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 60 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 39 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 57 " pdb=" ZN t 201 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 110 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 99 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 96 " pdb=" ZN w 602 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 35 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 19 " Number of angles added : 12 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13538 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 77 sheets defined 33.0% alpha, 14.5% beta 1037 base pairs and 1758 stacking pairs defined. Time for finding SS restraints: 40.57 Creating SS restraints... Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.888A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.658A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'D' and resid 31 through 43 removed outlier: 3.909A pdb=" N SER D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.563A pdb=" N THR D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.630A pdb=" N GLY D 139 " --> pdb=" O VAL D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 removed outlier: 3.595A pdb=" N GLU D 157 " --> pdb=" O THR D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.744A pdb=" N ALA D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 252 through 263 removed outlier: 4.090A pdb=" N LYS D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.910A pdb=" N ILE D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 320 through 328 removed outlier: 3.697A pdb=" N LEU D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 338 through 342 removed outlier: 4.052A pdb=" N LYS D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.828A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 35 removed outlier: 3.718A pdb=" N THR E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 removed outlier: 3.729A pdb=" N LEU E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 85 removed outlier: 3.853A pdb=" N GLU E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.772A pdb=" N VAL E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR E 139 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.792A pdb=" N LYS E 153 " --> pdb=" O ASN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'F' and resid 63 through 84 removed outlier: 3.705A pdb=" N ALA F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 150 through 165 removed outlier: 4.036A pdb=" N GLN F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 150 removed outlier: 4.268A pdb=" N VAL G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA G 147 " --> pdb=" O LYS G 143 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 removed outlier: 4.307A pdb=" N GLN H 59 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 83 through 96 Processing helix chain 'H' and resid 101 through 116 removed outlier: 3.516A pdb=" N LYS H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 145 Processing helix chain 'H' and resid 165 through 173 Processing helix chain 'H' and resid 182 through 190 removed outlier: 4.002A pdb=" N LEU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.698A pdb=" N ALA H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 239 through 247 removed outlier: 4.276A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 3.701A pdb=" N SER J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 removed outlier: 3.549A pdb=" N ALA J 39 " --> pdb=" O ARG J 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 39' Processing helix chain 'J' and resid 45 through 58 removed outlier: 3.701A pdb=" N TYR J 53 " --> pdb=" O ASN J 49 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE J 56 " --> pdb=" O LYS J 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG J 58 " --> pdb=" O HIS J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 93 through 98 Processing helix chain 'J' and resid 119 through 122 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'J' and resid 148 through 183 removed outlier: 3.678A pdb=" N VAL J 152 " --> pdb=" O TYR J 148 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS J 154 " --> pdb=" O ASP J 150 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU J 165 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER J 179 " --> pdb=" O LYS J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 197 removed outlier: 3.598A pdb=" N LEU J 193 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE J 196 " --> pdb=" O GLN J 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 28 No H-bonds generated for 'chain 'K' and resid 26 through 28' Processing helix chain 'K' and resid 29 through 46 removed outlier: 3.792A pdb=" N VAL K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.784A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 122 removed outlier: 3.793A pdb=" N ALA K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN K 114 " --> pdb=" O ASP K 110 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU K 116 " --> pdb=" O ASN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'K' and resid 165 through 186 removed outlier: 3.814A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY K 181 " --> pdb=" O LYS K 177 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE K 182 " --> pdb=" O LYS K 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.653A pdb=" N ALA L 130 " --> pdb=" O TRP L 126 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 110 Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.618A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN M 126 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 77 through 82 removed outlier: 4.007A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 removed outlier: 4.108A pdb=" N ASP N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 131 through 142 removed outlier: 3.921A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 11 Processing helix chain 'O' and resid 16 through 32 removed outlier: 3.957A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 removed outlier: 3.959A pdb=" N ARG O 50 " --> pdb=" O ASP O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.600A pdb=" N GLN O 87 " --> pdb=" O PRO O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 108 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 148 through 157 Proline residue: O 154 - end of helix removed outlier: 3.952A pdb=" N LYS O 157 " --> pdb=" O PRO O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 173 removed outlier: 4.107A pdb=" N SER O 171 " --> pdb=" O THR O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 194 Processing helix chain 'P' and resid 9 through 14 removed outlier: 3.996A pdb=" N SER P 13 " --> pdb=" O SER P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 29 through 38 removed outlier: 3.960A pdb=" N ARG P 35 " --> pdb=" O TYR P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 86 Proline residue: P 84 - end of helix No H-bonds generated for 'chain 'P' and resid 81 through 86' Processing helix chain 'P' and resid 94 through 114 Processing helix chain 'P' and resid 157 through 170 removed outlier: 3.619A pdb=" N GLY P 161 " --> pdb=" O ALA P 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 200 removed outlier: 3.563A pdb=" N PHE P 200 " --> pdb=" O ARG P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 215 removed outlier: 4.310A pdb=" N ASP P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 224 removed outlier: 3.573A pdb=" N PHE P 219 " --> pdb=" O ASP P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 250 removed outlier: 3.690A pdb=" N SER P 242 " --> pdb=" O ASP P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 270 removed outlier: 3.717A pdb=" N SER P 269 " --> pdb=" O TYR P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 39 removed outlier: 4.311A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.702A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 75 through 78 removed outlier: 4.584A pdb=" N ASN Q 78 " --> pdb=" O GLY Q 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 78' Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 126 through 131 Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.863A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 47 removed outlier: 3.536A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 101 removed outlier: 3.693A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 112 removed outlier: 3.708A pdb=" N ALA R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 4.705A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 149 removed outlier: 3.723A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 46 Processing helix chain 'S' and resid 100 through 114 removed outlier: 3.822A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG S 113 " --> pdb=" O ASP S 109 " (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 26 through 30 Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.532A pdb=" N GLN T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 123 removed outlier: 4.048A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU T 107 " --> pdb=" O GLN T 103 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 35 Processing helix chain 'U' and resid 41 through 53 removed outlier: 4.138A pdb=" N TYR U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU U 49 " --> pdb=" O GLN U 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN U 50 " --> pdb=" O LYS U 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 77 Processing helix chain 'U' and resid 86 through 106 removed outlier: 4.055A pdb=" N LEU U 94 " --> pdb=" O PHE U 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN U 97 " --> pdb=" O GLY U 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 26 Processing helix chain 'V' and resid 29 through 41 Processing helix chain 'V' and resid 72 through 87 removed outlier: 3.669A pdb=" N LEU V 76 " --> pdb=" O SER V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 62 Processing helix chain 'W' and resid 71 through 79 removed outlier: 3.688A pdb=" N LYS W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU W 77 " --> pdb=" O MET W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 103 Processing helix chain 'W' and resid 131 through 140 Processing helix chain 'X' and resid 11 through 21 removed outlier: 3.597A pdb=" N TYR X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 30 removed outlier: 4.293A pdb=" N VAL X 29 " --> pdb=" O SER X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 44 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 115 through 123 Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 97 through 101 Processing helix chain 'Y' and resid 103 through 123 removed outlier: 4.137A pdb=" N VAL Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL Y 114 " --> pdb=" O ALA Y 110 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Y 121 " --> pdb=" O ALA Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 13 through 35 removed outlier: 3.796A pdb=" N ASP Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU Z 24 " --> pdb=" O GLN Z 20 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 68 removed outlier: 4.055A pdb=" N THR Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG Z 48 " --> pdb=" O ILE Z 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA Z 52 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL Z 57 " --> pdb=" O CYS Z 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU Z 64 " --> pdb=" O GLU Z 60 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL Z 66 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 91 Processing helix chain 'Z' and resid 101 through 111 Processing helix chain 'a' and resid 12 through 19 removed outlier: 4.217A pdb=" N ASN a 19 " --> pdb=" O LYS a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 57 removed outlier: 3.883A pdb=" N ASN a 42 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS a 48 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA a 57 " --> pdb=" O ALA a 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 72 removed outlier: 3.714A pdb=" N LYS b 38 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN b 61 " --> pdb=" O THR b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 106 removed outlier: 3.817A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 130 through 132 No H-bonds generated for 'chain 'b' and resid 130 through 132' Processing helix chain 'b' and resid 141 through 152 removed outlier: 3.697A pdb=" N LYS b 150 " --> pdb=" O GLN b 146 " (cutoff:3.500A) Processing helix chain 'b' and resid 166 through 174 removed outlier: 3.940A pdb=" N ASN b 172 " --> pdb=" O ILE b 168 " (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 182 through 190 removed outlier: 4.049A pdb=" N ILE b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 194 through 202 Processing helix chain 'b' and resid 235 through 241 removed outlier: 3.513A pdb=" N LEU b 239 " --> pdb=" O PHE b 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 20 Processing helix chain 'c' and resid 26 through 35 removed outlier: 3.671A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 63 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 43 removed outlier: 3.588A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS d 38 " --> pdb=" O LYS d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'e' and resid 78 through 83 removed outlier: 3.862A pdb=" N LEU e 82 " --> pdb=" O ASN e 78 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.701A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE e 108 " --> pdb=" O ASN e 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.592A pdb=" N LEU f 45 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 64 removed outlier: 3.609A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.685A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 34 through 49 removed outlier: 3.592A pdb=" N GLU h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 65 removed outlier: 3.636A pdb=" N ARG h 56 " --> pdb=" O PRO h 52 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY h 65 " --> pdb=" O ILE h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 78 removed outlier: 3.611A pdb=" N ARG h 70 " --> pdb=" O GLU h 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS h 71 " --> pdb=" O LYS h 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL h 72 " --> pdb=" O ARG h 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS h 74 " --> pdb=" O ARG h 70 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 100 removed outlier: 4.636A pdb=" N ALA h 85 " --> pdb=" O THR h 81 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 57 removed outlier: 3.653A pdb=" N HIS i 57 " --> pdb=" O ALA i 53 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 68 No H-bonds generated for 'chain 'i' and resid 66 through 68' Processing helix chain 'i' and resid 69 through 76 removed outlier: 3.719A pdb=" N ASN i 76 " --> pdb=" O ARG i 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 15 removed outlier: 3.727A pdb=" N PHE j 11 " --> pdb=" O ASP j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 69 removed outlier: 3.578A pdb=" N GLN j 67 " --> pdb=" O LYS j 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 19 Processing helix chain 'k' and resid 24 through 30 removed outlier: 3.530A pdb=" N LEU k 29 " --> pdb=" O TRP k 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 37 through 42 Processing helix chain 'l' and resid 42 through 47 Processing helix chain 'm' and resid 8 through 14 removed outlier: 3.871A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 34 removed outlier: 4.108A pdb=" N VAL m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 90 removed outlier: 3.813A pdb=" N VAL m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR m 82 " --> pdb=" O THR m 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 17 removed outlier: 3.881A pdb=" N PHE n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 36 removed outlier: 3.795A pdb=" N TYR n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 56 Processing helix chain 'n' and resid 58 through 63 removed outlier: 3.674A pdb=" N MET n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 87 removed outlier: 3.882A pdb=" N HIS n 83 " --> pdb=" O GLN n 79 " (cutoff:3.500A) removed outlier: 4.069A 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 124 through 134 removed outlier: 4.330A pdb=" N SER n 130 " --> pdb=" O GLU n 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 166 through 178 Processing helix chain 'n' and resid 211 through 224 removed outlier: 3.621A pdb=" N VAL n 217 " --> pdb=" O PRO n 213 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU n 224 " --> pdb=" O SER n 220 " (cutoff:3.500A) Processing helix chain 'z' and resid 379 through 387 removed outlier: 4.206A pdb=" N VAL z 386 " --> pdb=" O ASP z 382 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER z 387 " --> pdb=" O ARG z 383 " (cutoff:3.500A) Processing helix chain 'z' and resid 390 through 417 removed outlier: 3.666A pdb=" N LYS z 400 " --> pdb=" O LYS z 396 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA z 408 " --> pdb=" O LEU z 404 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE z 409 " --> pdb=" O GLU z 405 " (cutoff:3.500A) Processing helix chain 'z' and resid 418 through 421 removed outlier: 4.010A pdb=" N ASN z 421 " --> pdb=" O LYS z 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 418 through 421' Processing helix chain 'w' and resid 35 through 42 Processing helix chain 'w' and resid 79 through 88 removed outlier: 3.914A pdb=" N ALA w 83 " --> pdb=" O ARG w 79 " (cutoff:3.500A) Processing helix chain 'w' and resid 90 through 95 removed outlier: 4.137A pdb=" N THR w 93 " --> pdb=" O LYS w 90 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL w 95 " --> pdb=" O LEU w 92 " (cutoff:3.500A) Processing helix chain 'w' and resid 106 through 109 Processing helix chain 'w' and resid 169 through 182 removed outlier: 4.156A pdb=" N GLN w 176 " --> pdb=" O LEU w 172 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU w 179 " --> pdb=" O GLU w 175 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS w 180 " --> pdb=" O GLN w 176 " (cutoff:3.500A) Processing helix chain 'w' and resid 204 through 216 Processing helix chain 'w' and resid 260 through 267 Processing helix chain 'w' and resid 297 through 304 removed outlier: 4.215A pdb=" N TYR w 301 " --> pdb=" O SER w 297 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 42 Processing helix chain 'v' and resid 52 through 60 Processing helix chain 'o' and resid 147 through 173 removed outlier: 3.852A pdb=" N ASP o 152 " --> pdb=" O LYS o 148 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU o 155 " --> pdb=" O LEU o 151 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU o 169 " --> pdb=" O LYS o 165 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN o 170 " --> pdb=" O LEU o 166 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU o 171 " --> pdb=" O ALA o 167 " (cutoff:3.500A) Processing helix chain 'o' and resid 185 through 192 Processing helix chain 'o' and resid 209 through 213 removed outlier: 3.863A pdb=" N LEU o 212 " --> pdb=" O ASN o 209 " (cutoff:3.500A) Processing helix chain 'o' and resid 246 through 251 Processing helix chain 'o' and resid 418 through 427 removed outlier: 3.781A pdb=" N ARG o 427 " --> pdb=" O LEU o 423 " (cutoff:3.500A) Processing helix chain 'o' and resid 429 through 438 removed outlier: 3.804A pdb=" N ILE o 433 " --> pdb=" O PRO o 429 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA o 435 " --> pdb=" O TYR o 431 " (cutoff:3.500A) Processing helix chain 'o' and resid 463 through 468 Processing helix chain 'o' and resid 479 through 494 removed outlier: 4.556A pdb=" N ARG o 485 " --> pdb=" O PRO o 481 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR o 486 " --> pdb=" O ARG o 482 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 96 through 100 Processing helix chain 'p' and resid 140 through 145 Processing helix chain 'p' and resid 178 through 182 removed outlier: 3.534A pdb=" N UNK p 181 " --> pdb=" O UNK p 178 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N UNK p 182 " --> pdb=" O UNK p 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 178 through 182' Processing helix chain 'q' and resid 62 through 80 removed outlier: 3.997A pdb=" N TYR q 75 " --> pdb=" O CYS q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 84 Processing helix chain 'q' and resid 144 through 156 removed outlier: 3.821A pdb=" N GLU q 150 " --> pdb=" O ASP q 146 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 187 Processing helix chain 'q' and resid 205 through 212 removed outlier: 3.868A pdb=" N GLU q 212 " --> pdb=" O ASN q 208 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 89 removed outlier: 3.722A pdb=" N TYR t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 6.577A pdb=" N LEU B 58 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 48 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS B 60 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG B 64 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.481A 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 'C' and resid 42 through 43 removed outlier: 3.663A pdb=" N ALA C 42 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN C 184 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 157 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 88 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL C 87 " --> pdb=" O TRP C 106 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP C 106 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 89 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR C 104 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY C 91 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.663A pdb=" N ALA C 42 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN C 184 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 157 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 88 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 84 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.358A pdb=" N VAL C 57 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE C 359 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR C 55 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 339 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE C 215 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 282 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 325 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 284 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 58 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 74 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP C 80 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS C 50 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 227 Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 9 removed outlier: 7.251A pdb=" N VAL D 6 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN D 18 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL D 8 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.472A pdb=" N LEU D 150 " --> pdb=" O TRP D 250 " (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 'E' and resid 46 through 49 removed outlier: 3.686A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 46 through 49 removed outlier: 3.686A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 16 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 130 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.430A pdb=" N LEU E 91 " --> pdb=" O LEU E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 6 through 11 Processing sheet with id=AB5, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'F' and resid 132 through 135 removed outlier: 5.586A pdb=" N ARG F 91 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL F 181 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL F 93 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE F 179 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 100 through 105 removed outlier: 3.542A pdb=" N ARG F 124 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 77 through 79 removed outlier: 3.714A pdb=" N LYS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 177 through 179 removed outlier: 3.548A pdb=" N LEU H 150 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AC2, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC3, first strand: chain 'K' and resid 22 through 24 Processing sheet with id=AC4, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC5, first strand: chain 'K' and resid 123 through 125 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: 7.041A pdb=" N ASN L 33 " --> pdb=" O LYS L 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS L 63 " --> pdb=" O ASN L 33 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET L 59 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL L 39 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET L 57 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA L 99 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 7.457A 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: 6.288A pdb=" N PHE L 92 " --> pdb=" O LEU v 20 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL v 22 " --> pdb=" O PHE L 92 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR L 94 " --> pdb=" O VAL v 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AD1, first strand: chain 'M' and resid 55 through 59 removed outlier: 7.902A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA M 34 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 72 through 73 Processing sheet with id=AD3, first strand: chain 'N' and resid 101 through 103 removed outlier: 6.550A pdb=" N ILE N 102 " --> pdb=" O LYS N 126 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL N 125 " --> pdb=" O GLU N 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'O' and resid 36 through 39 removed outlier: 4.134A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR O 129 " --> pdb=" O TRP O 120 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TRP O 120 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU O 131 " --> pdb=" O SER O 118 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER O 118 " --> pdb=" O GLU O 131 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE O 133 " --> pdb=" O LEU O 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 73 through 79 removed outlier: 5.252A pdb=" N VAL P 74 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER P 66 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA P 76 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR P 49 " --> pdb=" O PHE P 145 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP P 147 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU P 51 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 120 through 122 removed outlier: 6.526A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 86 through 87 Processing sheet with id=AD8, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD9, first strand: chain 'S' and resid 56 through 63 removed outlier: 5.346A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 87 through 96 removed outlier: 6.863A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 83 through 92 removed outlier: 3.768A pdb=" N ARG T 83 " --> pdb=" O VAL T 80 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL T 67 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL T 63 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 139 through 141 Processing sheet with id=AE4, first strand: chain 'U' and resid 14 through 22 removed outlier: 3.991A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N HIS U 145 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL U 119 " --> pdb=" O HIS U 145 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU U 147 " --> pdb=" O ILE U 117 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE U 117 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL U 149 " --> pdb=" O SER U 115 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'U' and resid 128 through 131 removed outlier: 3.832A pdb=" N ARG U 135 " --> pdb=" O ARG U 131 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 54 through 57 removed outlier: 7.807A pdb=" N TYR V 103 " --> pdb=" O THR V 14 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR V 16 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU V 105 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP V 18 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N PHE V 107 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 42 through 43 Processing sheet with id=AE9, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.982A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS W 109 " --> pdb=" O ARG W 125 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AF2, first strand: chain 'X' and resid 94 through 98 removed outlier: 7.249A pdb=" N VAL X 85 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA X 79 " --> pdb=" O VAL X 73 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL X 73 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL X 85 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N GLU X 67 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU X 57 " --> pdb=" O ILE X 106 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE X 106 " --> pdb=" O LEU X 57 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 69 through 76 removed outlier: 7.108A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS Y 40 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU Y 42 " --> pdb=" O VAL Y 26 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE Y 46 " --> pdb=" O LYS Y 22 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS Y 22 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL Y 10 " --> pdb=" O THR Y 83 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 205 through 206 removed outlier: 4.686A pdb=" N SER b 113 " --> pdb=" O ARG b 88 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 153 through 156 Processing sheet with id=AF6, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.656A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 89 through 95 Processing sheet with id=AF8, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.955A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'f' and resid 9 through 18 removed outlier: 9.893A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.779A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL f 80 " --> pdb=" O THR f 74 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR f 74 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AG2, first strand: chain 'i' and resid 17 through 18 Processing sheet with id=AG3, first strand: chain 'j' and resid 3 through 5 removed outlier: 3.693A pdb=" N ARG j 3 " --> pdb=" O LEU j 51 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL j 55 " --> pdb=" O ILE j 5 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA j 23 " --> pdb=" O ASN j 76 " (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 12 removed outlier: 3.773A pdb=" N THR l 10 " --> pdb=" O THR l 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS l 19 " --> pdb=" O CYS l 12 " (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 18 through 20 Processing sheet with id=AG8, first strand: chain 'n' and resid 64 through 65 removed outlier: 3.523A pdb=" N GLN n 95 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL n 72 " --> pdb=" O GLN n 95 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'n' and resid 160 through 161 Processing sheet with id=AH1, first strand: chain 'n' and resid 198 through 199 Processing sheet with id=AH2, first strand: chain 'w' and resid 52 through 57 removed outlier: 5.878A pdb=" N ALA w 53 " --> pdb=" O ILE w 137 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE w 139 " --> pdb=" O ALA w 53 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE w 55 " --> pdb=" O ILE w 139 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG w 113 " --> pdb=" O ILE w 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'w' and resid 190 through 192 removed outlier: 3.535A pdb=" N GLU w 247 " --> pdb=" O LYS w 221 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS w 221 " --> pdb=" O GLU w 247 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'w' and resid 257 through 258 Processing sheet with id=AH5, first strand: chain 'w' and resid 283 through 286 Processing sheet with id=AH6, first strand: chain 'w' and resid 355 through 357 removed outlier: 4.031A pdb=" N VAL w 355 " --> pdb=" O ILE w 338 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP w 337 " --> pdb=" O VAL w 323 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL w 323 " --> pdb=" O ASP w 337 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR w 339 " --> pdb=" O LEU w 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU w 321 " --> pdb=" O THR w 339 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL w 396 " --> pdb=" O TYR w 372 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'v' and resid 4 through 5 Processing sheet with id=AH8, first strand: chain 'o' and resid 201 through 203 removed outlier: 6.246A pdb=" N VAL o 202 " --> pdb=" O VAL o 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'o' and resid 235 through 236 removed outlier: 6.728A pdb=" N VAL o 235 " --> pdb=" O TYR o 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'o' and resid 378 through 379 removed outlier: 3.914A pdb=" N LEU o 379 " --> pdb=" O VAL o 383 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL o 383 " --> pdb=" O LEU o 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'q' and resid 35 through 37 removed outlier: 3.996A pdb=" N PHE q 136 " --> pdb=" O LEU q 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS q 49 " --> pdb=" O SER q 168 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE q 166 " --> pdb=" O HIS q 51 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'q' and resid 59 through 61 removed outlier: 6.079A pdb=" N ILE q 99 " --> pdb=" O PRO q 122 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'q' and resid 190 through 192 Processing sheet with id=AI5, first strand: chain 't' and resid 102 through 103 1763 hydrogen bonds defined for protein. 4962 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2545 hydrogen bonds 4138 hydrogen bond angles 0 basepair planarities 1037 basepair parallelities 1758 stacking parallelities Total time for adding SS restraints: 193.52 Time building geometry restraints manager: 54.39 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: 22382 1.32 - 1.45: 55815 1.45 - 1.57: 54855 1.57 - 1.70: 6622 1.70 - 1.83: 203 Bond restraints: 139877 Sorted by residual: bond pdb=" CA ALA B 27 " pdb=" CB ALA B 27 " ideal model delta sigma weight residual 1.528 1.328 0.200 1.35e-02 5.49e+03 2.20e+02 bond pdb=" C LEU K 54 " pdb=" N ARG K 55 " ideal model delta sigma weight residual 1.327 1.208 0.119 1.39e-02 5.18e+03 7.34e+01 bond pdb=" CA GLU H 161 " pdb=" C GLU H 161 " ideal model delta sigma weight residual 1.525 1.430 0.095 1.35e-02 5.49e+03 4.91e+01 bond pdb=" C CYS w 143 " pdb=" N PRO w 144 " ideal model delta sigma weight residual 1.334 1.498 -0.164 2.34e-02 1.83e+03 4.89e+01 bond pdb=" CA ASN g 18 " pdb=" CB ASN g 18 " ideal model delta sigma weight residual 1.526 1.424 0.102 1.49e-02 4.50e+03 4.68e+01 ... (remaining 139872 not shown) Histogram of bond angle deviations from ideal: 93.17 - 102.09: 4523 102.09 - 111.01: 71231 111.01 - 119.93: 73422 119.93 - 128.85: 51377 128.85 - 137.77: 5110 Bond angle restraints: 205663 Sorted by residual: angle pdb=" C CYS w 143 " pdb=" N PRO w 144 " pdb=" CA PRO w 144 " ideal model delta sigma weight residual 119.84 137.77 -17.93 1.25e+00 6.40e-01 2.06e+02 angle pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 112.00 93.94 18.06 1.40e+00 5.10e-01 1.66e+02 angle pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" CD PRO C 18 " ideal model delta sigma weight residual 112.00 96.14 15.86 1.40e+00 5.10e-01 1.28e+02 angle pdb=" C PRO H 159 " pdb=" CA PRO H 159 " pdb=" CB PRO H 159 " ideal model delta sigma weight residual 111.56 125.70 -14.14 1.65e+00 3.67e-01 7.35e+01 angle pdb=" N VAL m 79 " pdb=" CA VAL m 79 " pdb=" C VAL m 79 " ideal model delta sigma weight residual 111.90 106.00 5.90 8.10e-01 1.52e+00 5.30e+01 ... (remaining 205658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 79678 35.96 - 71.93: 8086 71.93 - 107.89: 734 107.89 - 143.86: 24 143.86 - 179.82: 40 Dihedral angle restraints: 88562 sinusoidal: 67584 harmonic: 20978 Sorted by residual: dihedral pdb=" C5' C A3206 " pdb=" C4' C A3206 " pdb=" C3' C A3206 " pdb=" O3' C A3206 " ideal model delta sinusoidal sigma weight residual 147.00 72.96 74.04 1 8.00e+00 1.56e-02 1.09e+02 dihedral pdb=" C4' C A3206 " pdb=" C3' C A3206 " pdb=" C2' C A3206 " pdb=" C1' C A3206 " ideal model delta sinusoidal sigma weight residual -35.00 35.83 -70.83 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' C A3181 " pdb=" C1' C A3181 " pdb=" N1 C A3181 " pdb=" C2 C A3181 " ideal model delta sinusoidal sigma weight residual 200.00 20.58 179.42 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 88559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 24787 0.151 - 0.302: 978 0.302 - 0.453: 21 0.453 - 0.604: 1 0.604 - 0.755: 1 Chirality restraints: 25788 Sorted by residual: chirality pdb=" CA CYS l 77 " pdb=" N CYS l 77 " pdb=" C CYS l 77 " pdb=" CB CYS l 77 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" C PRO H 159 " pdb=" CB PRO H 159 " both_signs ideal model delta sigma weight residual False 2.72 2.18 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CB VAL Q 64 " pdb=" CA VAL Q 64 " pdb=" CG1 VAL Q 64 " pdb=" CG2 VAL Q 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 25785 not shown) Planarity restraints: 13359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 17 " 0.089 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO C 18 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 158 " 0.089 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO H 159 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS l 74 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C CYS l 74 " 0.074 2.00e-02 2.50e+03 pdb=" O CYS l 74 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL l 75 " -0.026 2.00e-02 2.50e+03 ... (remaining 13356 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.99: 6 1.99 - 2.72: 15385 2.72 - 3.45: 168976 3.45 - 4.17: 390824 4.17 - 4.90: 591562 Nonbonded interactions: 1166753 Sorted by model distance: nonbonded pdb=" OD1 ASP w 350 " pdb=" CB UNK p 123 " model vdw 1.267 3.440 nonbonded pdb=" CG ASP w 350 " pdb=" CB UNK p 123 " model vdw 1.340 3.670 nonbonded pdb=" C8 A A2468 " pdb=" CB UNK p 99 " model vdw 1.737 3.660 nonbonded pdb=" O ASP w 254 " pdb=" OH TYR w 372 " model vdw 1.962 2.440 nonbonded pdb=" O2' A A2468 " pdb=" O UNK p 99 " model vdw 1.977 2.440 ... (remaining 1166748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.120 Extract box with map and model: 13.870 Check model and map are aligned: 1.390 Set scattering table: 0.850 Process input model: 442.740 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 466.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.016 0.208 139877 Z= 1.013 Angle : 1.146 18.058 205663 Z= 0.589 Chirality : 0.072 0.755 25788 Planarity : 0.007 0.124 13359 Dihedral : 22.502 179.820 75024 Min Nonbonded Distance : 1.267 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.60 % Favored : 90.20 % Rotamer: Outliers : 1.01 % Allowed : 9.15 % Favored : 89.84 % Cbeta Deviations : 0.09 % 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: -4.60 (0.08), residues: 6938 helix: -3.22 (0.08), residues: 2142 sheet: -2.66 (0.13), residues: 1033 loop : -3.11 (0.08), residues: 3763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP O 120 HIS 0.023 0.003 HIS e 21 PHE 0.027 0.003 PHE Q 35 TYR 0.034 0.003 TYR C 154 ARG 0.015 0.001 ARG O 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1548 time to evaluate : 6.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "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 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: "ASN b 244 " (corrupted residue). Skipping it. revert: symmetry clash 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 revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 SER cc_start: 0.7339 (t) cc_final: 0.6936 (p) REVERT: D 153 SER cc_start: 0.8263 (t) cc_final: 0.7999 (p) REVERT: E 17 LEU cc_start: 0.7448 (tt) cc_final: 0.7220 (tp) REVERT: H 28 HIS cc_start: 0.3768 (m-70) cc_final: 0.3394 (t-170) REVERT: H 95 ASN cc_start: 0.7085 (m-40) cc_final: 0.6722 (m-40) REVERT: H 189 LEU cc_start: 0.8047 (mp) cc_final: 0.7821 (mp) REVERT: J 41 ASN cc_start: 0.6986 (m110) cc_final: 0.6710 (m-40) REVERT: L 4 ASN cc_start: 0.5347 (OUTLIER) cc_final: 0.4418 (p0) REVERT: L 40 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8179 (mmtm) REVERT: L 115 THR cc_start: 0.8509 (m) cc_final: 0.8294 (p) REVERT: N 86 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7901 (mptt) REVERT: O 87 GLN cc_start: 0.8194 (pt0) cc_final: 0.7722 (pt0) REVERT: P 148 ILE cc_start: 0.8567 (pt) cc_final: 0.8220 (pt) REVERT: Q 66 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8425 (ttm110) REVERT: S 152 LEU cc_start: 0.8444 (mt) cc_final: 0.8145 (mp) REVERT: T 140 ILE cc_start: 0.9004 (mt) cc_final: 0.8759 (tt) REVERT: Y 64 LYS cc_start: 0.7044 (ttpp) cc_final: 0.6436 (tptt) REVERT: b 200 ASN cc_start: 0.6644 (t0) cc_final: 0.6383 (t0) REVERT: c 38 LYS cc_start: 0.7105 (mmtp) cc_final: 0.6799 (mmtt) REVERT: f 40 ASP cc_start: 0.7100 (p0) cc_final: 0.6852 (p0) REVERT: h 91 ASN cc_start: 0.7572 (m-40) cc_final: 0.7342 (m110) REVERT: l 24 LYS cc_start: 0.7631 (mmtt) cc_final: 0.6958 (tptt) REVERT: l 61 LYS cc_start: 0.7163 (tttm) cc_final: 0.6718 (mttt) REVERT: m 83 ILE cc_start: 0.8235 (mt) cc_final: 0.7822 (mt) REVERT: n 1 MET cc_start: 0.4220 (tpt) cc_final: 0.3973 (tpt) REVERT: n 164 GLN cc_start: 0.6657 (mp10) cc_final: 0.5863 (tm-30) REVERT: n 171 GLU cc_start: 0.7435 (pt0) cc_final: 0.7216 (tt0) REVERT: n 223 ARG cc_start: 0.5348 (mmm-85) cc_final: 0.4703 (ttm-80) REVERT: w 38 CYS cc_start: 0.5386 (OUTLIER) cc_final: 0.4942 (p) REVERT: w 58 CYS cc_start: 0.0527 (t) cc_final: 0.0098 (p) REVERT: w 96 ARG cc_start: 0.1198 (OUTLIER) cc_final: 0.0468 (mtm180) REVERT: w 132 PHE cc_start: 0.3246 (p90) cc_final: 0.2772 (p90) REVERT: w 180 LYS cc_start: -0.0334 (ptpt) cc_final: -0.0738 (mttm) REVERT: w 221 LYS cc_start: 0.4824 (mmmt) cc_final: 0.4474 (tptt) REVERT: w 287 ASP cc_start: 0.3650 (t0) cc_final: 0.2944 (t70) REVERT: w 356 ARG cc_start: 0.1890 (pmt170) cc_final: 0.1432 (mtp85) REVERT: o 183 ARG cc_start: 0.5950 (mtp85) cc_final: 0.5727 (ttt180) REVERT: q 31 ILE cc_start: 0.8744 (tt) cc_final: 0.8473 (tp) REVERT: q 121 LYS cc_start: 0.6569 (tttt) cc_final: 0.6178 (ttpt) REVERT: q 166 ILE cc_start: 0.8794 (mm) cc_final: 0.8527 (mm) REVERT: q 208 ASN cc_start: 0.7841 (t0) cc_final: 0.7598 (m-40) REVERT: q 216 TYR cc_start: 0.6918 (t80) cc_final: 0.6619 (t80) REVERT: t 112 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7668 (mmtp) outliers start: 60 outliers final: 22 residues processed: 1597 average time/residue: 1.3188 time to fit residues: 3481.3107 Evaluate side-chains 903 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 878 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 PRO Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 159 PRO Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 17 CYS Chi-restraints excluded: chain l residue 57 VAL Chi-restraints excluded: chain n residue 224 LEU Chi-restraints excluded: chain w residue 19 CYS Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 38 CYS Chi-restraints excluded: chain w residue 96 ARG Chi-restraints excluded: chain o residue 175 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 879 optimal weight: 1.9990 chunk 789 optimal weight: 0.0050 chunk 438 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 532 optimal weight: 6.9990 chunk 421 optimal weight: 1.9990 chunk 816 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 496 optimal weight: 0.9990 chunk 607 optimal weight: 3.9990 chunk 946 optimal weight: 0.8980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 218 HIS ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 269 GLN C 279 ASN D 5 GLN F 64 HIS F 100 ASN G 4 GLN G 61 ASN H 45 ASN H 191 ASN J 121 GLN K 25 HIS K 28 GLN M 105 GLN N 67 HIS P 45 ASN P 90 HIS Q 15 HIS Q 145 ASN R 3 ASN R 39 ASN S 89 ASN S 114 HIS T 66 ASN T 131 GLN U 96 GLN U 137 ASN V 87 ASN ** W 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 120 GLN Z 62 GLN Z 113 GLN a 12 GLN a 43 HIS b 80 GLN b 199 ASN c 12 GLN c 36 GLN c 75 ASN d 87 ASN e 21 HIS ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 ASN i 20 ASN ** i 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 50 ASN l 23 HIS ** l 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN n 82 GLN ** n 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 125 ASN w 130 GLN w 160 GLN ** w 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 32 GLN o 236 ASN o 354 ASN o 451 ASN o 504 HIS q 95 HIS q 208 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 139877 Z= 0.167 Angle : 0.621 10.824 205663 Z= 0.315 Chirality : 0.036 0.281 25788 Planarity : 0.005 0.162 13359 Dihedral : 22.875 179.396 60995 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 2.34 % Allowed : 14.36 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.01 % 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: -3.02 (0.09), residues: 6938 helix: -1.61 (0.10), residues: 2151 sheet: -1.66 (0.15), residues: 1013 loop : -2.39 (0.09), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 196 HIS 0.010 0.001 HIS l 23 PHE 0.032 0.002 PHE b 229 TYR 0.022 0.001 TYR D 120 ARG 0.019 0.001 ARG K 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1129 time to evaluate : 6.235 Fit side-chains 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 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 revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 GLU cc_start: 0.7055 (pt0) cc_final: 0.6852 (pm20) REVERT: D 65 TRP cc_start: 0.8346 (m-10) cc_final: 0.8142 (m-10) REVERT: D 153 SER cc_start: 0.8252 (t) cc_final: 0.7812 (p) REVERT: E 20 ASN cc_start: 0.6984 (t0) cc_final: 0.6702 (t0) REVERT: E 35 LYS cc_start: 0.6406 (mttt) cc_final: 0.5777 (mttt) REVERT: F 162 GLN cc_start: 0.7747 (pp30) cc_final: 0.7097 (tm-30) REVERT: G 78 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7455 (mtm180) REVERT: G 80 ASN cc_start: 0.7241 (t0) cc_final: 0.7026 (t0) REVERT: G 105 TYR cc_start: 0.6068 (t80) cc_final: 0.5713 (t80) REVERT: G 134 ARG cc_start: 0.6670 (tpp80) cc_final: 0.6339 (tpp80) REVERT: H 28 HIS cc_start: 0.3754 (m-70) cc_final: 0.3280 (t-170) REVERT: J 95 LYS cc_start: 0.8264 (mttt) cc_final: 0.8029 (mttp) REVERT: J 169 LYS cc_start: 0.7582 (tmtt) cc_final: 0.7344 (tmtt) REVERT: K 184 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7404 (mp0) REVERT: L 4 ASN cc_start: 0.5454 (OUTLIER) cc_final: 0.4693 (m110) REVERT: L 32 ARG cc_start: 0.7519 (mmp80) cc_final: 0.7235 (mmt-90) REVERT: L 115 THR cc_start: 0.8455 (m) cc_final: 0.8212 (p) REVERT: M 116 GLU cc_start: 0.7108 (mp0) cc_final: 0.6751 (mp0) REVERT: M 126 GLN cc_start: 0.7609 (mp10) cc_final: 0.7131 (mp10) REVERT: O 87 GLN cc_start: 0.8230 (pt0) cc_final: 0.7912 (pt0) REVERT: P 155 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8422 (p) REVERT: P 183 TRP cc_start: 0.7261 (t60) cc_final: 0.6981 (t60) REVERT: Q 66 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8261 (ttm110) REVERT: S 27 MET cc_start: 0.8450 (mtp) cc_final: 0.8248 (mtp) REVERT: S 85 SER cc_start: 0.8021 (p) cc_final: 0.7670 (p) REVERT: T 49 GLN cc_start: 0.8628 (mp10) cc_final: 0.8304 (mp10) REVERT: T 140 ILE cc_start: 0.9053 (mt) cc_final: 0.8776 (tt) REVERT: U 64 ASN cc_start: 0.8947 (p0) cc_final: 0.8746 (p0) REVERT: V 20 SER cc_start: 0.6037 (p) cc_final: 0.5827 (m) REVERT: X 46 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (tttp) REVERT: c 38 LYS cc_start: 0.6896 (mmtp) cc_final: 0.6588 (mmtt) REVERT: e 1 MET cc_start: 0.4083 (ptm) cc_final: 0.3747 (tpt) REVERT: h 36 ARG cc_start: 0.7515 (tpt-90) cc_final: 0.7197 (ttt-90) REVERT: h 91 ASN cc_start: 0.8180 (m-40) cc_final: 0.7948 (m110) REVERT: i 43 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8562 (mttt) REVERT: i 57 HIS cc_start: 0.8118 (m90) cc_final: 0.7698 (m170) REVERT: l 24 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6756 (tptt) REVERT: l 61 LYS cc_start: 0.7231 (tttm) cc_final: 0.6710 (mttt) REVERT: n 1 MET cc_start: 0.3611 (tpt) cc_final: 0.3095 (tpt) REVERT: n 4 ARG cc_start: 0.6114 (mtm180) cc_final: 0.5791 (mtm180) REVERT: n 85 ARG cc_start: 0.7415 (ttm170) cc_final: 0.7072 (ptt90) REVERT: n 164 GLN cc_start: 0.6918 (mp10) cc_final: 0.5752 (tm-30) REVERT: w 55 ILE cc_start: 0.2550 (tp) cc_final: 0.1869 (tt) REVERT: w 123 MET cc_start: 0.5786 (ttm) cc_final: 0.5519 (ttm) REVERT: w 221 LYS cc_start: 0.4982 (mmmt) cc_final: 0.4605 (tmtt) REVERT: o 153 ARG cc_start: 0.4229 (tpt170) cc_final: 0.3759 (mtt-85) REVERT: o 183 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5406 (ttt180) REVERT: o 212 LEU cc_start: 0.0346 (mt) cc_final: 0.0129 (tt) REVERT: o 354 ASN cc_start: 0.6007 (m-40) cc_final: 0.5211 (p0) REVERT: q 63 GLU cc_start: 0.7116 (mp0) cc_final: 0.6883 (mp0) REVERT: q 102 MET cc_start: 0.4149 (tmm) cc_final: 0.3460 (mtt) REVERT: q 166 ILE cc_start: 0.8802 (mm) cc_final: 0.8496 (mm) REVERT: q 208 ASN cc_start: 0.7976 (t0) cc_final: 0.7712 (m-40) REVERT: q 216 TYR cc_start: 0.6959 (t80) cc_final: 0.6655 (t80) outliers start: 139 outliers final: 91 residues processed: 1213 average time/residue: 1.1658 time to fit residues: 2411.8330 Evaluate side-chains 1014 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 920 time to evaluate : 6.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 159 PRO Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 21 SER Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain j residue 48 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 36 SER Chi-restraints excluded: chain n residue 52 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain o residue 239 ASP Chi-restraints excluded: chain o residue 241 LEU Chi-restraints excluded: chain o residue 341 LEU Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 159 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 525 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 787 optimal weight: 8.9990 chunk 644 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 947 optimal weight: 8.9990 chunk 1024 optimal weight: 10.0000 chunk 844 optimal weight: 8.9990 chunk 940 optimal weight: 1.9990 chunk 323 optimal weight: 9.9990 chunk 760 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 132 ASN B 187 HIS B 194 ASN B 215 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 GLN F 100 ASN F 157 ASN F 163 GLN G 97 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 HIS K 19 GLN N 40 HIS O 15 GLN P 45 ASN P 81 HIS P 90 HIS T 122 GLN U 96 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 ASN ** Y 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN e 35 GLN e 52 GLN e 104 ASN i 20 ASN j 28 ASN k 50 ASN ** l 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 GLN m 34 HIS n 95 GLN n 168 GLN ** n 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 425 HIS ** w 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 206 HIS ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 209 ASN q 14 ASN q 59 GLN q 133 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 139877 Z= 0.310 Angle : 0.651 12.396 205663 Z= 0.334 Chirality : 0.039 0.309 25788 Planarity : 0.006 0.156 13359 Dihedral : 22.657 179.954 60973 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % Rotamer: Outliers : 3.77 % Allowed : 16.85 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % 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: -2.40 (0.09), residues: 6938 helix: -1.06 (0.11), residues: 2164 sheet: -1.34 (0.15), residues: 1069 loop : -2.01 (0.09), residues: 3705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP o 188 HIS 0.010 0.002 HIS a 7 PHE 0.029 0.002 PHE b 229 TYR 0.051 0.002 TYR o 221 ARG 0.013 0.001 ARG o 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1059 time to evaluate : 6.373 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash 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 TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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 117 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 153 SER cc_start: 0.8151 (t) cc_final: 0.7683 (p) REVERT: E 35 LYS cc_start: 0.6438 (mttt) cc_final: 0.5816 (mttt) REVERT: E 157 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7849 (mm-30) REVERT: F 162 GLN cc_start: 0.8294 (pp30) cc_final: 0.7842 (tm-30) REVERT: G 78 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7437 (mtm180) REVERT: G 97 ASN cc_start: 0.6794 (OUTLIER) cc_final: 0.6349 (t0) REVERT: J 38 GLU cc_start: 0.7962 (pm20) cc_final: 0.7709 (pm20) REVERT: J 95 LYS cc_start: 0.8447 (mttt) cc_final: 0.8049 (mtpp) REVERT: J 133 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: J 169 LYS cc_start: 0.7768 (tmtt) cc_final: 0.7428 (tmtt) REVERT: J 173 PHE cc_start: 0.7454 (t80) cc_final: 0.6803 (m-80) REVERT: L 4 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5081 (p0) REVERT: L 73 VAL cc_start: 0.8881 (m) cc_final: 0.8583 (t) REVERT: L 88 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7272 (mtt180) REVERT: L 115 THR cc_start: 0.8633 (m) cc_final: 0.8117 (p) REVERT: L 125 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8774 (tt) REVERT: M 116 GLU cc_start: 0.7698 (mp0) cc_final: 0.7412 (mp0) REVERT: N 46 ASP cc_start: 0.8189 (m-30) cc_final: 0.7844 (m-30) REVERT: N 58 MET cc_start: 0.8882 (ptt) cc_final: 0.8559 (ptt) REVERT: O 87 GLN cc_start: 0.8353 (pt0) cc_final: 0.7949 (pt0) REVERT: P 95 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.7422 (t60) REVERT: P 155 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8686 (p) REVERT: T 140 ILE cc_start: 0.9153 (mt) cc_final: 0.8827 (tt) REVERT: U 64 ASN cc_start: 0.9058 (p0) cc_final: 0.8637 (p0) REVERT: V 20 SER cc_start: 0.6592 (p) cc_final: 0.6036 (m) REVERT: V 89 LEU cc_start: 0.7324 (mt) cc_final: 0.6947 (mp) REVERT: X 46 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8586 (tttp) REVERT: X 69 LYS cc_start: 0.8077 (pttt) cc_final: 0.7849 (mttt) REVERT: Y 64 LYS cc_start: 0.7127 (ttpp) cc_final: 0.6513 (tptt) REVERT: Z 20 GLN cc_start: 0.8256 (tp40) cc_final: 0.8049 (tp-100) REVERT: b 239 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8347 (tt) REVERT: e 1 MET cc_start: 0.4585 (ptm) cc_final: 0.4118 (tpt) REVERT: e 16 LYS cc_start: 0.8189 (tptt) cc_final: 0.7944 (tppt) REVERT: e 118 LYS cc_start: 0.8297 (tptt) cc_final: 0.7754 (tttt) REVERT: g 56 THR cc_start: 0.8722 (p) cc_final: 0.8499 (p) REVERT: g 67 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8642 (ttpt) REVERT: g 97 GLU cc_start: 0.7586 (tp30) cc_final: 0.6991 (tp30) REVERT: i 36 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8665 (t) REVERT: l 24 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7307 (tptt) REVERT: l 61 LYS cc_start: 0.7798 (tttm) cc_final: 0.7164 (mttt) REVERT: m 80 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7051 (mtt180) REVERT: n 4 ARG cc_start: 0.6374 (mtm180) cc_final: 0.6036 (mtm180) REVERT: n 57 ARG cc_start: 0.7433 (mtm180) cc_final: 0.7069 (mtm180) REVERT: n 164 GLN cc_start: 0.6980 (mp10) cc_final: 0.6728 (pm20) REVERT: n 187 ASN cc_start: 0.8002 (m110) cc_final: 0.7479 (m110) REVERT: w 22 CYS cc_start: 0.6091 (t) cc_final: 0.5761 (t) REVERT: w 55 ILE cc_start: 0.3650 (tp) cc_final: 0.3142 (tt) REVERT: w 58 CYS cc_start: -0.0236 (t) cc_final: -0.0469 (t) REVERT: w 210 MET cc_start: 0.3905 (tpp) cc_final: 0.2513 (ttt) REVERT: w 221 LYS cc_start: 0.4499 (mmmt) cc_final: 0.3945 (tmtt) REVERT: w 356 ARG cc_start: 0.3470 (ttm-80) cc_final: 0.3234 (ttm110) REVERT: v 1 MET cc_start: 0.1759 (ptt) cc_final: 0.0099 (tpp) REVERT: o 133 ASP cc_start: 0.0507 (OUTLIER) cc_final: 0.0173 (p0) REVERT: o 146 MET cc_start: 0.1893 (tpt) cc_final: 0.1291 (tpt) REVERT: o 153 ARG cc_start: 0.4463 (tpt170) cc_final: 0.3950 (mtt-85) REVERT: o 241 LEU cc_start: 0.1675 (OUTLIER) cc_final: 0.1292 (mp) REVERT: o 354 ASN cc_start: 0.6209 (m-40) cc_final: 0.5481 (p0) REVERT: q 7 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8574 (ttp-110) REVERT: q 102 MET cc_start: 0.4629 (tmm) cc_final: 0.3318 (mtt) outliers start: 224 outliers final: 153 residues processed: 1198 average time/residue: 1.2015 time to fit residues: 2479.1520 Evaluate side-chains 1085 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 919 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain G residue 97 ASN Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 213 ASP Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 239 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 48 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 80 ARG Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 36 SER Chi-restraints excluded: chain n residue 52 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 128 LEU Chi-restraints excluded: chain n residue 185 THR Chi-restraints excluded: chain n residue 198 VAL Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 103 ILE Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 170 THR Chi-restraints excluded: chain w residue 171 PHE Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 373 PHE Chi-restraints excluded: chain o residue 133 ASP Chi-restraints excluded: chain o residue 209 ASN Chi-restraints excluded: chain o residue 241 LEU Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 97 LEU Chi-restraints excluded: chain q residue 123 HIS Chi-restraints excluded: chain q residue 149 VAL Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 205 SER Chi-restraints excluded: chain t residue 91 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 936 optimal weight: 0.0020 chunk 712 optimal weight: 3.9990 chunk 491 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 452 optimal weight: 0.7980 chunk 636 optimal weight: 4.9990 chunk 951 optimal weight: 9.9990 chunk 1007 optimal weight: 0.4980 chunk 497 optimal weight: 0.0870 chunk 901 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 overall best weight: 1.0768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS B 86 GLN B 218 HIS ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 307 GLN F 157 ASN G 80 ASN G 97 ASN H 28 HIS H 38 GLN H 232 HIS J 121 GLN L 81 GLN O 15 GLN O 95 GLN ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS T 16 GLN U 96 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 65 GLN W 111 ASN X 4 GLN X 98 ASN Y 40 HIS b 80 GLN d 105 GLN h 63 ASN i 20 ASN l 47 GLN ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN ** n 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 203 GLN ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 209 ASN q 55 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 139877 Z= 0.134 Angle : 0.526 12.151 205663 Z= 0.272 Chirality : 0.034 0.296 25788 Planarity : 0.004 0.145 13359 Dihedral : 22.619 178.570 60967 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 3.10 % Allowed : 18.96 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.86 (0.10), residues: 6938 helix: -0.52 (0.11), residues: 2169 sheet: -1.04 (0.15), residues: 1065 loop : -1.74 (0.10), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 142 HIS 0.005 0.001 HIS C 259 PHE 0.029 0.001 PHE b 229 TYR 0.016 0.001 TYR D 194 ARG 0.006 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1028 time to evaluate : 6.493 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash 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: "ASN b 244 " (corrupted residue). Skipping it. revert: symmetry clash 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: symmetry clash REVERT: B 117 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8130 (mt-10) REVERT: B 118 GLU cc_start: 0.7254 (pt0) cc_final: 0.6984 (pm20) REVERT: D 153 SER cc_start: 0.8228 (t) cc_final: 0.7759 (p) REVERT: D 307 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: E 17 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8089 (tp) REVERT: E 35 LYS cc_start: 0.6392 (mttt) cc_final: 0.5920 (mttt) REVERT: E 52 TYR cc_start: 0.6848 (m-80) cc_final: 0.6643 (m-80) REVERT: E 157 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7926 (mm-30) REVERT: F 51 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7352 (mp10) REVERT: F 162 GLN cc_start: 0.8207 (pp30) cc_final: 0.7759 (tm-30) REVERT: F 166 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7339 (ptm160) REVERT: F 168 ARG cc_start: 0.6646 (tpp-160) cc_final: 0.6361 (tpp-160) REVERT: H 38 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.6088 (mt0) REVERT: H 207 ASP cc_start: 0.7838 (t0) cc_final: 0.7603 (t0) REVERT: J 38 GLU cc_start: 0.7967 (pm20) cc_final: 0.7683 (pm20) REVERT: J 95 LYS cc_start: 0.8502 (mttt) cc_final: 0.8106 (mtpp) REVERT: J 169 LYS cc_start: 0.7820 (tmtt) cc_final: 0.7618 (tmtt) REVERT: J 173 PHE cc_start: 0.7368 (t80) cc_final: 0.6767 (m-80) REVERT: K 114 GLN cc_start: 0.7779 (tp40) cc_final: 0.7386 (tp40) REVERT: L 4 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5073 (p0) REVERT: L 70 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7897 (ptp-170) REVERT: L 115 THR cc_start: 0.8650 (m) cc_final: 0.8114 (p) REVERT: L 125 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8946 (tt) REVERT: M 66 THR cc_start: 0.8668 (m) cc_final: 0.8145 (p) REVERT: M 126 GLN cc_start: 0.7855 (mt0) cc_final: 0.7645 (mp10) REVERT: N 46 ASP cc_start: 0.8168 (m-30) cc_final: 0.7828 (m-30) REVERT: O 87 GLN cc_start: 0.8210 (pt0) cc_final: 0.7863 (pt0) REVERT: P 95 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.7434 (t60) REVERT: P 155 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8515 (p) REVERT: P 216 GLU cc_start: 0.7087 (pm20) cc_final: 0.6119 (tt0) REVERT: P 273 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6682 (mmm-85) REVERT: R 20 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8028 (ptt180) REVERT: T 13 TYR cc_start: 0.8621 (m-80) cc_final: 0.8337 (m-80) REVERT: T 140 ILE cc_start: 0.9117 (mt) cc_final: 0.8774 (tt) REVERT: V 20 SER cc_start: 0.6645 (p) cc_final: 0.6059 (m) REVERT: W 64 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7428 (mt-10) REVERT: X 46 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8463 (tttp) REVERT: Y 64 LYS cc_start: 0.7080 (ttpp) cc_final: 0.6454 (tptt) REVERT: Y 119 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7409 (mm-30) REVERT: d 38 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7450 (ttmm) REVERT: e 1 MET cc_start: 0.4167 (ptm) cc_final: 0.3906 (tpt) REVERT: e 16 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8057 (tppt) REVERT: g 97 GLU cc_start: 0.7428 (tp30) cc_final: 0.6985 (tp30) REVERT: k 29 LEU cc_start: 0.8766 (mt) cc_final: 0.8207 (mt) REVERT: l 24 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7237 (tptt) REVERT: l 61 LYS cc_start: 0.7792 (tttm) cc_final: 0.7120 (mttt) REVERT: m 80 ARG cc_start: 0.7448 (mtt-85) cc_final: 0.7149 (mtt180) REVERT: n 4 ARG cc_start: 0.6397 (mtm180) cc_final: 0.6116 (mtm180) REVERT: n 139 ARG cc_start: 0.4902 (ptt180) cc_final: 0.4537 (ptt180) REVERT: n 164 GLN cc_start: 0.7082 (mp10) cc_final: 0.6877 (pm20) REVERT: n 187 ASN cc_start: 0.7960 (m110) cc_final: 0.7552 (m110) REVERT: w 55 ILE cc_start: 0.4283 (tp) cc_final: 0.3922 (tt) REVERT: w 203 GLN cc_start: 0.0704 (OUTLIER) cc_final: -0.0208 (tp40) REVERT: w 210 MET cc_start: 0.4014 (tpp) cc_final: 0.2541 (ttt) REVERT: o 133 ASP cc_start: 0.0466 (m-30) cc_final: 0.0219 (p0) REVERT: o 153 ARG cc_start: 0.4448 (tpt170) cc_final: 0.4001 (mtt-85) REVERT: o 183 ARG cc_start: 0.5780 (ttp-110) cc_final: 0.5580 (ttp-170) REVERT: o 212 LEU cc_start: 0.0970 (mt) cc_final: 0.0646 (tt) REVERT: o 241 LEU cc_start: 0.1690 (OUTLIER) cc_final: 0.1305 (mp) REVERT: o 344 TYR cc_start: 0.3483 (t80) cc_final: 0.2731 (t80) REVERT: o 354 ASN cc_start: 0.6294 (m-40) cc_final: 0.5477 (p0) REVERT: o 482 ARG cc_start: 0.2785 (ttm-80) cc_final: 0.1862 (ttm-80) REVERT: q 7 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8587 (ttp-110) REVERT: q 102 MET cc_start: 0.4760 (tmm) cc_final: 0.3531 (mtt) outliers start: 184 outliers final: 119 residues processed: 1146 average time/residue: 1.1408 time to fit residues: 2255.2312 Evaluate side-chains 1054 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 921 time to evaluate : 6.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 121 GLN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain e residue 16 LYS Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 52 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 185 THR Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain w residue 103 ILE Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 171 PHE Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 203 GLN Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 283 VAL Chi-restraints excluded: chain w residue 350 ASP Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 241 LEU Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 137 SER Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 838 optimal weight: 4.9990 chunk 571 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 749 optimal weight: 20.0000 chunk 415 optimal weight: 9.9990 chunk 859 optimal weight: 1.9990 chunk 696 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 514 optimal weight: 9.9990 chunk 904 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN G 80 ASN G 97 ASN H 155 ASN H 232 HIS K 19 GLN ** K 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN L 28 ASN M 56 GLN O 15 GLN ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS S 154 HIS U 72 GLN U 96 GLN U 120 ASN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN Z 61 GLN Z 113 GLN b 80 GLN g 33 GLN h 63 ASN i 20 ASN m 34 HIS ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN n 187 ASN w 203 GLN ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 209 ASN ** o 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 139877 Z= 0.262 Angle : 0.584 12.176 205663 Z= 0.300 Chirality : 0.037 0.406 25788 Planarity : 0.005 0.148 13359 Dihedral : 22.545 179.931 60966 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 4.33 % Allowed : 18.77 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.68 (0.10), residues: 6938 helix: -0.36 (0.11), residues: 2157 sheet: -0.91 (0.15), residues: 1055 loop : -1.63 (0.10), residues: 3726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 194 HIS 0.006 0.001 HIS R 141 PHE 0.029 0.002 PHE b 229 TYR 0.021 0.002 TYR E 128 ARG 0.011 0.001 ARG w 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 939 time to evaluate : 6.467 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. 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. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. 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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8208 (mt-10) REVERT: C 308 MET cc_start: 0.8655 (mmm) cc_final: 0.8301 (mtp) REVERT: D 153 SER cc_start: 0.8143 (t) cc_final: 0.7684 (p) REVERT: E 17 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8133 (tp) REVERT: E 35 LYS cc_start: 0.6675 (mttt) cc_final: 0.6204 (mttt) REVERT: E 40 LEU cc_start: 0.6842 (pp) cc_final: 0.6070 (tp) REVERT: E 52 TYR cc_start: 0.6966 (m-80) cc_final: 0.6678 (m-80) REVERT: E 157 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7891 (mm-30) REVERT: F 51 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7391 (mp10) REVERT: F 78 MET cc_start: 0.8931 (mtp) cc_final: 0.8681 (mtp) REVERT: F 162 GLN cc_start: 0.8257 (pp30) cc_final: 0.7836 (tm-30) REVERT: H 177 TYR cc_start: 0.8873 (p90) cc_final: 0.8646 (p90) REVERT: H 207 ASP cc_start: 0.7977 (t0) cc_final: 0.7695 (t0) REVERT: J 95 LYS cc_start: 0.8467 (mttt) cc_final: 0.8071 (mtpp) REVERT: J 133 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8139 (mtpp) REVERT: J 169 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7624 (tmtt) REVERT: J 173 PHE cc_start: 0.7444 (t80) cc_final: 0.6770 (m-80) REVERT: K 114 GLN cc_start: 0.7932 (tp40) cc_final: 0.7688 (tp40) REVERT: K 118 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7117 (mt-10) REVERT: L 70 ARG cc_start: 0.8266 (ptp90) cc_final: 0.8053 (ptp90) REVERT: L 125 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8955 (tt) REVERT: M 66 THR cc_start: 0.8802 (m) cc_final: 0.8250 (p) REVERT: M 126 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: N 46 ASP cc_start: 0.8211 (m-30) cc_final: 0.7903 (m-30) REVERT: N 58 MET cc_start: 0.8774 (ptt) cc_final: 0.8407 (ptt) REVERT: O 87 GLN cc_start: 0.8374 (pt0) cc_final: 0.8036 (pt0) REVERT: P 95 TRP cc_start: 0.8717 (OUTLIER) cc_final: 0.7758 (t60) REVERT: P 155 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8595 (p) REVERT: P 262 LYS cc_start: 0.7561 (tptm) cc_final: 0.7351 (tptp) REVERT: R 20 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7853 (ptt180) REVERT: T 140 ILE cc_start: 0.9159 (mt) cc_final: 0.8799 (tt) REVERT: U 146 ILE cc_start: 0.9322 (mt) cc_final: 0.9107 (mt) REVERT: V 20 SER cc_start: 0.6618 (p) cc_final: 0.6073 (m) REVERT: W 64 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7520 (mt-10) REVERT: W 133 LEU cc_start: 0.8325 (mm) cc_final: 0.8115 (mt) REVERT: Y 64 LYS cc_start: 0.7191 (ttpp) cc_final: 0.6351 (tptt) REVERT: b 239 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8246 (tt) REVERT: d 38 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7539 (ttmm) REVERT: e 1 MET cc_start: 0.4457 (ptm) cc_final: 0.4053 (tpt) REVERT: e 16 LYS cc_start: 0.8369 (tptt) cc_final: 0.8163 (tppt) REVERT: e 118 LYS cc_start: 0.8312 (tptt) cc_final: 0.7852 (tttt) REVERT: g 97 GLU cc_start: 0.7515 (tp30) cc_final: 0.6989 (tp30) REVERT: i 36 SER cc_start: 0.8990 (p) cc_final: 0.8672 (t) REVERT: l 24 LYS cc_start: 0.7663 (mmtt) cc_final: 0.7320 (tptt) REVERT: l 45 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7988 (ttt90) REVERT: l 61 LYS cc_start: 0.7923 (tttm) cc_final: 0.7189 (mttt) REVERT: n 4 ARG cc_start: 0.6484 (mtm180) cc_final: 0.6222 (mtm180) REVERT: n 164 GLN cc_start: 0.7173 (mp10) cc_final: 0.6918 (pm20) REVERT: n 187 ASN cc_start: 0.7899 (m-40) cc_final: 0.7540 (m-40) REVERT: w 55 ILE cc_start: 0.4035 (tp) cc_final: 0.3712 (tt) REVERT: w 200 PHE cc_start: 0.4615 (m-80) cc_final: 0.3269 (t80) REVERT: w 203 GLN cc_start: 0.0143 (OUTLIER) cc_final: -0.0464 (tp40) REVERT: o 133 ASP cc_start: 0.0772 (m-30) cc_final: 0.0570 (p0) REVERT: o 212 LEU cc_start: 0.1029 (mt) cc_final: 0.0716 (tt) REVERT: o 241 LEU cc_start: 0.1448 (OUTLIER) cc_final: 0.1050 (mp) REVERT: o 344 TYR cc_start: 0.3568 (t80) cc_final: 0.2771 (t80) REVERT: o 354 ASN cc_start: 0.6307 (m-40) cc_final: 0.5460 (p0) REVERT: o 482 ARG cc_start: 0.4183 (ttm-80) cc_final: 0.3139 (ttm-80) REVERT: q 102 MET cc_start: 0.4783 (tmm) cc_final: 0.3529 (mtt) outliers start: 257 outliers final: 190 residues processed: 1104 average time/residue: 1.1594 time to fit residues: 2229.1058 Evaluate side-chains 1096 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 896 time to evaluate : 6.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 126 GLN Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 144 VAL Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 213 ASP Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 96 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 172 ASN Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 239 LEU Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 99 LYS Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 72 VAL Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain l residue 3 ASN Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 52 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 185 THR Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 103 ILE Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 158 THR Chi-restraints excluded: chain w residue 170 THR Chi-restraints excluded: chain w residue 171 PHE Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 203 GLN Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 350 ASP Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 209 ASN Chi-restraints excluded: chain o residue 241 LEU Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 137 SER Chi-restraints excluded: chain q residue 149 VAL Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 338 optimal weight: 5.9990 chunk 907 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 591 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 1008 optimal weight: 10.0000 chunk 836 optimal weight: 0.0170 chunk 466 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 333 optimal weight: 0.4980 chunk 529 optimal weight: 1.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 157 ASN G 80 ASN H 137 ASN H 232 HIS J 121 GLN ** K 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 HIS ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN b 80 GLN i 20 ASN j 67 GLN m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN w 203 GLN ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 209 ASN ** o 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 139877 Z= 0.164 Angle : 0.526 13.446 205663 Z= 0.271 Chirality : 0.034 0.393 25788 Planarity : 0.004 0.144 13359 Dihedral : 22.526 178.656 60962 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 3.59 % Allowed : 19.78 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.41 (0.10), residues: 6938 helix: -0.09 (0.11), residues: 2162 sheet: -0.80 (0.15), residues: 1059 loop : -1.49 (0.10), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 162 HIS 0.022 0.001 HIS S 122 PHE 0.028 0.001 PHE b 229 TYR 0.019 0.001 TYR J 167 ARG 0.019 0.000 ARG m 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 951 time to evaluate : 6.330 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. 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. 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: "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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 308 MET cc_start: 0.8633 (mmm) cc_final: 0.8320 (mtp) REVERT: D 153 SER cc_start: 0.8173 (t) cc_final: 0.7708 (p) REVERT: E 35 LYS cc_start: 0.6632 (mttt) cc_final: 0.6244 (mttt) REVERT: E 40 LEU cc_start: 0.6773 (pp) cc_final: 0.6108 (tp) REVERT: E 52 TYR cc_start: 0.6963 (m-80) cc_final: 0.6550 (m-80) REVERT: F 7 GLU cc_start: 0.7475 (pt0) cc_final: 0.7129 (tt0) REVERT: F 51 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7383 (mp10) REVERT: F 162 GLN cc_start: 0.8207 (pp30) cc_final: 0.7909 (tm-30) REVERT: F 166 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7215 (ptm160) REVERT: H 177 TYR cc_start: 0.8842 (p90) cc_final: 0.8449 (p90) REVERT: H 207 ASP cc_start: 0.7909 (t0) cc_final: 0.7580 (t0) REVERT: J 95 LYS cc_start: 0.8508 (mttt) cc_final: 0.8107 (mtpp) REVERT: J 173 PHE cc_start: 0.7378 (t80) cc_final: 0.6724 (m-80) REVERT: K 118 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7172 (mt-10) REVERT: L 70 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7935 (ptp90) REVERT: M 66 THR cc_start: 0.8826 (m) cc_final: 0.8470 (p) REVERT: N 46 ASP cc_start: 0.8057 (m-30) cc_final: 0.7764 (m-30) REVERT: O 87 GLN cc_start: 0.8263 (pt0) cc_final: 0.7924 (pt0) REVERT: P 95 TRP cc_start: 0.8676 (OUTLIER) cc_final: 0.7789 (t60) REVERT: P 155 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8523 (p) REVERT: P 273 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6693 (mmm-85) REVERT: R 20 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7886 (ptt180) REVERT: T 140 ILE cc_start: 0.9162 (mt) cc_final: 0.8792 (tt) REVERT: U 146 ILE cc_start: 0.9292 (mt) cc_final: 0.9060 (mt) REVERT: V 20 SER cc_start: 0.6828 (p) cc_final: 0.6295 (m) REVERT: V 94 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7505 (ptm160) REVERT: W 64 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7501 (mt-10) REVERT: W 133 LEU cc_start: 0.8187 (mm) cc_final: 0.7939 (mt) REVERT: Y 64 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6335 (tptt) REVERT: Y 84 ARG cc_start: 0.7369 (ptm160) cc_final: 0.7159 (ptm160) REVERT: d 38 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7318 (ttmt) REVERT: d 69 TYR cc_start: 0.8846 (m-80) cc_final: 0.8632 (m-80) REVERT: e 1 MET cc_start: 0.4245 (ptm) cc_final: 0.3907 (tpt) REVERT: e 118 LYS cc_start: 0.8288 (tptt) cc_final: 0.7859 (tttt) REVERT: g 97 GLU cc_start: 0.7567 (tp30) cc_final: 0.7066 (tp30) REVERT: i 36 SER cc_start: 0.8981 (p) cc_final: 0.8689 (t) REVERT: k 29 LEU cc_start: 0.8706 (mt) cc_final: 0.8158 (mt) REVERT: l 24 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7272 (tptt) REVERT: l 61 LYS cc_start: 0.7860 (tttm) cc_final: 0.7089 (mttt) REVERT: n 164 GLN cc_start: 0.7133 (mp10) cc_final: 0.6909 (pm20) REVERT: n 187 ASN cc_start: 0.7969 (m-40) cc_final: 0.7624 (m110) REVERT: w 200 PHE cc_start: 0.4535 (m-80) cc_final: 0.3256 (t80) REVERT: w 203 GLN cc_start: 0.0629 (OUTLIER) cc_final: 0.0022 (tp40) REVERT: w 370 MET cc_start: -0.0736 (mmm) cc_final: -0.2480 (ptm) REVERT: o 133 ASP cc_start: 0.0820 (m-30) cc_final: 0.0528 (p0) REVERT: o 146 MET cc_start: 0.5251 (pmm) cc_final: 0.4352 (ptm) REVERT: o 212 LEU cc_start: 0.1005 (mt) cc_final: 0.0670 (tt) REVERT: o 344 TYR cc_start: 0.3532 (t80) cc_final: 0.2718 (t80) REVERT: o 354 ASN cc_start: 0.6223 (m-40) cc_final: 0.5290 (p0) REVERT: o 482 ARG cc_start: 0.4044 (ttm-80) cc_final: 0.3104 (ttm-80) REVERT: q 102 MET cc_start: 0.4928 (tmm) cc_final: 0.3668 (mtt) outliers start: 213 outliers final: 172 residues processed: 1077 average time/residue: 1.1091 time to fit residues: 2085.9069 Evaluate side-chains 1085 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 908 time to evaluate : 6.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain J residue 121 GLN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 213 ASP Chi-restraints excluded: chain P residue 275 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain X residue 5 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 47 ASN Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 52 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 185 THR Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 82 LEU Chi-restraints excluded: chain w residue 103 ILE Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 171 PHE Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 203 GLN Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 350 ASP Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 136 VAL Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 209 ASN Chi-restraints excluded: chain o residue 384 MET Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 972 optimal weight: 40.0000 chunk 113 optimal weight: 10.0000 chunk 574 optimal weight: 8.9990 chunk 736 optimal weight: 0.9980 chunk 570 optimal weight: 0.9980 chunk 848 optimal weight: 0.9990 chunk 562 optimal weight: 9.9990 chunk 1004 optimal weight: 0.2980 chunk 628 optimal weight: 7.9990 chunk 612 optimal weight: 0.9990 chunk 463 optimal weight: 20.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN K 137 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN P 90 HIS S 108 GLN S 122 HIS ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 ASN a 42 ASN ** b 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 GLN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 95 GLN n 168 GLN w 203 GLN ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 378 ASN ** o 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 GLN q 133 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 139877 Z= 0.121 Angle : 0.505 16.125 205663 Z= 0.258 Chirality : 0.032 0.328 25788 Planarity : 0.004 0.141 13359 Dihedral : 22.488 177.610 60962 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 2.97 % Allowed : 20.94 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.15 (0.10), residues: 6938 helix: 0.18 (0.11), residues: 2157 sheet: -0.67 (0.16), residues: 1046 loop : -1.36 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 142 HIS 0.004 0.001 HIS S 122 PHE 0.025 0.001 PHE b 229 TYR 0.021 0.001 TYR J 167 ARG 0.008 0.000 ARG o 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 968 time to evaluate : 6.025 Fit side-chains 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: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE T 160 " (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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 308 MET cc_start: 0.8593 (mmm) cc_final: 0.8270 (mtp) REVERT: D 153 SER cc_start: 0.8208 (t) cc_final: 0.7738 (p) REVERT: E 35 LYS cc_start: 0.6559 (mttt) cc_final: 0.6278 (mttt) REVERT: E 40 LEU cc_start: 0.6897 (pp) cc_final: 0.6142 (tp) REVERT: F 7 GLU cc_start: 0.7201 (pt0) cc_final: 0.6941 (tt0) REVERT: F 51 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7356 (mp10) REVERT: F 162 GLN cc_start: 0.8078 (pp30) cc_final: 0.7770 (tm-30) REVERT: F 166 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7084 (ptm160) REVERT: H 177 TYR cc_start: 0.8823 (p90) cc_final: 0.8320 (p90) REVERT: H 207 ASP cc_start: 0.7951 (t0) cc_final: 0.7591 (t0) REVERT: J 95 LYS cc_start: 0.8527 (mttt) cc_final: 0.8124 (mtpp) REVERT: J 173 PHE cc_start: 0.7347 (t80) cc_final: 0.6652 (m-80) REVERT: L 115 THR cc_start: 0.8653 (m) cc_final: 0.8073 (p) REVERT: M 121 MET cc_start: 0.7865 (tpp) cc_final: 0.7138 (tpp) REVERT: N 46 ASP cc_start: 0.8128 (m-30) cc_final: 0.7837 (m-30) REVERT: O 87 GLN cc_start: 0.8195 (pt0) cc_final: 0.7897 (pt0) REVERT: P 95 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.7744 (t60) REVERT: P 155 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8485 (p) REVERT: P 273 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6569 (mmm-85) REVERT: Q 173 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7471 (mm-30) REVERT: S 27 MET cc_start: 0.8453 (mtp) cc_final: 0.8227 (mtp) REVERT: T 140 ILE cc_start: 0.9137 (mt) cc_final: 0.8766 (tt) REVERT: U 4 TYR cc_start: 0.7987 (m-10) cc_final: 0.7553 (m-10) REVERT: U 10 ASN cc_start: 0.7874 (t0) cc_final: 0.7667 (t0) REVERT: V 70 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7771 (mmtt) REVERT: V 94 ARG cc_start: 0.7861 (ptm-80) cc_final: 0.7396 (ptm160) REVERT: W 64 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7486 (mt-10) REVERT: W 133 LEU cc_start: 0.8060 (mm) cc_final: 0.7835 (mt) REVERT: Y 72 ILE cc_start: 0.8886 (mm) cc_final: 0.8639 (tp) REVERT: Y 84 ARG cc_start: 0.7304 (ptm160) cc_final: 0.7098 (ptm160) REVERT: d 69 TYR cc_start: 0.8788 (m-80) cc_final: 0.8557 (m-80) REVERT: e 118 LYS cc_start: 0.8207 (tptt) cc_final: 0.7834 (tttt) REVERT: h 92 ASN cc_start: 0.8490 (m-40) cc_final: 0.8216 (m110) REVERT: k 29 LEU cc_start: 0.8649 (mt) cc_final: 0.8120 (mt) REVERT: l 24 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7303 (tptt) REVERT: l 61 LYS cc_start: 0.7825 (tttm) cc_final: 0.7034 (mttt) REVERT: n 93 LYS cc_start: 0.6735 (tppt) cc_final: 0.6351 (tppt) REVERT: n 187 ASN cc_start: 0.8079 (m-40) cc_final: 0.7663 (m110) REVERT: w 65 LEU cc_start: 0.0321 (OUTLIER) cc_final: 0.0017 (tt) REVERT: w 200 PHE cc_start: 0.4450 (m-80) cc_final: 0.3255 (t80) REVERT: w 203 GLN cc_start: -0.0044 (OUTLIER) cc_final: -0.0714 (mm-40) REVERT: v 1 MET cc_start: 0.2247 (ptm) cc_final: 0.0679 (ppp) REVERT: o 146 MET cc_start: 0.5286 (pmm) cc_final: 0.4395 (ptm) REVERT: o 153 ARG cc_start: 0.4365 (tpt170) cc_final: 0.4030 (mtt-85) REVERT: o 354 ASN cc_start: 0.6296 (m-40) cc_final: 0.5350 (p0) REVERT: o 482 ARG cc_start: 0.3891 (ttm-80) cc_final: 0.3093 (ttm-80) REVERT: q 76 MET cc_start: 0.8360 (mmm) cc_final: 0.7971 (tpp) REVERT: q 102 MET cc_start: 0.4868 (tmm) cc_final: 0.3666 (mtt) REVERT: t 79 GLU cc_start: 0.7461 (tp30) cc_final: 0.7235 (tp30) outliers start: 176 outliers final: 136 residues processed: 1071 average time/residue: 1.1208 time to fit residues: 2077.7283 Evaluate side-chains 1043 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 902 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 129 ASP Chi-restraints excluded: chain X residue 5 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 60 GLU Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 44 MET Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain n residue 185 THR Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 65 LEU Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 203 GLN Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 136 VAL Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 123 HIS Chi-restraints excluded: chain q residue 137 SER Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 621 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 599 optimal weight: 9.9990 chunk 302 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 638 optimal weight: 7.9990 chunk 684 optimal weight: 4.9990 chunk 496 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 789 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 80 ASN H 137 ASN H 232 HIS J 121 GLN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 GLN M 56 GLN O 95 GLN ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN S 108 GLN S 122 HIS U 96 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 ASN i 20 ASN m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 83 HIS ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN ** w 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 GLN q 133 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 139877 Z= 0.344 Angle : 0.633 13.333 205663 Z= 0.323 Chirality : 0.039 0.300 25788 Planarity : 0.005 0.147 13359 Dihedral : 22.517 179.890 60962 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.30 % Favored : 93.61 % Rotamer: Outliers : 3.96 % Allowed : 20.56 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 6938 helix: -0.07 (0.11), residues: 2159 sheet: -0.80 (0.16), residues: 1051 loop : -1.47 (0.10), residues: 3728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP o 142 HIS 0.007 0.001 HIS a 7 PHE 0.030 0.002 PHE b 229 TYR 0.027 0.002 TYR P 172 ARG 0.014 0.001 ARG w 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 920 time to evaluate : 6.545 Fit side-chains revert: symmetry clash revert: symmetry clash 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 308 MET cc_start: 0.8718 (mmm) cc_final: 0.8408 (mtp) REVERT: E 35 LYS cc_start: 0.6670 (mttt) cc_final: 0.6437 (mtmt) REVERT: E 40 LEU cc_start: 0.6836 (pp) cc_final: 0.6110 (tp) REVERT: F 162 GLN cc_start: 0.8267 (pp30) cc_final: 0.7908 (tm-30) REVERT: H 177 TYR cc_start: 0.8857 (p90) cc_final: 0.8574 (p90) REVERT: H 207 ASP cc_start: 0.7995 (t0) cc_final: 0.7653 (t0) REVERT: J 95 LYS cc_start: 0.8505 (mttt) cc_final: 0.8113 (mtpp) REVERT: J 173 PHE cc_start: 0.7459 (t80) cc_final: 0.6748 (m-80) REVERT: L 4 ASN cc_start: 0.5749 (OUTLIER) cc_final: 0.4942 (p0) REVERT: N 46 ASP cc_start: 0.8117 (m-30) cc_final: 0.7862 (m-30) REVERT: N 58 MET cc_start: 0.8888 (ptt) cc_final: 0.8554 (ptt) REVERT: O 29 GLU cc_start: 0.8109 (tp30) cc_final: 0.7869 (tp30) REVERT: O 87 GLN cc_start: 0.8460 (pt0) cc_final: 0.8141 (pt0) REVERT: P 95 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.7834 (t60) REVERT: P 155 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8659 (p) REVERT: R 140 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7932 (mt-10) REVERT: S 152 LEU cc_start: 0.8652 (mt) cc_final: 0.8281 (mp) REVERT: T 140 ILE cc_start: 0.9193 (mt) cc_final: 0.8841 (tt) REVERT: W 64 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7506 (mt-10) REVERT: W 133 LEU cc_start: 0.8242 (mm) cc_final: 0.8039 (mt) REVERT: b 239 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8327 (tt) REVERT: g 97 GLU cc_start: 0.7454 (tp30) cc_final: 0.6991 (tp30) REVERT: h 26 ILE cc_start: 0.6429 (tp) cc_final: 0.6036 (mp) REVERT: i 36 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8746 (t) REVERT: k 29 LEU cc_start: 0.8674 (mt) cc_final: 0.8135 (mt) REVERT: l 24 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7263 (tptt) REVERT: l 61 LYS cc_start: 0.7954 (tttm) cc_final: 0.7139 (mttt) REVERT: n 187 ASN cc_start: 0.8034 (m-40) cc_final: 0.7642 (m110) REVERT: w 156 ARG cc_start: 0.5308 (mtt180) cc_final: 0.3307 (mmp-170) REVERT: v 1 MET cc_start: 0.2888 (ptm) cc_final: 0.0346 (tpp) REVERT: o 146 MET cc_start: 0.4991 (pmm) cc_final: 0.4345 (ptp) REVERT: o 183 ARG cc_start: 0.5894 (ttp-110) cc_final: 0.5619 (ttp-110) REVERT: o 354 ASN cc_start: 0.6309 (m-40) cc_final: 0.5358 (p0) REVERT: o 400 LYS cc_start: 0.3659 (pttt) cc_final: 0.1837 (tmtt) REVERT: q 102 MET cc_start: 0.4798 (tmm) cc_final: 0.3459 (mtt) outliers start: 235 outliers final: 186 residues processed: 1069 average time/residue: 1.1168 time to fit residues: 2082.0031 Evaluate side-chains 1069 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 878 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 6 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 213 ASP Chi-restraints excluded: chain P residue 231 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 5 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 239 LEU Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 40 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 78 THR Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 82 LEU Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 131 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 136 VAL Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 97 LEU Chi-restraints excluded: chain q residue 149 VAL Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain q residue 186 GLU Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 913 optimal weight: 5.9990 chunk 962 optimal weight: 9.9990 chunk 877 optimal weight: 0.9980 chunk 935 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 563 optimal weight: 0.9980 chunk 407 optimal weight: 0.9990 chunk 734 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 845 optimal weight: 10.0000 chunk 885 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN J 121 GLN P 90 HIS S 108 GLN S 122 HIS T 103 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 17 HIS i 20 ASN m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN ** n 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 203 GLN ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 139877 Z= 0.189 Angle : 0.546 12.594 205663 Z= 0.280 Chirality : 0.035 0.308 25788 Planarity : 0.004 0.144 13359 Dihedral : 22.515 179.803 60962 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 3.15 % Allowed : 21.40 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.23 (0.10), residues: 6938 helix: 0.09 (0.11), residues: 2151 sheet: -0.76 (0.16), residues: 1054 loop : -1.37 (0.10), residues: 3733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP o 142 HIS 0.030 0.001 HIS S 122 PHE 0.029 0.001 PHE b 229 TYR 0.030 0.001 TYR J 167 ARG 0.012 0.000 ARG w 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 922 time to evaluate : 6.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash 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. 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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 308 MET cc_start: 0.8675 (mmm) cc_final: 0.8351 (mtp) REVERT: C 370 PHE cc_start: 0.7745 (m-10) cc_final: 0.7517 (m-10) REVERT: E 35 LYS cc_start: 0.6604 (mttt) cc_final: 0.6131 (mtmt) REVERT: E 40 LEU cc_start: 0.6863 (pp) cc_final: 0.6185 (tp) REVERT: F 7 GLU cc_start: 0.7347 (pt0) cc_final: 0.6964 (tt0) REVERT: F 150 SER cc_start: 0.8220 (t) cc_final: 0.7829 (t) REVERT: F 162 GLN cc_start: 0.8233 (pp30) cc_final: 0.7911 (tm-30) REVERT: H 177 TYR cc_start: 0.8872 (p90) cc_final: 0.8456 (p90) REVERT: H 207 ASP cc_start: 0.7940 (t0) cc_final: 0.7593 (t0) REVERT: J 95 LYS cc_start: 0.8485 (mttt) cc_final: 0.8096 (mtpp) REVERT: J 173 PHE cc_start: 0.7475 (t80) cc_final: 0.6764 (m-80) REVERT: L 70 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7922 (ptp90) REVERT: N 46 ASP cc_start: 0.8105 (m-30) cc_final: 0.7869 (m-30) REVERT: O 29 GLU cc_start: 0.8076 (tp30) cc_final: 0.7848 (tp30) REVERT: O 87 GLN cc_start: 0.8363 (pt0) cc_final: 0.8077 (pt0) REVERT: P 95 TRP cc_start: 0.8720 (OUTLIER) cc_final: 0.7860 (t60) REVERT: P 155 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8531 (p) REVERT: P 273 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6538 (mmm-85) REVERT: Q 173 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7441 (mm-30) REVERT: R 140 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7888 (mt-10) REVERT: R 146 LYS cc_start: 0.6676 (pttp) cc_final: 0.5348 (tptt) REVERT: T 140 ILE cc_start: 0.9167 (mt) cc_final: 0.8805 (tt) REVERT: V 89 LEU cc_start: 0.7434 (mt) cc_final: 0.7174 (tp) REVERT: V 94 ARG cc_start: 0.7909 (ptm-80) cc_final: 0.7538 (ptm160) REVERT: W 64 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7493 (mt-10) REVERT: W 133 LEU cc_start: 0.8231 (mm) cc_final: 0.8021 (mt) REVERT: d 82 GLU cc_start: 0.5580 (pp20) cc_final: 0.4878 (pp20) REVERT: g 97 GLU cc_start: 0.7508 (tp30) cc_final: 0.7062 (tp30) REVERT: h 26 ILE cc_start: 0.6386 (tp) cc_final: 0.5971 (mp) REVERT: i 36 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8700 (t) REVERT: k 29 LEU cc_start: 0.8631 (mt) cc_final: 0.8110 (mt) REVERT: l 24 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7233 (tptt) REVERT: l 61 LYS cc_start: 0.7979 (tttm) cc_final: 0.7181 (mttt) REVERT: n 50 HIS cc_start: 0.8324 (m90) cc_final: 0.8008 (m90) REVERT: n 164 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6752 (mp10) REVERT: n 187 ASN cc_start: 0.8075 (m-40) cc_final: 0.7621 (m110) REVERT: w 123 MET cc_start: 0.5379 (ttp) cc_final: 0.5019 (ttt) REVERT: w 156 ARG cc_start: 0.5195 (mtt180) cc_final: 0.3083 (mmp-170) REVERT: w 203 GLN cc_start: 0.0958 (OUTLIER) cc_final: 0.0330 (tp40) REVERT: v 1 MET cc_start: 0.2818 (ptm) cc_final: 0.1402 (ppp) REVERT: o 146 MET cc_start: 0.5022 (pmm) cc_final: 0.4382 (ptm) REVERT: o 183 ARG cc_start: 0.5597 (ttp-110) cc_final: 0.5360 (ttp-110) REVERT: o 400 LYS cc_start: 0.3631 (pttt) cc_final: 0.1821 (tmtt) REVERT: q 102 MET cc_start: 0.5016 (tmm) cc_final: 0.3762 (mtt) REVERT: q 154 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7525 (mtp85) REVERT: t 79 GLU cc_start: 0.7311 (tp30) cc_final: 0.7072 (tp30) outliers start: 187 outliers final: 161 residues processed: 1037 average time/residue: 1.1321 time to fit residues: 2049.8101 Evaluate side-chains 1058 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 893 time to evaluate : 6.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 121 GLN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain X residue 5 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 82 LEU Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 131 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 203 GLN Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 136 VAL Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 97 LEU Chi-restraints excluded: chain q residue 152 LEU Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 932 optimal weight: 7.9990 chunk 614 optimal weight: 0.9980 chunk 989 optimal weight: 10.0000 chunk 604 optimal weight: 20.0000 chunk 469 optimal weight: 5.9990 chunk 687 optimal weight: 0.8980 chunk 1038 optimal weight: 10.0000 chunk 955 optimal weight: 6.9990 chunk 826 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 638 optimal weight: 0.7980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN P 90 HIS R 130 ASN S 108 GLN S 122 HIS T 103 GLN U 101 ASN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 168 GLN ** n 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 139877 Z= 0.189 Angle : 0.593 59.194 205663 Z= 0.320 Chirality : 0.035 0.910 25788 Planarity : 0.005 0.157 13359 Dihedral : 22.515 179.815 60962 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 3.07 % Allowed : 21.53 % Favored : 75.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.22 (0.10), residues: 6938 helix: 0.10 (0.11), residues: 2151 sheet: -0.75 (0.16), residues: 1053 loop : -1.38 (0.10), residues: 3734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 142 HIS 0.023 0.001 HIS S 122 PHE 0.029 0.001 PHE b 229 TYR 0.024 0.001 TYR J 167 ARG 0.010 0.000 ARG w 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 896 time to evaluate : 6.359 Fit side-chains 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. TARDY: cannot create tardy model for: "ILE T 160 " (corrupted residue). Skipping it. 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 revert: symmetry clash TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8304 (mt-10) REVERT: C 308 MET cc_start: 0.8674 (mmm) cc_final: 0.8351 (mtp) REVERT: E 35 LYS cc_start: 0.6602 (mttt) cc_final: 0.6132 (mtmt) REVERT: E 40 LEU cc_start: 0.6860 (pp) cc_final: 0.6186 (tp) REVERT: E 131 MET cc_start: 0.7191 (pmm) cc_final: 0.6715 (pmm) REVERT: F 7 GLU cc_start: 0.7350 (pt0) cc_final: 0.6964 (tt0) REVERT: F 150 SER cc_start: 0.8220 (t) cc_final: 0.7834 (t) REVERT: F 162 GLN cc_start: 0.8232 (pp30) cc_final: 0.7911 (tm-30) REVERT: H 177 TYR cc_start: 0.8892 (p90) cc_final: 0.8470 (p90) REVERT: H 207 ASP cc_start: 0.7942 (t0) cc_final: 0.7591 (t0) REVERT: J 95 LYS cc_start: 0.8484 (mttt) cc_final: 0.8096 (mtpp) REVERT: J 121 GLN cc_start: 0.8583 (pt0) cc_final: 0.8255 (pt0) REVERT: J 136 THR cc_start: 0.8997 (m) cc_final: 0.8714 (p) REVERT: J 173 PHE cc_start: 0.7426 (t80) cc_final: 0.6700 (m-80) REVERT: L 70 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7920 (ptp90) REVERT: L 108 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: N 46 ASP cc_start: 0.8116 (m-30) cc_final: 0.7866 (m-30) REVERT: O 29 GLU cc_start: 0.8075 (tp30) cc_final: 0.7849 (tp30) REVERT: O 87 GLN cc_start: 0.8363 (pt0) cc_final: 0.8078 (pt0) REVERT: P 95 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.7859 (t60) REVERT: P 136 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.5818 (pp20) REVERT: P 155 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8530 (p) REVERT: P 273 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6540 (mmm-85) REVERT: Q 173 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7442 (mm-30) REVERT: R 140 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7887 (mt-10) REVERT: R 146 LYS cc_start: 0.6674 (pttp) cc_final: 0.5348 (tptt) REVERT: T 140 ILE cc_start: 0.9168 (mt) cc_final: 0.8804 (tt) REVERT: V 89 LEU cc_start: 0.7431 (mt) cc_final: 0.7173 (tp) REVERT: V 94 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7558 (ptm160) REVERT: W 64 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7493 (mt-10) REVERT: W 133 LEU cc_start: 0.8228 (mm) cc_final: 0.8022 (mt) REVERT: g 97 GLU cc_start: 0.7493 (tp30) cc_final: 0.7043 (tp30) REVERT: h 26 ILE cc_start: 0.6384 (tp) cc_final: 0.5969 (mp) REVERT: i 36 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8700 (t) REVERT: k 29 LEU cc_start: 0.8634 (mt) cc_final: 0.8109 (mt) REVERT: l 24 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7232 (tptt) REVERT: l 61 LYS cc_start: 0.7980 (tttm) cc_final: 0.7179 (mttt) REVERT: n 50 HIS cc_start: 0.8321 (m90) cc_final: 0.8007 (m90) REVERT: n 93 LYS cc_start: 0.6738 (tppt) cc_final: 0.6329 (tppt) REVERT: n 164 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6752 (mp10) REVERT: n 187 ASN cc_start: 0.8072 (m-40) cc_final: 0.7620 (m110) REVERT: w 123 MET cc_start: 0.5370 (ttp) cc_final: 0.5011 (ttt) REVERT: w 156 ARG cc_start: 0.5191 (mtt180) cc_final: 0.3086 (mmp-170) REVERT: v 1 MET cc_start: 0.2792 (ptm) cc_final: 0.1406 (ppp) REVERT: o 146 MET cc_start: 0.5027 (pmm) cc_final: 0.4386 (ptm) REVERT: o 183 ARG cc_start: 0.5597 (ttp-110) cc_final: 0.5362 (ttp-110) REVERT: o 193 ARG cc_start: 0.2987 (OUTLIER) cc_final: 0.2543 (tpt170) REVERT: o 400 LYS cc_start: 0.3630 (pttt) cc_final: 0.1822 (tmtt) REVERT: q 102 MET cc_start: 0.5036 (tmm) cc_final: 0.3764 (mtt) REVERT: q 154 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7525 (mtp85) REVERT: t 79 GLU cc_start: 0.7312 (tp30) cc_final: 0.7070 (tp30) outliers start: 182 outliers final: 171 residues processed: 1010 average time/residue: 1.1222 time to fit residues: 1979.6601 Evaluate side-chains 1062 residues out of total 5935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 885 time to evaluate : 6.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 123 PHE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 84 SER Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain P residue 95 TRP Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 158 THR Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 117 ILE Chi-restraints excluded: chain V residue 56 VAL Chi-restraints excluded: chain V residue 92 TRP Chi-restraints excluded: chain W residue 59 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 107 VAL Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain X residue 5 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain b residue 113 SER Chi-restraints excluded: chain b residue 175 LYS Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 100 HIS Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 26 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 36 SER Chi-restraints excluded: chain i residue 46 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 3 ARG Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain m residue 5 THR Chi-restraints excluded: chain m residue 39 CYS Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 62 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain z residue 379 THR Chi-restraints excluded: chain z residue 420 VAL Chi-restraints excluded: chain w residue 60 ASN Chi-restraints excluded: chain w residue 82 LEU Chi-restraints excluded: chain w residue 117 THR Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 131 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 248 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain o residue 136 VAL Chi-restraints excluded: chain o residue 143 ASN Chi-restraints excluded: chain o residue 193 ARG Chi-restraints excluded: chain o residue 411 ILE Chi-restraints excluded: chain o residue 460 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 97 LEU Chi-restraints excluded: chain q residue 152 LEU Chi-restraints excluded: chain q residue 159 PHE Chi-restraints excluded: chain q residue 168 SER Chi-restraints excluded: chain q residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1042 random chunks: chunk 506 optimal weight: 2.9990 chunk 656 optimal weight: 5.9990 chunk 880 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 762 optimal weight: 3.9990 chunk 122 optimal weight: 40.0000 chunk 229 optimal weight: 40.0000 chunk 827 optimal weight: 0.8980 chunk 346 optimal weight: 0.9980 chunk 850 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN G 80 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN P 90 HIS R 130 ASN S 108 GLN S 122 HIS T 103 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 ASN m 34 HIS ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098206 restraints weight = 254091.743| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.42 r_work: 0.3107 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 139877 Z= 0.226 Angle : 0.593 59.200 205663 Z= 0.316 Chirality : 0.036 0.510 25788 Planarity : 0.005 0.162 13359 Dihedral : 22.513 179.791 60962 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 3.27 % Allowed : 21.50 % Favored : 75.23 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.22 (0.10), residues: 6938 helix: 0.09 (0.11), residues: 2152 sheet: -0.75 (0.16), residues: 1054 loop : -1.37 (0.10), residues: 3732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 142 HIS 0.019 0.001 HIS S 122 PHE 0.029 0.001 PHE b 229 TYR 0.023 0.001 TYR J 167 ARG 0.011 0.000 ARG w 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34483.77 seconds wall clock time: 602 minutes 52.47 seconds (36172.47 seconds total)