Starting phenix.real_space_refine on Sat Feb 17 17:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qik_4560/02_2024/6qik_4560.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.022 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 3419 5.49 5 S 125 5.16 5 C 67737 2.51 5 N 23673 2.21 5 O 33608 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 74": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 337": "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 88": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K GLU 118": "OE1" <-> "OE2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O GLU 104": "OE1" <-> "OE2" Residue "P GLU 124": "OE1" <-> "OE2" Residue "P ARG 140": "NH1" <-> "NH2" Residue "P ARG 158": "NH1" <-> "NH2" Residue "P GLU 177": "OE1" <-> "OE2" Residue "P GLU 186": "OE1" <-> "OE2" Residue "P GLU 193": "OE1" <-> "OE2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P GLU 221": "OE1" <-> "OE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S GLU 104": "OE1" <-> "OE2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 18": "NH1" <-> "NH2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U GLU 103": "OE1" <-> "OE2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W GLU 64": "OE1" <-> "OE2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Z TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 102": "OE1" <-> "OE2" Residue "a PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 29": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 39": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "b GLU 170": "OE1" <-> "OE2" Residue "b GLU 234": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d GLU 110": "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 GLU 88": "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 TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n GLU 8": "OE1" <-> "OE2" Residue "n GLU 39": "OE1" <-> "OE2" Residue "n GLU 41": "OE1" <-> "OE2" Residue "n GLU 98": "OE1" <-> "OE2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n GLU 124": "OE1" <-> "OE2" Residue "n GLU 172": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "n GLU 214": "OE1" <-> "OE2" Residue "z GLU 391": "OE1" <-> "OE2" Residue "z GLU 416": "OE1" <-> "OE2" Residue "z ARG 419": "NH1" <-> "NH2" Residue "z ARG 427": "NH1" <-> "NH2" Residue "w ARG 51": "NH1" <-> "NH2" Residue "w GLU 62": "OE1" <-> "OE2" 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 ARG 111": "NH1" <-> "NH2" Residue "w GLU 133": "OE1" <-> "OE2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w GLU 192": "OE1" <-> "OE2" Residue "w GLU 227": "OE1" <-> "OE2" Residue "w GLU 247": "OE1" <-> "OE2" Residue "w ARG 303": "NH1" <-> "NH2" Residue "w ARG 330": "NH1" <-> "NH2" Residue "w ARG 333": "NH1" <-> "NH2" Residue "w ARG 342": "NH1" <-> "NH2" Residue "w ARG 404": "NH1" <-> "NH2" Residue "v ARG 17": "NH1" <-> "NH2" Residue "o GLU 141": "OE1" <-> "OE2" Residue "o GLU 144": "OE1" <-> "OE2" Residue "o ARG 153": "NH1" <-> "NH2" Residue "o GLU 171": "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 ARG 267": "NH1" <-> "NH2" Residue "o GLU 303": "OE1" <-> "OE2" Residue "o GLU 402": "OE1" <-> "OE2" Residue "o ARG 427": "NH1" <-> "NH2" Residue "o ARG 446": "NH1" <-> "NH2" Residue "o GLU 448": "OE1" <-> "OE2" Residue "o ARG 466": "NH1" <-> "NH2" Residue "o ARG 468": "NH1" <-> "NH2" Residue "o ARG 482": "NH1" <-> "NH2" Residue "o ARG 485": "NH1" <-> "NH2" Residue "o GLU 506": "OE1" <-> "OE2" Residue "t GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 128569 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 67292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3146, 67292 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "'] Classifications: {'RNA': 3146} Modifications used: {'5*END': 2, 'rna2p_pur': 318, 'rna2p_pyr': 202, 'rna3p_pur': 1430, 'rna3p_pyr': 1196} Link IDs: {'rna2p': 520, 'rna3p': 2625} Chain breaks: 3 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1878 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain: "C" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3039 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 14, 'TRANS': 366} Chain: "D" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1399 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1742 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "J" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1486 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1002 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1045 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "N" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1172 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1719 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2176 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "Q" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1440 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1275 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1222 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain: "V" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 786 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Y" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 963 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 415 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "b" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1760 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "c" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 741 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 872 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 849 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "g" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 812 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "h" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 763 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "j" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 435 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "l" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 756 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "m" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 680 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "n" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1691 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "z" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 491 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "w" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3076 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 14, 'TRANS': 374} Chain: "v" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 500 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2593 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 17, 'TRANS': 304} Chain breaks: 2 Chain: "p" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "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': 13, 'rna3p_pur': 62, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 126} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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 A06JQ SG CYS g 44 124.075 117.549 199.074 1.00 55.42 S ATOM A06K8 SG CYS g 47 121.269 117.094 200.074 1.00 56.11 S ATOM A06RA SG CYS g 81 122.074 118.699 203.554 1.00 59.95 S ATOM A06RT SG CYS g 84 122.896 115.720 202.195 1.00 61.02 S ATOM A07LJ SG CYS i 19 146.655 134.058 149.609 1.00 37.42 S ATOM A07M8 SG CYS i 22 146.643 136.177 145.704 1.00 34.65 S ATOM A07P0 SG CYS i 34 144.664 133.036 146.584 1.00 33.85 S ATOM A07PI SG CYS i 37 148.714 132.728 146.123 1.00 34.05 S ATOM A08VS SG CYS l 12 142.833 62.422 86.320 1.00 53.40 S ATOM A08WR SG CYS l 17 145.327 59.280 84.206 1.00 55.42 S ATOM A099N SG CYS l 74 142.031 59.199 86.510 1.00 49.93 S ATOM A09MW SG CYS m 39 108.666 105.419 196.908 1.00 58.58 S ATOM A09NJ SG CYS m 42 108.197 107.723 199.047 1.00 61.14 S ATOM A09QK SG CYS m 57 108.434 109.751 196.303 1.00 55.00 S ATOM A0BUH SG CYS w 58 65.810 96.704 110.220 1.00172.64 S ATOM A0BML SG CYS w 19 23.334 123.730 129.024 1.00135.89 S ATOM A0BN5 SG CYS w 22 20.977 122.393 127.662 1.00136.07 S ATOM A0BPH SG CYS w 35 23.667 118.936 129.560 1.00146.26 S ATOM A0BQ7 SG CYS w 38 24.144 121.926 125.888 1.00149.36 S ATOM A0HDM SG CYS t 110 54.702 135.944 78.075 1.00158.48 S ATOM A0HEW SG CYS t 115 58.313 134.789 78.007 1.00150.84 S Time building chain proxies: 43.45, per 1000 atoms: 0.34 Number of scatterers: 128569 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 125 16.00 P 3419 15.00 O 33608 8.00 N 23673 7.00 C 67737 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: 48.19 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 22 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 19 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 37 " pdb=" ZN l 201 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 12 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 74 " pdb="ZN ZN l 201 " - pdb=" SG CYS l 17 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 42 " 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 115 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 110 " pdb=" ZN w 601 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 58 " pdb=" ZN w 602 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 19 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 22 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 38 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 35 " Number of angles added : 18 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13182 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 75 sheets defined 34.8% alpha, 16.1% beta 1028 base pairs and 1743 stacking pairs defined. Time for finding SS restraints: 40.91 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 173 through 177 Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 132 through 140 removed outlier: 3.539A pdb=" N LYS C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.964A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 removed outlier: 3.599A pdb=" N ASP C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 31 through 43 removed outlier: 4.193A pdb=" N THR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.764A pdb=" N ALA D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 removed outlier: 3.701A pdb=" N VAL D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) 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 262 removed outlier: 4.327A pdb=" N ASP D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TRP D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.679A pdb=" N ILE D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 328 Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 339 through 342 removed outlier: 3.930A pdb=" N LYS D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 339 through 342' Processing helix chain 'D' and resid 352 through 360 removed outlier: 4.019A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.691A pdb=" N VAL E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.947A pdb=" N GLU E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 4.013A pdb=" N LEU E 112 " --> pdb=" O HIS E 109 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY E 113 " --> pdb=" O ILE E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 109 through 113' Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.004A pdb=" N VAL E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.710A pdb=" N LYS E 153 " --> pdb=" O ASN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.628A pdb=" N SER E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 85 removed outlier: 4.393A pdb=" N ARG F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 82 " --> pdb=" O MET F 78 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 165 removed outlier: 4.012A pdb=" N GLN F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 133 through 150 removed outlier: 3.991A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 161 Processing helix chain 'H' and resid 46 through 50 removed outlier: 4.126A pdb=" N VAL H 50 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 69 removed outlier: 3.694A pdb=" N GLN H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'H' and resid 83 through 95 Processing helix chain 'H' and resid 101 through 115 Processing helix chain 'H' and resid 116 through 118 No H-bonds generated for 'chain 'H' and resid 116 through 118' Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.692A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 165 through 173 Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.637A pdb=" N LEU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 219 Processing helix chain 'H' and resid 225 through 231 removed outlier: 4.005A pdb=" N LYS H 231 " --> pdb=" O ASP H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 247 removed outlier: 3.608A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 4.010A pdb=" N THR J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 removed outlier: 3.698A 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 Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.772A pdb=" N GLY J 68 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 85 Processing helix chain 'J' and resid 91 through 100 Processing helix chain 'J' and resid 108 through 113 removed outlier: 3.759A pdb=" N LYS J 113 " --> pdb=" O PRO J 109 " (cutoff:3.500A) 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 145 Processing helix chain 'J' and resid 148 through 182 removed outlier: 3.833A pdb=" N VAL J 152 " --> pdb=" O TYR J 148 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS J 154 " --> pdb=" O ASP J 150 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA J 172 " --> pdb=" O ALA J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 185 No H-bonds generated for 'chain 'J' and resid 183 through 185' Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'K' and resid 27 through 46 removed outlier: 3.976A pdb=" N SER K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 84 Processing helix chain 'K' and resid 86 through 93 removed outlier: 3.555A pdb=" N ARG K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE K 93 " --> pdb=" O TYR K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 122 Processing helix chain 'K' and resid 165 through 179 removed outlier: 3.860A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 187 Processing helix chain 'L' and resid 119 through 124 Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.792A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 77 through 81 Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.932A pdb=" N ASP N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 4.641A 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 132 through 142 Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 16 through 33 removed outlier: 3.633A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.774A 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 148 through 152 removed outlier: 3.609A pdb=" N ILE O 151 " --> pdb=" O TYR O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 157 removed outlier: 3.565A pdb=" N HIS O 156 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 163 removed outlier: 3.557A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 186 through 195 removed outlier: 3.521A pdb=" N TRP O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 16 removed outlier: 3.702A 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: 4.369A pdb=" N ARG P 35 " --> pdb=" O TYR P 31 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 86 Processing helix chain 'P' and resid 94 through 114 removed outlier: 3.613A pdb=" N GLN P 111 " --> pdb=" O ARG P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 170 removed outlier: 3.694A pdb=" N ALA P 162 " --> pdb=" O ARG P 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 200 Processing helix chain 'P' and resid 204 through 212 Processing helix chain 'P' and resid 215 through 223 Processing helix chain 'P' and resid 223 through 229 removed outlier: 3.638A pdb=" N LEU P 227 " --> pdb=" O PHE P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 250 removed outlier: 4.165A pdb=" N THR P 241 " --> pdb=" O GLU P 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU P 245 " --> pdb=" O THR P 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 270 removed outlier: 3.536A pdb=" N SER P 269 " --> pdb=" O TYR P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 39 removed outlier: 3.591A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.275A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.686A pdb=" N LYS Q 113 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.792A pdb=" N VAL Q 129 " --> pdb=" O ASP Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.780A pdb=" N ARG R 9 " --> pdb=" O ARG R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 38 through 48 removed outlier: 3.707A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU R 44 " --> pdb=" O ALA R 40 " (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 112 removed outlier: 3.601A pdb=" N LEU R 102 " --> pdb=" O ARG R 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.940A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 148 removed outlier: 3.566A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.587A pdb=" N TRP S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN S 46 " --> pdb=" O TRP S 42 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU S 48 " --> pdb=" O PHE S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 removed outlier: 3.683A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (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 removed outlier: 3.779A pdb=" N THR T 29 " --> pdb=" O HIS T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.712A pdb=" N GLN T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 122 removed outlier: 4.096A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE T 105 " --> pdb=" O CYS T 101 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA T 114 " --> pdb=" O LYS T 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 12 No H-bonds generated for 'chain 'U' and resid 10 through 12' Processing helix chain 'U' and resid 25 through 35 removed outlier: 3.728A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 53 removed outlier: 3.531A pdb=" N GLU U 49 " --> pdb=" O GLN U 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'V' and resid 19 through 25 removed outlier: 3.656A pdb=" N THR V 23 " --> pdb=" O VAL V 19 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 41 Processing helix chain 'V' and resid 72 through 87 Processing helix chain 'W' and resid 58 through 62 Processing helix chain 'W' and resid 71 through 79 removed outlier: 4.140A pdb=" N LYS W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 4.926A 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 removed outlier: 3.720A pdb=" N ILE W 135 " --> pdb=" O ASP W 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 21 Processing helix chain 'X' and resid 26 through 31 Processing helix chain 'X' and resid 38 through 43 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 122 Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 104 through 125 removed outlier: 3.738A pdb=" N GLU Y 108 " --> pdb=" O PRO Y 104 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 removed outlier: 3.502A pdb=" N SER Y 132 " --> pdb=" O TRP Y 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 10 Processing helix chain 'Z' and resid 13 through 35 removed outlier: 3.576A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU Z 27 " --> pdb=" O ASP Z 23 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 71 removed outlier: 4.380A pdb=" N THR Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL Z 47 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL Z 57 " --> pdb=" O CYS Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 91 Processing helix chain 'Z' and resid 93 through 98 Processing helix chain 'Z' and resid 101 through 111 Processing helix chain 'a' and resid 11 through 17 Processing helix chain 'a' and resid 36 through 55 removed outlier: 3.550A pdb=" N ASN a 42 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS a 45 " --> pdb=" O ARG a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 73 removed outlier: 3.584A pdb=" N ALA b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 106 removed outlier: 3.662A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 128 removed outlier: 3.974A pdb=" N GLU b 125 " --> pdb=" O LYS b 121 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU b 126 " --> pdb=" O ALA b 122 " (cutoff:3.500A) 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 151 Processing helix chain 'b' and resid 166 through 174 removed outlier: 4.006A 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 180 through 190 Processing helix chain 'b' and resid 194 through 202 Processing helix chain 'b' and resid 235 through 241 removed outlier: 3.776A pdb=" N LEU b 239 " --> pdb=" O PHE b 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 18 removed outlier: 4.011A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE c 18 " --> pdb=" O LEU c 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 35 removed outlier: 3.733A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.784A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) 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 41 removed outlier: 4.137A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 removed outlier: 4.170A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) 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 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.758A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.725A pdb=" N LEU f 45 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 64 removed outlier: 3.601A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.666A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 29 Processing helix chain 'h' and resid 34 through 49 removed outlier: 3.661A pdb=" N PHE h 39 " --> pdb=" O ASN h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 62 removed outlier: 3.509A pdb=" N LEU h 60 " --> pdb=" O ARG h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 78 removed outlier: 3.752A pdb=" N ARG h 70 " --> pdb=" O GLU h 66 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS h 75 " --> pdb=" O LYS h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 100 removed outlier: 3.830A pdb=" N LYS h 84 " --> pdb=" O PHE h 80 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA h 85 " --> pdb=" O THR h 81 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 9 removed outlier: 3.623A pdb=" N PHE i 8 " --> pdb=" O THR i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 58 removed outlier: 3.807A pdb=" N ARG i 55 " --> pdb=" O ALA i 51 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.616A pdb=" N ASN i 76 " --> pdb=" O ARG i 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 15 removed outlier: 3.820A pdb=" N PHE j 11 " --> pdb=" O ASP j 7 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU j 12 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 67 removed outlier: 3.655A pdb=" N GLN j 67 " --> pdb=" O LYS j 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 20 removed outlier: 3.930A pdb=" N LYS k 12 " --> pdb=" O ARG k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 28 Processing helix chain 'l' and resid 37 through 48 removed outlier: 3.877A pdb=" N TYR l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 14 removed outlier: 3.508A pdb=" N GLY m 12 " --> pdb=" O GLY m 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 35 removed outlier: 4.355A pdb=" N GLN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 89 removed outlier: 4.114A pdb=" N VAL m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR m 82 " --> pdb=" O THR m 78 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU m 88 " --> pdb=" O ARG m 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 40 removed outlier: 4.071A pdb=" N PHE n 38 " --> pdb=" O PHE n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 56 removed outlier: 3.596A pdb=" N GLY n 55 " --> pdb=" O THR n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 63 removed outlier: 3.643A pdb=" N MET n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 86 Processing helix chain 'n' and resid 103 through 107 Processing helix chain 'n' and resid 122 through 134 removed outlier: 3.560A pdb=" N GLU n 127 " --> pdb=" O ARG n 123 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU n 128 " --> pdb=" O GLU n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 147 through 151 Processing helix chain 'n' and resid 166 through 178 Processing helix chain 'n' and resid 192 through 197 Processing helix chain 'n' and resid 211 through 222 removed outlier: 3.808A pdb=" N VAL n 217 " --> pdb=" O PRO n 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE n 222 " --> pdb=" O ILE n 218 " (cutoff:3.500A) Processing helix chain 'z' and resid 379 through 387 Processing helix chain 'z' and resid 390 through 415 removed outlier: 3.648A pdb=" N THR z 411 " --> pdb=" O ASN z 407 " (cutoff:3.500A) Processing helix chain 'z' and resid 417 through 421 removed outlier: 4.119A pdb=" N VAL z 420 " --> pdb=" O ILE z 417 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN z 421 " --> pdb=" O LYS z 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 417 through 421' Processing helix chain 'w' and resid 35 through 42 Processing helix chain 'w' and resid 79 through 88 removed outlier: 3.853A pdb=" N ALA w 83 " --> pdb=" O ARG w 79 " (cutoff:3.500A) Processing helix chain 'w' and resid 90 through 95 removed outlier: 4.305A pdb=" N THR w 93 " --> pdb=" O LYS w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 143 through 149 removed outlier: 3.742A pdb=" N SER w 149 " --> pdb=" O ASP w 145 " (cutoff:3.500A) Processing helix chain 'w' and resid 168 through 182 removed outlier: 3.656A pdb=" N LEU w 172 " --> pdb=" O LYS w 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE w 173 " --> pdb=" O ARG w 169 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 215 removed outlier: 3.530A pdb=" N ALA w 207 " --> pdb=" O GLN w 203 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS w 209 " --> pdb=" O ASN w 205 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 265 Processing helix chain 'w' and resid 297 through 302 Processing helix chain 'w' and resid 383 through 387 Processing helix chain 'w' and resid 388 through 392 Processing helix chain 'v' and resid 33 through 42 Processing helix chain 'v' and resid 45 through 49 Processing helix chain 'v' and resid 52 through 60 Processing helix chain 'o' and resid 147 through 169 removed outlier: 3.998A pdb=" N GLU o 155 " --> pdb=" O LEU o 151 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA o 158 " --> pdb=" O GLN o 154 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG o 164 " --> pdb=" O LEU o 160 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS o 165 " --> pdb=" O GLU o 161 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU o 166 " --> pdb=" O TRP o 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 184 through 191 Processing helix chain 'o' and resid 194 through 199 Processing helix chain 'o' and resid 217 through 222 Processing helix chain 'o' and resid 242 through 256 removed outlier: 3.722A pdb=" N ILE o 247 " --> pdb=" O LYS o 243 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA o 248 " --> pdb=" O LYS o 244 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR o 252 " --> pdb=" O ALA o 248 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE o 253 " --> pdb=" O TRP o 249 " (cutoff:3.500A) Processing helix chain 'o' and resid 348 through 353 removed outlier: 4.242A pdb=" N ILE o 353 " --> pdb=" O LYS o 349 " (cutoff:3.500A) Processing helix chain 'o' and resid 418 through 427 removed outlier: 4.861A pdb=" N VAL o 424 " --> pdb=" O PRO o 420 " (cutoff:3.500A) Processing helix chain 'o' and resid 429 through 436 removed outlier: 3.966A pdb=" N ILE o 433 " --> pdb=" O PRO o 429 " (cutoff:3.500A) Processing helix chain 'o' and resid 460 through 469 removed outlier: 3.747A pdb=" N ARG o 466 " --> pdb=" O VAL o 462 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA o 467 " --> pdb=" O ALA o 463 " (cutoff:3.500A) Processing helix chain 'o' and resid 487 through 492 removed outlier: 3.532A pdb=" N VAL o 492 " --> pdb=" O LEU o 488 " (cutoff:3.500A) Processing helix chain 'p' and resid 6 through 14 removed outlier: 3.891A pdb=" N UNK p 10 " --> pdb=" O UNK p 6 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N UNK p 12 " --> pdb=" O UNK p 8 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N UNK p 14 " --> pdb=" O UNK p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 80 through 86 Processing helix chain 'p' and resid 121 through 125 removed outlier: 3.547A pdb=" N UNK p 125 " --> pdb=" O UNK p 122 " (cutoff:3.500A) Processing helix chain 'p' and resid 138 through 148 removed outlier: 3.866A pdb=" N UNK p 142 " --> pdb=" O UNK p 138 " (cutoff:3.500A) Processing helix chain 'p' and resid 178 through 185 removed outlier: 4.038A pdb=" N UNK p 182 " --> pdb=" O UNK p 179 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N UNK p 183 " --> pdb=" O UNK p 180 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N UNK p 184 " --> pdb=" O UNK p 181 " (cutoff:3.500A) Processing helix chain 't' and resid 79 through 91 removed outlier: 4.420A pdb=" N TYR t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN t 90 " --> pdb=" O ALA t 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 6.565A pdb=" N LEU B 58 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 48 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 60 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG B 64 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.391A 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 removed outlier: 6.306A pdb=" N ARG B 147 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N HIS B 139 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 145 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.533A pdb=" N ALA C 42 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 184 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 157 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL C 87 " --> pdb=" O TRP C 106 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP C 106 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 89 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR C 104 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 6.880A 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: 3.533A pdb=" N ALA C 42 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 184 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 158 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 157 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.594A pdb=" N VAL C 57 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE C 359 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 55 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE C 215 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS C 281 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 323 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL C 285 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE C 321 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 74 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 52 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP C 80 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 50 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 225 through 227 Processing sheet with id=AA7, first strand: chain 'D' and resid 15 through 21 removed outlier: 6.163A pdb=" N ASN D 18 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 8 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 151 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 150 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 206 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR D 251 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 208 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 207 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 63 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: 3.845A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE E 102 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 11 Processing sheet with id=AB3, first strand: chain 'F' and resid 33 through 37 removed outlier: 7.577A pdb=" N LYS M 8 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 20 " --> pdb=" O LYS M 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 133 through 136 removed outlier: 6.402A pdb=" N LYS F 87 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS F 184 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS F 89 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 100 through 105 removed outlier: 3.551A pdb=" N ARG F 124 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.720A pdb=" N LEU G 64 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR G 38 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL G 39 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.553A pdb=" N LEU H 150 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 5 through 9 removed outlier: 6.259A pdb=" N VAL J 6 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL J 35 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE J 8 " --> pdb=" O VAL J 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC1, first strand: chain 'K' and resid 22 through 24 Processing sheet with id=AC2, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC3, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AC4, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AC5, first strand: chain 'L' and resid 22 through 25 removed outlier: 6.850A pdb=" N MET L 59 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL L 39 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N MET L 57 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA L 99 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE L 102 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AC7, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.745A pdb=" N SER L 133 " --> pdb=" O ILE L 114 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N GLY L 116 " --> pdb=" O SER L 133 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL L 135 " --> pdb=" O GLY L 116 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 58 through 59 removed outlier: 8.067A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 101 through 103 removed outlier: 6.743A pdb=" N ILE N 102 " --> pdb=" O LYS N 126 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL N 125 " --> pdb=" O GLU N 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'N' and resid 111 through 112 Processing sheet with id=AD2, first strand: chain 'O' and resid 36 through 39 removed outlier: 4.326A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR O 129 " --> pdb=" O VAL O 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN O 117 " --> pdb=" O ILE O 133 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL O 135 " --> pdb=" O VAL O 115 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL O 115 " --> pdb=" O VAL O 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 72 through 79 removed outlier: 6.758A pdb=" N ILE P 64 " --> pdb=" O LEU P 75 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA P 77 " --> pdb=" O CYS P 62 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS P 62 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR P 79 " --> pdb=" O ILE P 60 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE P 60 " --> pdb=" O TYR P 79 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP P 147 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL P 53 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 183 through 184 Processing sheet with id=AD5, first strand: chain 'Q' and resid 61 through 63 removed outlier: 6.408A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 61 through 63 removed outlier: 6.408A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD8, first strand: chain 'S' and resid 56 through 63 removed outlier: 5.288A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU S 24 " --> pdb=" O GLN T 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 87 through 94 removed outlier: 4.596A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 83 through 92 removed outlier: 3.648A pdb=" N ASN T 66 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL T 64 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 139 through 142 Processing sheet with id=AE3, first strand: chain 'U' and resid 14 through 22 removed outlier: 3.810A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS U 145 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL U 119 " --> pdb=" O HIS U 145 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU U 147 " --> pdb=" O ILE U 117 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE U 117 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL U 149 " --> pdb=" O SER U 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'U' and resid 126 through 131 removed outlier: 3.978A pdb=" N ARG U 135 " --> pdb=" O ARG U 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 54 through 57 removed outlier: 7.162A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 42 through 43 Processing sheet with id=AE8, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.904A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS W 109 " --> pdb=" O ARG W 125 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AF1, first strand: chain 'X' and resid 94 through 99 removed outlier: 3.511A pdb=" N ILE X 97 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL X 85 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N LEU X 99 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N ASP X 83 " --> pdb=" O LEU X 99 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA X 79 " --> pdb=" O VAL X 73 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL X 73 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL X 85 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N GLU X 67 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU X 55 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 69 through 76 removed outlier: 7.386A pdb=" N LYS Y 69 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA Y 44 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE Y 25 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE Y 46 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL Y 23 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 10 " --> pdb=" O THR Y 83 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 205 through 206 removed outlier: 4.460A pdb=" N SER b 113 " --> pdb=" O ARG b 88 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL b 134 " --> pdb=" O SER b 228 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS b 221 " --> pdb=" O PHE b 229 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ASN b 231 " --> pdb=" O LYS b 221 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 153 through 156 Processing sheet with id=AF5, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.878A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 49 through 51 removed outlier: 3.656A pdb=" N GLU d 11 " --> pdb=" O VAL d 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 72 through 76 Processing sheet with id=AF8, first strand: chain 'f' and resid 9 through 18 removed outlier: 9.957A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.374A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.601A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 16 through 18 Processing sheet with id=AG2, first strand: chain 'j' and resid 3 through 5 removed outlier: 6.626A pdb=" N ARG j 3 " --> pdb=" O THR j 53 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL j 55 " --> pdb=" O ARG j 3 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE j 5 " --> pdb=" O VAL j 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG j 46 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR j 22 " --> pdb=" O ARG j 46 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA j 23 " --> pdb=" O ASN j 76 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'l' and resid 3 through 5 removed outlier: 6.646A pdb=" N VAL l 4 " --> pdb=" O GLY l 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'l' and resid 7 through 11 removed outlier: 6.965A pdb=" N LYS l 66 " --> pdb=" O ARG l 87 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG l 87 " --> pdb=" O LYS l 66 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL l 68 " --> pdb=" O LEU l 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'm' and resid 37 through 38 removed outlier: 3.727A pdb=" N TYR m 37 " --> pdb=" O VAL m 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL m 47 " --> pdb=" O TYR m 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'n' and resid 2 through 5 Processing sheet with id=AG7, first strand: chain 'n' and resid 18 through 19 removed outlier: 3.556A pdb=" N VAL n 49 " --> pdb=" O CYS n 24 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'n' and resid 64 through 65 Processing sheet with id=AG9, first strand: chain 'n' and resid 108 through 110 removed outlier: 6.294A pdb=" N ALA n 115 " --> pdb=" O PHE n 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 152 through 154 Processing sheet with id=AH2, first strand: chain 'w' and resid 52 through 57 removed outlier: 3.831A pdb=" N THR w 117 " --> pdb=" O VAL w 98 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'w' and resid 52 through 57 removed outlier: 4.190A pdb=" N ARG w 113 " --> pdb=" O ILE w 103 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'w' and resid 189 through 192 removed outlier: 4.081A pdb=" N SER w 189 " --> pdb=" O PHE w 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER w 191 " --> pdb=" O ASP w 198 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'w' and resid 189 through 192 removed outlier: 4.081A pdb=" N SER w 189 " --> pdb=" O PHE w 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER w 191 " --> pdb=" O ASP w 198 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N THR w 239 " --> pdb=" O ILE w 229 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'w' and resid 256 through 258 removed outlier: 6.838A pdb=" N GLN w 284 " --> pdb=" O SER w 277 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN w 292 " --> pdb=" O ASP w 287 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'w' and resid 353 through 355 removed outlier: 6.814A pdb=" N THR w 339 " --> pdb=" O LEU w 321 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER w 368 " --> pdb=" O LYS w 400 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS w 400 " --> pdb=" O SER w 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET w 370 " --> pdb=" O VAL w 398 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'w' and resid 329 through 330 Processing sheet with id=AH9, first strand: chain 'v' and resid 4 through 5 Processing sheet with id=AI1, first strand: chain 'v' and resid 19 through 22 Processing sheet with id=AI2, first strand: chain 'o' and resid 203 through 204 removed outlier: 5.946A pdb=" N ILE o 339 " --> pdb=" O CYS o 386 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 't' and resid 102 through 103 1828 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2534 hydrogen bonds 4102 hydrogen bond angles 0 basepair planarities 1028 basepair parallelities 1743 stacking parallelities Total time for adding SS restraints: 183.17 Time building geometry restraints manager: 52.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 12050 1.27 - 1.41: 45763 1.41 - 1.55: 73381 1.55 - 1.68: 6886 1.68 - 1.82: 195 Bond restraints: 138275 Sorted by residual: bond pdb=" N PRO w 25 " pdb=" CA PRO w 25 " ideal model delta sigma weight residual 1.469 1.709 -0.241 1.28e-02 6.10e+03 3.53e+02 bond pdb=" N PRO o 394 " pdb=" CA PRO o 394 " ideal model delta sigma weight residual 1.469 1.698 -0.229 1.28e-02 6.10e+03 3.21e+02 bond pdb=" C CYS w 19 " pdb=" O CYS w 19 " ideal model delta sigma weight residual 1.236 1.130 0.106 1.28e-02 6.10e+03 6.89e+01 bond pdb=" C THR o 179 " pdb=" N PRO o 180 " ideal model delta sigma weight residual 1.334 1.501 -0.167 2.34e-02 1.83e+03 5.12e+01 bond pdb=" C1' U A2258 " pdb=" N1 U A2258 " ideal model delta sigma weight residual 1.480 1.572 -0.092 1.50e-02 4.44e+03 3.77e+01 ... (remaining 138270 not shown) Histogram of bond angle deviations from ideal: 89.12 - 99.29: 41 99.29 - 109.46: 50606 109.46 - 119.63: 92532 119.63 - 129.80: 57866 129.80 - 139.97: 2474 Bond angle restraints: 203519 Sorted by residual: angle pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" CD PRO C 18 " ideal model delta sigma weight residual 112.00 89.12 22.88 1.40e+00 5.10e-01 2.67e+02 angle pdb=" C PHE o 393 " pdb=" N PRO o 394 " pdb=" CA PRO o 394 " ideal model delta sigma weight residual 119.84 139.97 -20.13 1.25e+00 6.40e-01 2.59e+02 angle pdb=" C THR w 24 " pdb=" N PRO w 25 " pdb=" CA PRO w 25 " ideal model delta sigma weight residual 119.84 137.86 -18.02 1.25e+00 6.40e-01 2.08e+02 angle pdb=" C THR o 179 " pdb=" N PRO o 180 " pdb=" CA PRO o 180 " ideal model delta sigma weight residual 119.84 136.75 -16.91 1.25e+00 6.40e-01 1.83e+02 angle pdb=" CA PRO o 394 " pdb=" N PRO o 394 " pdb=" CD PRO o 394 " ideal model delta sigma weight residual 112.00 99.91 12.09 1.40e+00 5.10e-01 7.46e+01 ... (remaining 203514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 78797 35.95 - 71.89: 7941 71.89 - 107.84: 753 107.84 - 143.79: 31 143.79 - 179.73: 42 Dihedral angle restraints: 87564 sinusoidal: 67137 harmonic: 20427 Sorted by residual: dihedral pdb=" O4' U A3306 " pdb=" C1' U A3306 " pdb=" N1 U A3306 " pdb=" C2 U A3306 " ideal model delta sinusoidal sigma weight residual 200.00 25.32 174.68 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' C A3181 " pdb=" C1' C A3181 " pdb=" N1 C A3181 " pdb=" C2 C A3181 " ideal model delta sinusoidal sigma weight residual -160.00 13.01 -173.01 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U A2506 " pdb=" C1' U A2506 " pdb=" N1 U A2506 " pdb=" C2 U A2506 " ideal model delta sinusoidal sigma weight residual -160.00 12.88 -172.88 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 87561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 20283 0.073 - 0.147: 4668 0.147 - 0.220: 538 0.220 - 0.294: 70 0.294 - 0.367: 8 Chirality restraints: 25567 Sorted by residual: 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 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB VAL J 35 " pdb=" CA VAL J 35 " pdb=" CG1 VAL J 35 " pdb=" CG2 VAL J 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" C PRO C 18 " pdb=" CB PRO C 18 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 25564 not shown) Planarity restraints: 13083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 120 " 0.026 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C PRO B 120 " -0.088 2.00e-02 2.50e+03 pdb=" O PRO B 120 " 0.032 2.00e-02 2.50e+03 pdb=" N GLY B 121 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 17 " -0.092 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO C 18 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A y 88 " 0.050 2.00e-02 2.50e+03 2.26e-02 1.40e+01 pdb=" N9 A y 88 " -0.050 2.00e-02 2.50e+03 pdb=" C8 A y 88 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A y 88 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A y 88 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A y 88 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A y 88 " 0.021 2.00e-02 2.50e+03 pdb=" N1 A y 88 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A y 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A y 88 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A y 88 " -0.002 2.00e-02 2.50e+03 ... (remaining 13080 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 632 2.48 - 3.08: 85391 3.08 - 3.69: 221968 3.69 - 4.29: 341728 4.29 - 4.90: 502424 Nonbonded interactions: 1152143 Sorted by model distance: nonbonded pdb=" O ALA w 147 " pdb=" N SER w 149 " model vdw 1.872 2.520 nonbonded pdb=" O GLN n 140 " pdb=" CG2 THR n 141 " model vdw 1.921 3.460 nonbonded pdb=" O ASP o 133 " pdb=" OD1 ASP o 217 " model vdw 1.968 3.040 nonbonded pdb=" O LYS O 192 " pdb=" OG1 THR O 196 " model vdw 1.993 2.440 nonbonded pdb=" OP1 U A2282 " pdb=" O2' G A2973 " model vdw 1.996 2.440 ... (remaining 1152138 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 13.450 Check model and map are aligned: 1.230 Set scattering table: 0.800 Process input model: 422.890 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 447.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.014 0.241 138275 Z= 0.851 Angle : 0.989 22.885 203519 Z= 0.513 Chirality : 0.062 0.367 25567 Planarity : 0.006 0.125 13083 Dihedral : 22.403 179.733 74382 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.31 % Favored : 91.49 % Rotamer: Outliers : 0.80 % Allowed : 6.05 % Favored : 93.16 % Cbeta Deviations : 0.03 % 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: -4.17 (0.08), residues: 6753 helix: -2.80 (0.08), residues: 2147 sheet: -2.11 (0.14), residues: 1042 loop : -3.00 (0.08), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 95 HIS 0.013 0.002 HIS C 163 PHE 0.025 0.002 PHE J 63 TYR 0.043 0.003 TYR C 154 ARG 0.018 0.001 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1029 time to evaluate : 6.166 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL L 137 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "VAL Q 186 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash 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: B 123 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7840 (mtp180) REVERT: B 144 ASN cc_start: 0.7869 (t0) cc_final: 0.7501 (t0) REVERT: B 155 LYS cc_start: 0.8283 (mttp) cc_final: 0.8057 (mttp) REVERT: C 67 PHE cc_start: 0.8423 (m-80) cc_final: 0.7877 (m-80) REVERT: C 302 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8257 (mmtp) REVERT: D 285 ASP cc_start: 0.7982 (t70) cc_final: 0.7549 (p0) REVERT: D 350 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7711 (mmmt) REVERT: D 360 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8408 (mttm) REVERT: E 154 THR cc_start: 0.8845 (p) cc_final: 0.8534 (p) REVERT: E 168 ASP cc_start: 0.7283 (m-30) cc_final: 0.7072 (m-30) REVERT: F 91 ARG cc_start: 0.7040 (mmm-85) cc_final: 0.6789 (mmm-85) REVERT: F 173 ARG cc_start: 0.6064 (tmm-80) cc_final: 0.4910 (mtm180) REVERT: L 42 SER cc_start: 0.8824 (p) cc_final: 0.8448 (p) REVERT: L 49 LEU cc_start: 0.9107 (pp) cc_final: 0.8899 (pp) REVERT: P 206 GLN cc_start: 0.8058 (mp10) cc_final: 0.7596 (mp10) REVERT: Q 11 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8710 (tttt) REVERT: Q 180 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7688 (mtt-85) REVERT: R 89 LEU cc_start: 0.8974 (tp) cc_final: 0.8756 (tp) REVERT: V 103 TYR cc_start: 0.8716 (m-80) cc_final: 0.8509 (m-80) REVERT: Y 25 ILE cc_start: 0.9223 (mt) cc_final: 0.8997 (mm) REVERT: Y 68 ILE cc_start: 0.8909 (mm) cc_final: 0.8661 (mm) REVERT: Y 133 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7406 (tptt) REVERT: Z 69 LEU cc_start: 0.8968 (tt) cc_final: 0.8707 (mp) REVERT: Z 75 TYR cc_start: 0.8477 (m-80) cc_final: 0.8271 (m-80) REVERT: Z 98 SER cc_start: 0.9065 (p) cc_final: 0.8862 (p) REVERT: b 78 GLU cc_start: 0.7770 (pm20) cc_final: 0.7488 (pm20) REVERT: b 118 LYS cc_start: 0.8629 (ttpt) cc_final: 0.8403 (tttt) REVERT: e 34 LYS cc_start: 0.9040 (tptm) cc_final: 0.8833 (ttmm) REVERT: g 14 ASN cc_start: 0.8810 (t0) cc_final: 0.8503 (t0) REVERT: i 21 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.8012 (ttp-170) REVERT: i 58 THR cc_start: 0.8504 (t) cc_final: 0.8224 (p) REVERT: j 65 LEU cc_start: 0.8799 (mp) cc_final: 0.8594 (mt) REVERT: l 27 GLN cc_start: 0.8792 (tt0) cc_final: 0.8498 (tt0) REVERT: l 58 PHE cc_start: 0.8379 (t80) cc_final: 0.8124 (t80) REVERT: n 23 TYR cc_start: 0.8560 (p90) cc_final: 0.8116 (p90) REVERT: n 151 TYR cc_start: 0.9222 (m-80) cc_final: 0.8780 (m-80) REVERT: w 203 GLN cc_start: 0.6743 (pm20) cc_final: 0.6386 (pm20) REVERT: w 247 GLU cc_start: 0.7527 (mp0) cc_final: 0.7239 (mp0) REVERT: v 5 ILE cc_start: 0.8608 (pt) cc_final: 0.8178 (tt) REVERT: v 12 LYS cc_start: 0.7927 (mttt) cc_final: 0.7655 (mttt) REVERT: v 44 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8382 (mmtt) REVERT: o 134 LEU cc_start: 0.2341 (OUTLIER) cc_final: 0.1825 (tp) REVERT: o 169 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5280 (tt) REVERT: o 400 LYS cc_start: 0.3286 (OUTLIER) cc_final: 0.2992 (ttmm) REVERT: o 431 TYR cc_start: 0.2838 (p90) cc_final: 0.2254 (m-80) outliers start: 46 outliers final: 29 residues processed: 1071 average time/residue: 1.3001 time to fit residues: 2287.9213 Evaluate side-chains 816 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 782 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 PRO Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain e residue 7 PRO Chi-restraints excluded: chain g residue 44 CYS Chi-restraints excluded: chain i residue 21 ARG Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 141 THR Chi-restraints excluded: chain n residue 142 ILE Chi-restraints excluded: chain w residue 59 ARG Chi-restraints excluded: chain w residue 146 CYS Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 164 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 169 LEU Chi-restraints excluded: chain o residue 171 GLU Chi-restraints excluded: chain o residue 178 LEU Chi-restraints excluded: chain o residue 181 PHE Chi-restraints excluded: chain o residue 223 LYS Chi-restraints excluded: chain o residue 400 LYS Chi-restraints excluded: chain o residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 864 optimal weight: 0.8980 chunk 776 optimal weight: 2.9990 chunk 430 optimal weight: 5.9990 chunk 265 optimal weight: 40.0000 chunk 523 optimal weight: 0.9990 chunk 414 optimal weight: 4.9990 chunk 802 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 3.9990 chunk 597 optimal weight: 0.8980 chunk 929 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 97 ASN B 218 HIS D 59 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN E 43 GLN F 5 GLN F 157 ASN F 163 GLN H 45 ASN H 79 GLN H 95 ASN H 123 GLN H 137 ASN K 25 HIS K 149 GLN L 98 ASN P 57 ASN Q 135 GLN S 49 HIS S 63 GLN S 88 HIS ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS U 28 ASN U 92 GLN W 85 GLN W 111 ASN X 91 ASN Y 127 ASN a 11 ASN b 80 GLN b 104 GLN c 36 GLN d 105 GLN f 88 ASN g 18 ASN i 76 ASN i 79 GLN j 28 ASN j 40 GLN k 25 GLN l 47 GLN l 59 HIS n 75 GLN n 82 GLN z 410 ASN w 206 HIS w 269 ASN w 351 GLN w 358 HIS w 364 HIS v 58 HIS o 338 ASN o 395 ASN ** o 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 138275 Z= 0.179 Angle : 0.563 12.851 203519 Z= 0.290 Chirality : 0.035 0.237 25567 Planarity : 0.005 0.157 13083 Dihedral : 22.814 179.621 60805 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 1.58 % Allowed : 11.40 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.09), residues: 6753 helix: -1.23 (0.10), residues: 2142 sheet: -1.49 (0.15), residues: 1062 loop : -2.32 (0.09), residues: 3549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 162 HIS 0.006 0.001 HIS w 364 PHE 0.032 0.001 PHE b 229 TYR 0.019 0.001 TYR o 417 ARG 0.007 0.001 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 955 time to evaluate : 6.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. 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. 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: B 238 ILE cc_start: 0.8416 (mm) cc_final: 0.8150 (mt) REVERT: C 246 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8943 (pp) REVERT: C 302 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8206 (mmtp) REVERT: D 285 ASP cc_start: 0.8011 (t70) cc_final: 0.7580 (p0) REVERT: D 360 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8369 (mtmt) REVERT: E 47 GLN cc_start: 0.8499 (mp10) cc_final: 0.7785 (mp10) REVERT: E 154 THR cc_start: 0.8930 (p) cc_final: 0.8689 (p) REVERT: E 168 ASP cc_start: 0.7226 (m-30) cc_final: 0.7016 (m-30) REVERT: F 5 GLN cc_start: 0.8177 (tt0) cc_final: 0.7949 (tt0) REVERT: F 7 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 63 LYS cc_start: 0.7208 (ttpt) cc_final: 0.6281 (tmtt) REVERT: F 69 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7550 (mmm-85) REVERT: F 173 ARG cc_start: 0.5991 (tmm-80) cc_final: 0.5039 (mtm180) REVERT: G 90 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8286 (mttm) REVERT: H 130 TYR cc_start: 0.8842 (m-80) cc_final: 0.8617 (m-80) REVERT: J 31 LYS cc_start: 0.8591 (mttt) cc_final: 0.8123 (mtpt) REVERT: K 110 ASP cc_start: 0.8656 (m-30) cc_final: 0.8454 (m-30) REVERT: K 176 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7684 (mp0) REVERT: L 42 SER cc_start: 0.9028 (p) cc_final: 0.8653 (p) REVERT: L 61 THR cc_start: 0.9294 (m) cc_final: 0.8992 (p) REVERT: L 106 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8246 (mtpt) REVERT: N 45 MET cc_start: 0.8544 (mmm) cc_final: 0.8332 (mmm) REVERT: N 60 TYR cc_start: 0.8708 (t80) cc_final: 0.8028 (t80) REVERT: P 254 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7822 (ptmm) REVERT: Q 120 GLU cc_start: 0.7671 (pt0) cc_final: 0.7309 (pt0) REVERT: Q 130 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7896 (mtt180) REVERT: W 73 MET cc_start: 0.7583 (mmm) cc_final: 0.7259 (mmm) REVERT: W 74 LYS cc_start: 0.7632 (mtpt) cc_final: 0.7300 (mtpp) REVERT: W 77 GLU cc_start: 0.7932 (mp0) cc_final: 0.7665 (mp0) REVERT: Y 133 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7361 (tptt) REVERT: b 78 GLU cc_start: 0.7785 (pm20) cc_final: 0.7506 (pm20) REVERT: f 10 LYS cc_start: 0.9133 (ptpt) cc_final: 0.8566 (mtpt) REVERT: f 63 LYS cc_start: 0.8755 (mttt) cc_final: 0.8467 (mttm) REVERT: f 75 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8593 (t70) REVERT: j 76 ASN cc_start: 0.8477 (t0) cc_final: 0.8239 (t0) REVERT: m 84 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.6988 (ptm-80) REVERT: n 23 TYR cc_start: 0.8720 (p90) cc_final: 0.8227 (p90) REVERT: w 195 ASP cc_start: 0.8557 (p0) cc_final: 0.7957 (p0) REVERT: w 286 MET cc_start: 0.8162 (ttp) cc_final: 0.7716 (tmm) REVERT: w 370 MET cc_start: 0.8381 (mmt) cc_final: 0.8050 (mmt) REVERT: v 1 MET cc_start: 0.3585 (ttp) cc_final: 0.3278 (ttp) REVERT: v 5 ILE cc_start: 0.8632 (pt) cc_final: 0.8293 (tt) REVERT: v 12 LYS cc_start: 0.7900 (mttt) cc_final: 0.7560 (mttt) REVERT: o 134 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.1788 (tt) REVERT: o 148 LYS cc_start: 0.1774 (tptm) cc_final: 0.0805 (pptt) REVERT: o 165 LYS cc_start: 0.4200 (OUTLIER) cc_final: 0.2824 (mmtp) outliers start: 91 outliers final: 59 residues processed: 1008 average time/residue: 1.1866 time to fit residues: 2011.4642 Evaluate side-chains 900 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 837 time to evaluate : 6.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL 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 115 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain O residue 198 SER Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 135 ARG Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain a residue 31 SER Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 170 GLU Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 93 LEU Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 387 SER Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 171 GLU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 402 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 516 optimal weight: 0.1980 chunk 288 optimal weight: 8.9990 chunk 773 optimal weight: 0.9980 chunk 633 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 931 optimal weight: 1.9990 chunk 1006 optimal weight: 10.0000 chunk 829 optimal weight: 7.9990 chunk 923 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 747 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS D 201 GLN E 43 GLN E 150 ASN G 80 ASN H 45 ASN H 79 GLN K 13 HIS K 149 GLN M 126 GLN N 14 HIS Q 126 GLN ** Q 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 HIS ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 GLN e 6 HIS e 52 GLN g 61 GLN j 40 GLN m 32 GLN w 364 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 138275 Z= 0.271 Angle : 0.561 13.397 203519 Z= 0.290 Chirality : 0.036 0.239 25567 Planarity : 0.004 0.155 13083 Dihedral : 22.684 179.328 60753 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.51 % Favored : 94.48 % Rotamer: Outliers : 3.01 % Allowed : 13.81 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.09), residues: 6753 helix: -0.71 (0.11), residues: 2166 sheet: -1.23 (0.15), residues: 1054 loop : -1.96 (0.09), residues: 3533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 120 HIS 0.010 0.001 HIS D 115 PHE 0.031 0.001 PHE b 229 TYR 0.026 0.002 TYR E 167 ARG 0.007 0.000 ARG j 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 907 time to evaluate : 6.194 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (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: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7527 (mmt90) REVERT: C 246 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8963 (pp) REVERT: C 302 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8323 (mmtp) REVERT: D 285 ASP cc_start: 0.8098 (t70) cc_final: 0.7632 (p0) REVERT: D 311 HIS cc_start: 0.8315 (t-90) cc_final: 0.8087 (t70) REVERT: D 360 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8420 (mtmt) REVERT: E 47 GLN cc_start: 0.8497 (mp10) cc_final: 0.7893 (mp10) REVERT: E 154 THR cc_start: 0.9008 (p) cc_final: 0.8766 (p) REVERT: F 5 GLN cc_start: 0.8158 (tt0) cc_final: 0.7933 (tt0) REVERT: F 62 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8111 (ttm170) REVERT: F 63 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6468 (tmtt) REVERT: F 168 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7400 (mtp-110) REVERT: F 173 ARG cc_start: 0.6225 (tmm-80) cc_final: 0.5356 (mtp180) REVERT: G 48 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8573 (mtm110) REVERT: G 90 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8315 (mttm) REVERT: H 130 TYR cc_start: 0.8890 (m-80) cc_final: 0.8531 (m-80) REVERT: J 31 LYS cc_start: 0.8588 (mttt) cc_final: 0.8209 (mtpt) REVERT: L 42 SER cc_start: 0.9203 (p) cc_final: 0.8845 (p) REVERT: L 106 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8305 (mtpt) REVERT: M 14 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8794 (pp) REVERT: R 28 GLU cc_start: 0.7885 (mp0) cc_final: 0.7567 (mp0) REVERT: R 43 LYS cc_start: 0.8090 (tttt) cc_final: 0.7777 (mttm) REVERT: S 109 ASP cc_start: 0.7515 (p0) cc_final: 0.7106 (p0) REVERT: V 36 TYR cc_start: 0.8845 (t80) cc_final: 0.8571 (t80) REVERT: V 55 THR cc_start: 0.7744 (m) cc_final: 0.7485 (t) REVERT: Y 106 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: Y 123 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: b 62 ILE cc_start: 0.8694 (pt) cc_final: 0.8422 (mt) REVERT: b 78 GLU cc_start: 0.7780 (pm20) cc_final: 0.7511 (pm20) REVERT: b 100 ARG cc_start: 0.8390 (ptm-80) cc_final: 0.7901 (ttp-110) REVERT: d 87 ASN cc_start: 0.7598 (m110) cc_final: 0.7320 (m110) REVERT: d 92 TYR cc_start: 0.9073 (t80) cc_final: 0.8549 (t80) REVERT: d 94 GLU cc_start: 0.8312 (pt0) cc_final: 0.8039 (pt0) REVERT: f 75 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8610 (t70) REVERT: m 30 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7408 (mt-10) REVERT: m 84 ARG cc_start: 0.7501 (ptm-80) cc_final: 0.7100 (ptm-80) REVERT: w 370 MET cc_start: 0.8213 (mmt) cc_final: 0.8006 (mmt) REVERT: v 1 MET cc_start: 0.3636 (ttp) cc_final: 0.3187 (ttp) REVERT: v 12 LYS cc_start: 0.7892 (mttt) cc_final: 0.7595 (mttt) REVERT: o 134 LEU cc_start: 0.2532 (OUTLIER) cc_final: 0.1938 (tt) REVERT: o 148 LYS cc_start: 0.1716 (tptm) cc_final: 0.1269 (tppt) outliers start: 174 outliers final: 119 residues processed: 1017 average time/residue: 1.1637 time to fit residues: 2007.1087 Evaluate side-chains 976 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 851 time to evaluate : 6.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 132 VAL 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 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 56 ASP Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 27 LEU Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 106 GLN Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain a residue 31 SER Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 387 SER Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 164 LYS Chi-restraints excluded: chain w residue 170 THR Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 171 GLU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 310 ILE Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 920 optimal weight: 6.9990 chunk 700 optimal weight: 1.9990 chunk 483 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 625 optimal weight: 0.8980 chunk 934 optimal weight: 0.5980 chunk 989 optimal weight: 30.0000 chunk 488 optimal weight: 2.9990 chunk 886 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN D 201 GLN E 150 ASN F 59 ASN F 157 ASN G 80 ASN H 45 ASN H 79 GLN J 49 ASN K 149 GLN N 65 GLN N 89 GLN Q 126 GLN Q 135 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 157 GLN U 34 GLN U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 122 HIS Z 59 ASN e 31 ASN f 106 ASN w 364 HIS o 338 ASN t 117 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 138275 Z= 0.224 Angle : 0.525 12.357 203519 Z= 0.273 Chirality : 0.035 0.231 25567 Planarity : 0.004 0.151 13083 Dihedral : 22.641 179.972 60751 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.08 % Favored : 94.91 % Rotamer: Outliers : 3.34 % Allowed : 15.12 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 6753 helix: -0.39 (0.11), residues: 2162 sheet: -1.03 (0.15), residues: 1048 loop : -1.77 (0.10), residues: 3543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 120 HIS 0.011 0.001 HIS D 115 PHE 0.032 0.001 PHE b 229 TYR 0.020 0.001 TYR D 194 ARG 0.006 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 911 time to evaluate : 6.214 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. 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: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 72 ARG cc_start: 0.7824 (mmt90) cc_final: 0.7545 (mmt90) REVERT: B 246 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7362 (tp) REVERT: C 70 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7225 (mtp180) REVERT: C 246 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8939 (pt) REVERT: C 302 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8428 (mmtp) REVERT: D 285 ASP cc_start: 0.8060 (t70) cc_final: 0.7590 (p0) REVERT: D 311 HIS cc_start: 0.8278 (t-90) cc_final: 0.7909 (t-90) REVERT: D 360 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8415 (mttt) REVERT: E 47 GLN cc_start: 0.8519 (mp10) cc_final: 0.7955 (mp10) REVERT: E 154 THR cc_start: 0.9015 (p) cc_final: 0.8786 (p) REVERT: F 1 MET cc_start: 0.8672 (ptm) cc_final: 0.8008 (ptm) REVERT: F 7 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7381 (mt-10) REVERT: F 62 ARG cc_start: 0.8440 (mtp180) cc_final: 0.8032 (ttm170) REVERT: F 63 LYS cc_start: 0.7313 (ttpt) cc_final: 0.6503 (tmtt) REVERT: F 111 PHE cc_start: 0.8180 (m-80) cc_final: 0.7820 (m-80) REVERT: F 129 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.6862 (mmt-90) REVERT: F 168 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7255 (mtp-110) REVERT: F 173 ARG cc_start: 0.6482 (tmm-80) cc_final: 0.5396 (mtp180) REVERT: F 183 HIS cc_start: 0.7424 (t70) cc_final: 0.7144 (t70) REVERT: G 48 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8621 (mtm110) REVERT: G 90 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8113 (mttm) REVERT: H 130 TYR cc_start: 0.8918 (m-80) cc_final: 0.8544 (m-80) REVERT: H 177 TYR cc_start: 0.9357 (p90) cc_final: 0.9000 (p90) REVERT: H 226 TYR cc_start: 0.8563 (t80) cc_final: 0.8336 (t80) REVERT: J 31 LYS cc_start: 0.8583 (mttt) cc_final: 0.8173 (mtpt) REVERT: L 106 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8325 (mtpt) REVERT: M 14 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8810 (pp) REVERT: Q 55 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8454 (t) REVERT: R 28 GLU cc_start: 0.7863 (mp0) cc_final: 0.7600 (mp0) REVERT: R 43 LYS cc_start: 0.8086 (tttt) cc_final: 0.7767 (mttm) REVERT: S 109 ASP cc_start: 0.7469 (p0) cc_final: 0.7108 (p0) REVERT: U 31 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8209 (mm-30) REVERT: V 33 TYR cc_start: 0.8279 (t80) cc_final: 0.8015 (t80) REVERT: V 36 TYR cc_start: 0.8908 (t80) cc_final: 0.8637 (t80) REVERT: V 55 THR cc_start: 0.7806 (m) cc_final: 0.7579 (t) REVERT: W 129 ASP cc_start: 0.8303 (p0) cc_final: 0.7974 (p0) REVERT: Y 85 TYR cc_start: 0.8847 (m-80) cc_final: 0.8603 (m-80) REVERT: Y 106 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: Y 119 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7221 (mt-10) REVERT: Y 123 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: b 78 GLU cc_start: 0.7751 (pm20) cc_final: 0.7539 (pm20) REVERT: b 100 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.7874 (ttp-170) REVERT: b 180 SER cc_start: 0.8655 (p) cc_final: 0.8420 (p) REVERT: d 87 ASN cc_start: 0.7635 (m110) cc_final: 0.7357 (m110) REVERT: e 52 GLN cc_start: 0.8695 (mt0) cc_final: 0.8441 (mt0) REVERT: f 10 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8271 (mttt) REVERT: f 75 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8656 (t70) REVERT: g 94 LEU cc_start: 0.8997 (mt) cc_final: 0.8795 (mt) REVERT: m 84 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7092 (ptm-80) REVERT: m 87 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8515 (ttm170) REVERT: w 121 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.4306 (mt-10) REVERT: v 1 MET cc_start: 0.3769 (ttp) cc_final: 0.3194 (ttp) REVERT: v 12 LYS cc_start: 0.7886 (mttt) cc_final: 0.7588 (mttt) REVERT: o 134 LEU cc_start: 0.2596 (OUTLIER) cc_final: 0.2043 (tp) REVERT: o 148 LYS cc_start: 0.1707 (tptm) cc_final: 0.0525 (pptt) outliers start: 193 outliers final: 141 residues processed: 1029 average time/residue: 1.1381 time to fit residues: 1993.5481 Evaluate side-chains 1017 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 866 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain K residue 63 VAL 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 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP 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 80 VAL Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 91 ASP Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 106 GLN Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 31 SER Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 387 SER Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 255 ASP Chi-restraints excluded: chain w residue 273 PHE Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 171 GLU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 824 optimal weight: 6.9990 chunk 561 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 736 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 chunk 844 optimal weight: 9.9990 chunk 684 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 505 optimal weight: 0.4980 chunk 888 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN F 5 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 79 GLN H 243 GLN J 49 ASN K 149 GLN M 56 GLN Q 126 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN Y 78 ASN ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 ASN n 164 GLN w 206 HIS w 269 ASN w 364 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 138275 Z= 0.276 Angle : 0.550 23.593 203519 Z= 0.284 Chirality : 0.036 0.237 25567 Planarity : 0.004 0.192 13083 Dihedral : 22.622 179.934 60751 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.41 % Favored : 94.58 % Rotamer: Outliers : 4.11 % Allowed : 15.33 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.10), residues: 6753 helix: -0.27 (0.11), residues: 2162 sheet: -0.94 (0.15), residues: 1035 loop : -1.67 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 120 HIS 0.011 0.001 HIS D 115 PHE 0.032 0.001 PHE b 229 TYR 0.027 0.002 TYR N 60 ARG 0.009 0.000 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 908 time to evaluate : 6.182 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. 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: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 72 ARG cc_start: 0.7792 (mmt90) cc_final: 0.7507 (mmt90) REVERT: C 70 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7217 (mtp180) REVERT: C 246 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8768 (pp) REVERT: D 285 ASP cc_start: 0.8153 (t70) cc_final: 0.7552 (p0) REVERT: D 311 HIS cc_start: 0.8291 (t-90) cc_final: 0.7572 (t-90) REVERT: D 360 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8365 (mtmt) REVERT: E 47 GLN cc_start: 0.8535 (mp10) cc_final: 0.7996 (mp10) REVERT: E 154 THR cc_start: 0.9054 (p) cc_final: 0.8839 (p) REVERT: F 7 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7554 (mt-10) REVERT: F 62 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8059 (ttm170) REVERT: F 63 LYS cc_start: 0.7272 (ttpt) cc_final: 0.6542 (tmtt) REVERT: F 94 TYR cc_start: 0.7905 (p90) cc_final: 0.7357 (p90) REVERT: F 111 PHE cc_start: 0.8216 (m-80) cc_final: 0.7835 (m-80) REVERT: F 163 GLN cc_start: 0.7855 (mm110) cc_final: 0.7407 (mt0) REVERT: F 168 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7223 (mtp-110) REVERT: G 48 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8641 (mtm-85) REVERT: G 90 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8087 (mttm) REVERT: H 130 TYR cc_start: 0.8966 (m-80) cc_final: 0.8632 (m-80) REVERT: H 177 TYR cc_start: 0.9388 (p90) cc_final: 0.9093 (p90) REVERT: J 31 LYS cc_start: 0.8580 (mttt) cc_final: 0.8177 (mtpt) REVERT: K 137 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: M 14 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8787 (pp) REVERT: R 28 GLU cc_start: 0.7896 (mp0) cc_final: 0.7589 (mp0) REVERT: R 43 LYS cc_start: 0.8092 (tttt) cc_final: 0.7780 (mttm) REVERT: S 27 MET cc_start: 0.8923 (mtp) cc_final: 0.8587 (mtp) REVERT: S 109 ASP cc_start: 0.7441 (p0) cc_final: 0.7002 (p0) REVERT: U 75 GLU cc_start: 0.8009 (pt0) cc_final: 0.7750 (tt0) REVERT: V 36 TYR cc_start: 0.8932 (t80) cc_final: 0.8697 (t80) REVERT: V 55 THR cc_start: 0.7883 (m) cc_final: 0.7608 (p) REVERT: W 77 GLU cc_start: 0.7594 (mp0) cc_final: 0.7378 (mp0) REVERT: W 129 ASP cc_start: 0.8446 (p0) cc_final: 0.8159 (p0) REVERT: Y 85 TYR cc_start: 0.8859 (m-80) cc_final: 0.8530 (m-80) REVERT: Y 123 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: b 78 GLU cc_start: 0.7818 (pm20) cc_final: 0.7575 (pm20) REVERT: b 100 ARG cc_start: 0.8462 (ptm-80) cc_final: 0.7949 (ttp-170) REVERT: b 180 SER cc_start: 0.8733 (p) cc_final: 0.8505 (p) REVERT: d 48 ASP cc_start: 0.7820 (t0) cc_final: 0.7559 (t0) REVERT: d 73 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8916 (mt) REVERT: d 87 ASN cc_start: 0.7664 (m110) cc_final: 0.7389 (m110) REVERT: f 5 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5731 (m90) REVERT: f 75 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8736 (t70) REVERT: g 38 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8796 (mp) REVERT: g 94 LEU cc_start: 0.9004 (mt) cc_final: 0.8729 (mt) REVERT: h 20 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7566 (ttm) REVERT: k 25 GLN cc_start: 0.8372 (mm110) cc_final: 0.8158 (mm110) REVERT: m 84 ARG cc_start: 0.7525 (ptm-80) cc_final: 0.7052 (ptm-80) REVERT: m 87 ARG cc_start: 0.8764 (ttp-110) cc_final: 0.8524 (ttm170) REVERT: w 121 GLU cc_start: 0.4717 (OUTLIER) cc_final: 0.4263 (mt-10) REVERT: v 12 LYS cc_start: 0.7887 (mttt) cc_final: 0.7585 (mttt) REVERT: o 134 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1876 (tp) REVERT: o 165 LYS cc_start: 0.4793 (OUTLIER) cc_final: 0.4512 (pmtt) REVERT: o 307 ILE cc_start: 0.0974 (OUTLIER) cc_final: 0.0735 (pt) outliers start: 237 outliers final: 181 residues processed: 1050 average time/residue: 1.0724 time to fit residues: 1927.2300 Evaluate side-chains 1065 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 871 time to evaluate : 6.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 203 VAL 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 K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP 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 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 31 SER Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 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 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER 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 l residue 26 THR Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 40 SER Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 387 SER Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 240 TYR Chi-restraints excluded: chain w residue 269 ASN Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 281 ASN Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 307 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 333 optimal weight: 1.9990 chunk 891 optimal weight: 0.0270 chunk 195 optimal weight: 7.9990 chunk 581 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 990 optimal weight: 50.0000 chunk 822 optimal weight: 20.0000 chunk 458 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 327 optimal weight: 6.9990 chunk 520 optimal weight: 3.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 79 GLN J 49 ASN K 28 GLN K 149 GLN M 56 GLN N 89 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN j 57 ASN n 82 GLN ** w 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN w 364 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 138275 Z= 0.281 Angle : 0.550 15.577 203519 Z= 0.284 Chirality : 0.036 0.241 25567 Planarity : 0.004 0.169 13083 Dihedral : 22.617 179.795 60748 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.48 % Favored : 94.51 % Rotamer: Outliers : 4.23 % Allowed : 16.13 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 6753 helix: -0.17 (0.11), residues: 2155 sheet: -0.90 (0.15), residues: 1028 loop : -1.62 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 120 HIS 0.011 0.001 HIS w 206 PHE 0.033 0.001 PHE b 229 TYR 0.029 0.001 TYR N 60 ARG 0.009 0.000 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 907 time to evaluate : 6.275 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (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: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. 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: B 109 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 246 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7147 (tp) REVERT: C 70 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7218 (ttp-170) REVERT: C 74 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: C 246 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8776 (pp) REVERT: D 285 ASP cc_start: 0.8194 (t70) cc_final: 0.7537 (p0) REVERT: D 311 HIS cc_start: 0.8327 (t-90) cc_final: 0.7635 (t-90) REVERT: D 360 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8307 (mtmt) REVERT: E 25 GLU cc_start: 0.6840 (pp20) cc_final: 0.6172 (pp20) REVERT: E 47 GLN cc_start: 0.8559 (mp10) cc_final: 0.8034 (mp10) REVERT: E 154 THR cc_start: 0.9116 (p) cc_final: 0.8908 (p) REVERT: F 62 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7993 (ttm-80) REVERT: F 63 LYS cc_start: 0.7326 (ttpt) cc_final: 0.6617 (tmtt) REVERT: F 94 TYR cc_start: 0.7872 (p90) cc_final: 0.7415 (p90) REVERT: F 111 PHE cc_start: 0.8225 (m-80) cc_final: 0.7852 (m-80) REVERT: F 183 HIS cc_start: 0.7450 (t70) cc_final: 0.7187 (t70) REVERT: G 48 ARG cc_start: 0.9085 (mtm-85) cc_final: 0.8687 (mtm-85) REVERT: G 90 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8031 (mttm) REVERT: H 130 TYR cc_start: 0.8959 (m-80) cc_final: 0.8621 (m-80) REVERT: J 31 LYS cc_start: 0.8573 (mttt) cc_final: 0.8175 (mtpt) REVERT: J 47 PHE cc_start: 0.8139 (p90) cc_final: 0.7826 (p90) REVERT: K 137 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: M 14 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8750 (pp) REVERT: R 43 LYS cc_start: 0.8141 (tttt) cc_final: 0.7788 (mttm) REVERT: S 27 MET cc_start: 0.8926 (mtp) cc_final: 0.8563 (mtp) REVERT: S 109 ASP cc_start: 0.7436 (p0) cc_final: 0.6984 (p0) REVERT: U 25 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8486 (t) REVERT: W 77 GLU cc_start: 0.7581 (mp0) cc_final: 0.7369 (mp0) REVERT: W 129 ASP cc_start: 0.8421 (p0) cc_final: 0.8182 (p0) REVERT: Y 85 TYR cc_start: 0.8858 (m-80) cc_final: 0.8516 (m-80) REVERT: Y 123 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: b 78 GLU cc_start: 0.7809 (pm20) cc_final: 0.7556 (pm20) REVERT: b 100 ARG cc_start: 0.8398 (ptm-80) cc_final: 0.7900 (ttp-170) REVERT: b 180 SER cc_start: 0.8740 (p) cc_final: 0.8508 (p) REVERT: d 48 ASP cc_start: 0.7872 (t0) cc_final: 0.7573 (t70) REVERT: d 73 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8954 (mt) REVERT: d 87 ASN cc_start: 0.7627 (m110) cc_final: 0.7365 (m110) REVERT: e 87 MET cc_start: 0.7519 (mpp) cc_final: 0.7261 (ptp) REVERT: f 5 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.5879 (m90) REVERT: f 10 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8235 (mttt) REVERT: f 75 HIS cc_start: 0.9026 (OUTLIER) cc_final: 0.8750 (t70) REVERT: g 38 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8815 (mp) REVERT: h 20 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7498 (ttm) REVERT: l 25 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (t) REVERT: m 84 ARG cc_start: 0.7489 (ptm-80) cc_final: 0.6978 (ptm-80) REVERT: m 87 ARG cc_start: 0.8761 (ttp-110) cc_final: 0.8527 (ttm170) REVERT: n 82 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8169 (mm110) REVERT: w 34 MET cc_start: 0.4262 (mmp) cc_final: 0.3912 (mmt) REVERT: w 121 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4303 (mt-10) REVERT: v 12 LYS cc_start: 0.7892 (mttt) cc_final: 0.7582 (mttt) REVERT: o 134 LEU cc_start: 0.2226 (OUTLIER) cc_final: 0.2005 (tp) REVERT: o 307 ILE cc_start: 0.0993 (OUTLIER) cc_final: 0.0771 (pt) outliers start: 244 outliers final: 194 residues processed: 1050 average time/residue: 1.1059 time to fit residues: 2002.6605 Evaluate side-chains 1086 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 875 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 207 ASP 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 K residue 63 VAL Chi-restraints excluded: chain K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP 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 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain a residue 31 SER Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 170 GLU Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain d residue 44 MET Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 92 LYS Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 43 ASN Chi-restraints excluded: chain l residue 25 VAL Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 387 SER Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 127 ILE Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 240 TYR Chi-restraints excluded: chain w residue 255 ASP Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 370 MET Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 307 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 955 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 chunk 564 optimal weight: 2.9990 chunk 723 optimal weight: 3.9990 chunk 560 optimal weight: 4.9990 chunk 834 optimal weight: 0.1980 chunk 553 optimal weight: 5.9990 chunk 986 optimal weight: 40.0000 chunk 617 optimal weight: 6.9990 chunk 601 optimal weight: 3.9990 chunk 455 optimal weight: 0.0570 overall best weight: 2.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 ASN E 150 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 79 GLN J 49 ASN K 149 GLN N 89 GLN Q 15 HIS U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 ASN k 25 GLN n 164 GLN ** n 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN w 364 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 138275 Z= 0.199 Angle : 0.523 12.493 203519 Z= 0.272 Chirality : 0.035 0.232 25567 Planarity : 0.004 0.159 13083 Dihedral : 22.631 179.925 60748 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.45 % Favored : 94.54 % Rotamer: Outliers : 3.78 % Allowed : 17.22 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.10), residues: 6753 helix: -0.07 (0.11), residues: 2157 sheet: -0.85 (0.16), residues: 1026 loop : -1.56 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 120 HIS 0.009 0.001 HIS D 115 PHE 0.031 0.001 PHE b 229 TYR 0.030 0.001 TYR N 60 ARG 0.009 0.000 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 896 time to evaluate : 6.457 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (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: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. 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: B 246 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7110 (tp) REVERT: C 70 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7216 (ttp-170) REVERT: C 74 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: C 246 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8747 (pp) REVERT: D 285 ASP cc_start: 0.8187 (t70) cc_final: 0.7539 (p0) REVERT: D 311 HIS cc_start: 0.8286 (t-90) cc_final: 0.7626 (t-90) REVERT: D 360 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8301 (mtmt) REVERT: E 25 GLU cc_start: 0.6912 (pp20) cc_final: 0.6281 (pp20) REVERT: E 47 GLN cc_start: 0.8555 (mp10) cc_final: 0.8033 (mp10) REVERT: E 154 THR cc_start: 0.9091 (p) cc_final: 0.8884 (p) REVERT: F 7 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7467 (mt-10) REVERT: F 62 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7972 (ttm-80) REVERT: F 63 LYS cc_start: 0.7307 (ttpt) cc_final: 0.6600 (tmtt) REVERT: F 94 TYR cc_start: 0.7856 (p90) cc_final: 0.7414 (p90) REVERT: F 183 HIS cc_start: 0.7546 (t70) cc_final: 0.7196 (t70) REVERT: G 48 ARG cc_start: 0.9087 (mtm-85) cc_final: 0.8707 (mtm-85) REVERT: G 90 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8022 (mttm) REVERT: H 130 TYR cc_start: 0.8955 (m-80) cc_final: 0.8633 (m-80) REVERT: J 31 LYS cc_start: 0.8568 (mttt) cc_final: 0.8170 (mtpt) REVERT: J 47 PHE cc_start: 0.8115 (p90) cc_final: 0.7868 (p90) REVERT: K 137 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: L 61 THR cc_start: 0.9298 (m) cc_final: 0.9002 (p) REVERT: M 14 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8751 (pp) REVERT: R 43 LYS cc_start: 0.8107 (tttt) cc_final: 0.7760 (mttm) REVERT: S 27 MET cc_start: 0.8922 (mtp) cc_final: 0.8558 (mtp) REVERT: S 109 ASP cc_start: 0.7413 (p0) cc_final: 0.6973 (p0) REVERT: U 25 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8492 (t) REVERT: W 77 GLU cc_start: 0.7569 (mp0) cc_final: 0.7369 (mp0) REVERT: W 129 ASP cc_start: 0.8358 (p0) cc_final: 0.8150 (p0) REVERT: Y 85 TYR cc_start: 0.8837 (m-80) cc_final: 0.8475 (m-80) REVERT: Y 123 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: b 100 ARG cc_start: 0.8385 (ptm-80) cc_final: 0.7894 (ttp-170) REVERT: b 180 SER cc_start: 0.8709 (p) cc_final: 0.8469 (p) REVERT: d 48 ASP cc_start: 0.7808 (t0) cc_final: 0.7517 (t70) REVERT: d 73 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8936 (mt) REVERT: d 74 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8252 (ttp-170) REVERT: d 87 ASN cc_start: 0.7634 (m110) cc_final: 0.7373 (m110) REVERT: e 87 MET cc_start: 0.7540 (mpp) cc_final: 0.7294 (ptp) REVERT: f 5 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5832 (m90) REVERT: f 10 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8254 (mttt) REVERT: f 75 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8737 (t70) REVERT: g 38 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8802 (mp) REVERT: h 20 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7464 (ttm) REVERT: m 84 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.6956 (ptm-80) REVERT: m 87 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.8514 (ttm170) REVERT: w 20 CYS cc_start: 0.6317 (OUTLIER) cc_final: 0.6052 (m) REVERT: w 34 MET cc_start: 0.4329 (mmp) cc_final: 0.4123 (mmt) REVERT: w 121 GLU cc_start: 0.4880 (OUTLIER) cc_final: 0.4279 (mt-10) REVERT: w 141 MET cc_start: 0.0123 (ptt) cc_final: -0.0131 (ttp) REVERT: v 12 LYS cc_start: 0.7888 (mttt) cc_final: 0.7575 (mttt) REVERT: o 134 LEU cc_start: 0.2135 (OUTLIER) cc_final: 0.1924 (tp) REVERT: o 148 LYS cc_start: 0.1154 (tptm) cc_final: 0.0113 (pptt) REVERT: o 307 ILE cc_start: 0.0984 (OUTLIER) cc_final: 0.0770 (pt) outliers start: 218 outliers final: 179 residues processed: 1033 average time/residue: 1.1374 time to fit residues: 2023.5721 Evaluate side-chains 1074 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 877 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 207 ASP 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 K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 15 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP 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 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 96 GLN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 135 ARG Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 124 LEU Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER 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 43 ASN Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 93 LEU Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 20 CYS Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 127 ILE Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 269 ASN Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 281 ASN Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 370 MET Chi-restraints excluded: chain w residue 382 ASP Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 307 ILE Chi-restraints excluded: chain o residue 310 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Chi-restraints excluded: chain o residue 488 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 610 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 589 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 627 optimal weight: 0.9990 chunk 672 optimal weight: 3.9990 chunk 487 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 775 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 ASN E 150 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 79 GLN J 49 ASN K 149 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN l 23 HIS ** n 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN w 364 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 138275 Z= 0.238 Angle : 0.527 11.229 203519 Z= 0.273 Chirality : 0.035 0.267 25567 Planarity : 0.004 0.154 13083 Dihedral : 22.585 179.989 60748 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 4.18 % Allowed : 17.12 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.10), residues: 6753 helix: 0.01 (0.11), residues: 2148 sheet: -0.80 (0.16), residues: 1016 loop : -1.50 (0.10), residues: 3589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 120 HIS 0.008 0.001 HIS D 115 PHE 0.032 0.001 PHE b 229 TYR 0.029 0.001 TYR N 60 ARG 0.008 0.000 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 904 time to evaluate : 6.263 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (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: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. 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: B 246 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7097 (tp) REVERT: C 70 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7252 (ttp-170) REVERT: C 74 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: C 246 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8720 (pp) REVERT: D 285 ASP cc_start: 0.8137 (t70) cc_final: 0.7436 (p0) REVERT: D 311 HIS cc_start: 0.8314 (t-90) cc_final: 0.7663 (t-90) REVERT: D 360 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8356 (mttt) REVERT: E 25 GLU cc_start: 0.6936 (pp20) cc_final: 0.6237 (pp20) REVERT: E 47 GLN cc_start: 0.8570 (mp10) cc_final: 0.8041 (mp10) REVERT: E 57 PHE cc_start: 0.7682 (m-80) cc_final: 0.6502 (m-80) REVERT: F 62 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7974 (ttm-80) REVERT: F 63 LYS cc_start: 0.7262 (ttpt) cc_final: 0.6607 (tmtt) REVERT: F 94 TYR cc_start: 0.7809 (p90) cc_final: 0.7370 (p90) REVERT: F 183 HIS cc_start: 0.7550 (t70) cc_final: 0.7190 (t70) REVERT: G 48 ARG cc_start: 0.9125 (mtm-85) cc_final: 0.8767 (mtm-85) REVERT: G 90 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7944 (mttm) REVERT: H 83 ASP cc_start: 0.7756 (p0) cc_final: 0.7543 (p0) REVERT: H 130 TYR cc_start: 0.8941 (m-80) cc_final: 0.8618 (m-80) REVERT: J 31 LYS cc_start: 0.8580 (mttt) cc_final: 0.8176 (mtpt) REVERT: K 137 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: L 121 GLU cc_start: 0.8881 (mp0) cc_final: 0.8566 (mp0) REVERT: M 14 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8726 (pp) REVERT: O 136 ASP cc_start: 0.8159 (p0) cc_final: 0.7701 (p0) REVERT: Q 55 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8456 (t) REVERT: R 43 LYS cc_start: 0.8098 (tttt) cc_final: 0.7738 (mttm) REVERT: R 86 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: S 27 MET cc_start: 0.8932 (mtp) cc_final: 0.8554 (mtp) REVERT: S 109 ASP cc_start: 0.7434 (p0) cc_final: 0.6990 (p0) REVERT: U 25 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8442 (t) REVERT: U 108 ASP cc_start: 0.7958 (p0) cc_final: 0.7619 (p0) REVERT: V 33 TYR cc_start: 0.7904 (t80) cc_final: 0.7620 (t80) REVERT: W 73 MET cc_start: 0.7487 (mmm) cc_final: 0.7156 (mmm) REVERT: W 77 GLU cc_start: 0.7593 (mp0) cc_final: 0.7383 (mp0) REVERT: Y 85 TYR cc_start: 0.8822 (m-80) cc_final: 0.8542 (m-80) REVERT: Y 123 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: b 100 ARG cc_start: 0.8463 (ptm-80) cc_final: 0.7966 (ttp-170) REVERT: b 180 SER cc_start: 0.8673 (p) cc_final: 0.8433 (p) REVERT: d 48 ASP cc_start: 0.7838 (t0) cc_final: 0.7510 (t70) REVERT: d 73 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8928 (mt) REVERT: d 74 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8322 (ttp-170) REVERT: d 87 ASN cc_start: 0.7643 (m110) cc_final: 0.7389 (m110) REVERT: e 87 MET cc_start: 0.7512 (mpp) cc_final: 0.7279 (ptp) REVERT: f 5 HIS cc_start: 0.6295 (OUTLIER) cc_final: 0.5769 (m90) REVERT: f 10 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8240 (mttt) REVERT: f 75 HIS cc_start: 0.8982 (OUTLIER) cc_final: 0.8710 (t70) REVERT: g 38 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8807 (mp) REVERT: g 94 LEU cc_start: 0.9022 (mt) cc_final: 0.8789 (mt) REVERT: g 98 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: h 20 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7460 (ttm) REVERT: m 84 ARG cc_start: 0.7535 (ptm-80) cc_final: 0.6974 (ptm-80) REVERT: m 87 ARG cc_start: 0.8717 (ttp-110) cc_final: 0.8494 (ttm170) REVERT: w 121 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.4310 (mt-10) REVERT: w 141 MET cc_start: 0.0077 (ptt) cc_final: -0.0176 (ttp) REVERT: v 12 LYS cc_start: 0.7891 (mttt) cc_final: 0.7575 (mttt) REVERT: o 148 LYS cc_start: 0.1383 (tptm) cc_final: 0.0386 (pptt) REVERT: o 307 ILE cc_start: 0.0938 (OUTLIER) cc_final: 0.0712 (pt) outliers start: 241 outliers final: 197 residues processed: 1052 average time/residue: 1.1297 time to fit residues: 2043.3616 Evaluate side-chains 1100 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 884 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 207 ASP 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 K residue 103 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 96 GLN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 135 ARG Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 170 GLU Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 43 ASN Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 20 CYS Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 121 GLU Chi-restraints excluded: chain w residue 127 ILE Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 240 TYR Chi-restraints excluded: chain w residue 269 ASN Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 281 ASN Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 382 ASP Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain v residue 39 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 307 ILE Chi-restraints excluded: chain o residue 310 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Chi-restraints excluded: chain o residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 897 optimal weight: 8.9990 chunk 945 optimal weight: 7.9990 chunk 862 optimal weight: 7.9990 chunk 919 optimal weight: 0.0980 chunk 553 optimal weight: 6.9990 chunk 400 optimal weight: 7.9990 chunk 722 optimal weight: 0.8980 chunk 282 optimal weight: 20.0000 chunk 831 optimal weight: 3.9990 chunk 869 optimal weight: 9.9990 chunk 916 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 ASN E 150 ASN F 5 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 79 GLN J 49 ASN K 28 GLN K 149 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN w 364 HIS ** o 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 138275 Z= 0.309 Angle : 0.563 10.999 203519 Z= 0.290 Chirality : 0.037 0.241 25567 Planarity : 0.004 0.153 13083 Dihedral : 22.587 179.963 60746 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.83 % Favored : 94.15 % Rotamer: Outliers : 4.23 % Allowed : 17.34 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 6753 helix: -0.04 (0.11), residues: 2152 sheet: -0.82 (0.16), residues: 1009 loop : -1.51 (0.10), residues: 3592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 203 HIS 0.009 0.001 HIS D 115 PHE 0.033 0.001 PHE b 229 TYR 0.035 0.002 TYR N 60 ARG 0.009 0.000 ARG P 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 897 time to evaluate : 6.357 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "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: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 70 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7235 (ttp-170) REVERT: C 74 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: C 246 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8755 (pp) REVERT: D 285 ASP cc_start: 0.8158 (t70) cc_final: 0.7448 (p0) REVERT: D 311 HIS cc_start: 0.8348 (t-90) cc_final: 0.7701 (t-90) REVERT: D 350 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7680 (mmmt) REVERT: D 360 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8377 (mttt) REVERT: E 25 GLU cc_start: 0.6963 (pp20) cc_final: 0.6202 (pp20) REVERT: E 47 GLN cc_start: 0.8549 (mp10) cc_final: 0.7981 (mp10) REVERT: E 57 PHE cc_start: 0.7714 (m-80) cc_final: 0.6593 (m-80) REVERT: F 63 LYS cc_start: 0.7328 (ttpt) cc_final: 0.6657 (tmtt) REVERT: F 94 TYR cc_start: 0.7852 (p90) cc_final: 0.7423 (p90) REVERT: F 183 HIS cc_start: 0.7554 (t70) cc_final: 0.7191 (t70) REVERT: G 48 ARG cc_start: 0.9126 (mtm-85) cc_final: 0.8767 (mtm-85) REVERT: G 90 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8092 (mtmm) REVERT: H 83 ASP cc_start: 0.7721 (p0) cc_final: 0.7495 (p0) REVERT: H 130 TYR cc_start: 0.8918 (m-80) cc_final: 0.8582 (m-80) REVERT: J 31 LYS cc_start: 0.8583 (mttt) cc_final: 0.8165 (mtpt) REVERT: K 137 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: L 121 GLU cc_start: 0.8858 (mp0) cc_final: 0.8507 (mp0) REVERT: M 14 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8731 (pp) REVERT: N 60 TYR cc_start: 0.8902 (t80) cc_final: 0.8490 (t80) REVERT: O 136 ASP cc_start: 0.8171 (p0) cc_final: 0.7739 (p0) REVERT: R 43 LYS cc_start: 0.8133 (tttt) cc_final: 0.7770 (mttm) REVERT: R 86 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: S 27 MET cc_start: 0.8930 (mtp) cc_final: 0.8587 (mtp) REVERT: S 157 GLN cc_start: 0.8275 (mt0) cc_final: 0.8027 (mt0) REVERT: U 25 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8476 (t) REVERT: U 108 ASP cc_start: 0.7997 (p0) cc_final: 0.7695 (p0) REVERT: V 33 TYR cc_start: 0.7887 (t80) cc_final: 0.7644 (t80) REVERT: V 40 HIS cc_start: 0.8292 (m90) cc_final: 0.8076 (m90) REVERT: W 73 MET cc_start: 0.7478 (mmm) cc_final: 0.7178 (mmm) REVERT: W 129 ASP cc_start: 0.8320 (p0) cc_final: 0.8116 (p0) REVERT: Y 85 TYR cc_start: 0.8838 (m-80) cc_final: 0.8504 (m-80) REVERT: Y 123 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: b 100 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.7909 (ttp-170) REVERT: b 180 SER cc_start: 0.8769 (p) cc_final: 0.8534 (p) REVERT: d 48 ASP cc_start: 0.7832 (t0) cc_final: 0.7513 (t70) REVERT: d 73 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8979 (mt) REVERT: d 74 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8255 (ttp-170) REVERT: d 87 ASN cc_start: 0.7680 (m110) cc_final: 0.7436 (m110) REVERT: e 87 MET cc_start: 0.7495 (mpp) cc_final: 0.7267 (ptp) REVERT: f 5 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5771 (m90) REVERT: f 10 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8315 (mttt) REVERT: f 75 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8784 (t70) REVERT: g 38 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8809 (mp) REVERT: h 20 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7472 (ttm) REVERT: m 84 ARG cc_start: 0.7585 (ptm-80) cc_final: 0.7000 (ptm-80) REVERT: m 87 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.8522 (ttm170) REVERT: w 20 CYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5771 (m) REVERT: v 12 LYS cc_start: 0.7918 (mttt) cc_final: 0.7608 (mttt) REVERT: o 148 LYS cc_start: 0.1055 (tptm) cc_final: -0.0019 (pptt) outliers start: 244 outliers final: 211 residues processed: 1048 average time/residue: 1.1198 time to fit residues: 2030.0534 Evaluate side-chains 1108 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 882 time to evaluate : 6.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 207 ASP 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 K residue 103 ASN Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 96 GLN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 135 ARG Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 170 GLU Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 43 ASN Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 20 CYS Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 39 ILE Chi-restraints excluded: chain w residue 127 ILE Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 240 TYR Chi-restraints excluded: chain w residue 269 ASN Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 281 ASN Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 382 ASP Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain v residue 39 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 178 LEU Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 310 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Chi-restraints excluded: chain o residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 603 optimal weight: 9.9990 chunk 972 optimal weight: 50.0000 chunk 593 optimal weight: 4.9990 chunk 461 optimal weight: 5.9990 chunk 676 optimal weight: 2.9990 chunk 1020 optimal weight: 10.0000 chunk 938 optimal weight: 4.9990 chunk 812 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 627 optimal weight: 0.9990 chunk 498 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 ASN E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN J 49 ASN K 28 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 142 GLN w 269 ASN w 364 HIS ** o 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 138275 Z= 0.309 Angle : 0.563 10.875 203519 Z= 0.291 Chirality : 0.037 0.263 25567 Planarity : 0.004 0.152 13083 Dihedral : 22.598 179.777 60746 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.88 % Favored : 94.11 % Rotamer: Outliers : 4.16 % Allowed : 17.69 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 6753 helix: -0.06 (0.11), residues: 2160 sheet: -0.80 (0.16), residues: 1019 loop : -1.49 (0.10), residues: 3574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 203 HIS 0.008 0.001 HIS D 115 PHE 0.034 0.001 PHE b 229 TYR 0.035 0.002 TYR N 60 ARG 0.009 0.000 ARG n 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13506 Ramachandran restraints generated. 6753 Oldfield, 0 Emsley, 6753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 885 time to evaluate : 6.373 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR J 198 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "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: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 74 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: C 246 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8776 (pp) REVERT: D 285 ASP cc_start: 0.8116 (t70) cc_final: 0.7425 (p0) REVERT: D 311 HIS cc_start: 0.8342 (t-90) cc_final: 0.7697 (t-90) REVERT: D 350 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7716 (mmmt) REVERT: D 360 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8369 (mttt) REVERT: E 25 GLU cc_start: 0.6969 (pp20) cc_final: 0.6160 (pp20) REVERT: E 47 GLN cc_start: 0.8546 (mp10) cc_final: 0.7982 (mp10) REVERT: E 57 PHE cc_start: 0.7728 (m-80) cc_final: 0.6693 (m-80) REVERT: F 63 LYS cc_start: 0.7363 (ttpt) cc_final: 0.6666 (tmtt) REVERT: F 94 TYR cc_start: 0.7806 (p90) cc_final: 0.7462 (p90) REVERT: F 183 HIS cc_start: 0.7558 (t70) cc_final: 0.7196 (t70) REVERT: G 48 ARG cc_start: 0.9124 (mtm-85) cc_final: 0.8754 (mtm-85) REVERT: G 90 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8079 (mtmm) REVERT: H 83 ASP cc_start: 0.7737 (p0) cc_final: 0.7533 (p0) REVERT: H 130 TYR cc_start: 0.8918 (m-80) cc_final: 0.8605 (m-80) REVERT: J 31 LYS cc_start: 0.8585 (mttt) cc_final: 0.8168 (mtpt) REVERT: K 137 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: L 121 GLU cc_start: 0.8880 (mp0) cc_final: 0.8527 (mp0) REVERT: M 14 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (pp) REVERT: N 60 TYR cc_start: 0.8880 (t80) cc_final: 0.8457 (t80) REVERT: O 136 ASP cc_start: 0.8118 (p0) cc_final: 0.7732 (p0) REVERT: P 189 GLU cc_start: 0.6538 (tm-30) cc_final: 0.5934 (tm-30) REVERT: R 43 LYS cc_start: 0.8125 (tttt) cc_final: 0.7761 (mttm) REVERT: R 86 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: S 27 MET cc_start: 0.8940 (mtp) cc_final: 0.8630 (mtp) REVERT: U 25 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8460 (t) REVERT: U 108 ASP cc_start: 0.8000 (p0) cc_final: 0.7700 (p0) REVERT: U 128 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7735 (mtt90) REVERT: W 73 MET cc_start: 0.7555 (mmm) cc_final: 0.7313 (mmm) REVERT: Y 85 TYR cc_start: 0.8803 (m-80) cc_final: 0.8522 (m-80) REVERT: Y 123 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: b 100 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.7942 (ttp-170) REVERT: b 180 SER cc_start: 0.8735 (p) cc_final: 0.8495 (p) REVERT: d 48 ASP cc_start: 0.7872 (t0) cc_final: 0.7510 (t70) REVERT: d 73 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9007 (mt) REVERT: d 74 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (ttp-170) REVERT: e 87 MET cc_start: 0.7490 (mpp) cc_final: 0.7264 (ptp) REVERT: f 5 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.5873 (m90) REVERT: f 10 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8336 (mttt) REVERT: f 75 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8795 (t70) REVERT: g 38 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8805 (mp) REVERT: g 98 GLN cc_start: 0.7923 (tt0) cc_final: 0.7719 (tt0) REVERT: h 20 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7463 (ttm) REVERT: m 84 ARG cc_start: 0.7495 (ptm-80) cc_final: 0.6942 (ptm-80) REVERT: m 87 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8514 (ttm170) REVERT: w 20 CYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5773 (m) REVERT: v 12 LYS cc_start: 0.7921 (mttt) cc_final: 0.7607 (mttt) REVERT: o 148 LYS cc_start: 0.1386 (tptm) cc_final: 0.0313 (pptt) outliers start: 240 outliers final: 211 residues processed: 1034 average time/residue: 1.1166 time to fit residues: 1994.1511 Evaluate side-chains 1101 residues out of total 5772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 875 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 161 GLU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 207 ASP 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 K residue 103 ASN Chi-restraints excluded: chain K residue 118 GLU Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 137 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 196 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 62 CYS Chi-restraints excluded: chain P residue 155 THR Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 206 GLN Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 80 ARG Chi-restraints excluded: chain S residue 134 ASP Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 18 ASP Chi-restraints excluded: chain T residue 80 VAL Chi-restraints excluded: chain T residue 90 ASN Chi-restraints excluded: chain T residue 138 SER Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 7 THR Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 96 GLN Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 135 ARG Chi-restraints excluded: chain U residue 151 THR Chi-restraints excluded: chain V residue 52 ASN Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 170 GLU Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 229 PHE Chi-restraints excluded: chain b residue 244 ASN Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 ASN Chi-restraints excluded: chain d residue 44 MET Chi-restraints excluded: chain d residue 73 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain f residue 75 HIS Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 96 GLU Chi-restraints excluded: chain h residue 20 MET Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 70 ARG Chi-restraints excluded: chain h residue 81 THR Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 80 THR Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 27 ILE Chi-restraints excluded: chain j residue 49 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 56 ILE Chi-restraints excluded: chain j residue 65 LEU Chi-restraints excluded: chain j residue 78 LEU Chi-restraints excluded: chain k residue 43 ASN Chi-restraints excluded: chain l residue 26 THR Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 72 LEU Chi-restraints excluded: chain l residue 79 THR Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 92 VAL Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain n residue 165 THR Chi-restraints excluded: chain z residue 377 THR Chi-restraints excluded: chain z residue 424 THR Chi-restraints excluded: chain w residue 20 CYS Chi-restraints excluded: chain w residue 34 MET Chi-restraints excluded: chain w residue 35 CYS Chi-restraints excluded: chain w residue 127 ILE Chi-restraints excluded: chain w residue 179 LEU Chi-restraints excluded: chain w residue 233 THR Chi-restraints excluded: chain w residue 240 TYR Chi-restraints excluded: chain w residue 269 ASN Chi-restraints excluded: chain w residue 274 VAL Chi-restraints excluded: chain w residue 281 ASN Chi-restraints excluded: chain w residue 317 GLU Chi-restraints excluded: chain w residue 320 VAL Chi-restraints excluded: chain w residue 352 VAL Chi-restraints excluded: chain w residue 382 ASP Chi-restraints excluded: chain v residue 19 THR Chi-restraints excluded: chain v residue 39 LEU Chi-restraints excluded: chain o residue 134 LEU Chi-restraints excluded: chain o residue 163 ARG Chi-restraints excluded: chain o residue 165 LYS Chi-restraints excluded: chain o residue 170 GLN Chi-restraints excluded: chain o residue 194 VAL Chi-restraints excluded: chain o residue 234 LEU Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 307 ILE Chi-restraints excluded: chain o residue 310 ILE Chi-restraints excluded: chain o residue 344 TYR Chi-restraints excluded: chain o residue 379 LEU Chi-restraints excluded: chain o residue 402 GLU Chi-restraints excluded: chain o residue 431 TYR Chi-restraints excluded: chain o residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 645 optimal weight: 2.9990 chunk 865 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 749 optimal weight: 10.0000 chunk 119 optimal weight: 60.0000 chunk 225 optimal weight: 40.0000 chunk 813 optimal weight: 3.9990 chunk 340 optimal weight: 3.9990 chunk 835 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN J 49 ASN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 ASN i 76 ASN m 34 HIS ** n 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 269 ASN w 364 HIS ** o 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090277 restraints weight = 208666.179| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.38 r_work: 0.2776 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 138275 Z= 0.337 Angle : 0.580 10.789 203519 Z= 0.299 Chirality : 0.038 0.247 25567 Planarity : 0.005 0.152 13083 Dihedral : 22.608 179.708 60746 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.07 % Favored : 93.91 % Rotamer: Outliers : 4.00 % Allowed : 18.09 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6753 helix: -0.11 (0.11), residues: 2162 sheet: -0.82 (0.16), residues: 1028 loop : -1.50 (0.10), residues: 3563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 203 HIS 0.008 0.001 HIS D 115 PHE 0.034 0.001 PHE b 229 TYR 0.038 0.002 TYR E 167 ARG 0.009 0.000 ARG n 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31964.23 seconds wall clock time: 560 minutes 1.76 seconds (33601.76 seconds total)