Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 18:34:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qtz_4636/04_2023/6qtz_4636.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.020 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 3418 5.49 5 S 131 5.16 5 C 68812 2.51 5 N 23993 2.21 5 O 33898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 200": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H ARG 185": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "K ARG 42": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K ARG 128": "NH1" <-> "NH2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ARG 171": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 180": "NH1" <-> "NH2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 128": "OE1" <-> "OE2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "P ARG 140": "NH1" <-> "NH2" Residue "P ARG 158": "NH1" <-> "NH2" Residue "P GLU 189": "OE1" <-> "OE2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q ARG 176": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 18": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 128": "NH1" <-> "NH2" Residue "U ARG 135": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 56": "NH1" <-> "NH2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W ARG 125": "NH1" <-> "NH2" Residue "W ARG 138": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y ARG 84": "NH1" <-> "NH2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 100": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "d GLU 54": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 72": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d GLU 111": "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 97": "OE1" <-> "OE2" Residue "h ARG 99": "NH1" <-> "NH2" Residue "i ARG 63": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 45": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "m ARG 36": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n GLU 172": "OE1" <-> "OE2" Residue "n ARG 188": "NH1" <-> "NH2" Residue "z GLU 405": "OE1" <-> "OE2" Residue "z ARG 419": "NH1" <-> "NH2" Residue "z ARG 427": "NH1" <-> "NH2" Residue "w ARG 51": "NH1" <-> "NH2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "w ARG 73": "NH1" <-> "NH2" Residue "w GLU 77": "OE1" <-> "OE2" Residue "w ARG 79": "NH1" <-> "NH2" Residue "w ARG 87": "NH1" <-> "NH2" Residue "w ARG 88": "NH1" <-> "NH2" Residue "w ARG 96": "NH1" <-> "NH2" Residue "w ARG 111": "NH1" <-> "NH2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 156": "NH1" <-> "NH2" Residue "w ARG 162": "NH1" <-> "NH2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 227": "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 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 426": "OE1" <-> "OE2" Residue "o ARG 427": "NH1" <-> "NH2" Residue "o GLU 434": "OE1" <-> "OE2" Residue "o ARG 446": "NH1" <-> "NH2" Residue "o ARG 466": "NH1" <-> "NH2" Residue "o ARG 468": "NH1" <-> "NH2" Residue "o ARG 482": "NH1" <-> "NH2" Residue "o ARG 485": "NH1" <-> "NH2" Residue "q ARG 4": "NH1" <-> "NH2" Residue "q ARG 24": "NH1" <-> "NH2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q GLU 58": "OE1" <-> "OE2" Residue "q ARG 139": "NH1" <-> "NH2" Residue "q ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 130259 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 67289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3146, 67289 Inner-chain residues flagged as termini: ['pdbres=" G A 494 "', 'pdbres=" U A1288 "'] Classifications: {'RNA': 3146} Modifications used: {'5*END': 3, 'rna2p_pur': 319, 'rna2p_pyr': 203, 'rna3p_pur': 1429, 'rna3p_pyr': 1195} Link IDs: {'rna2p': 522, 'rna3p': 2623} 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: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 17, 'TRANS': 307} Chain breaks: 2 Chain: "p" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "q" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1671 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain breaks: 1 Chain: "t" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "x" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2576 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 106} Chain: "y" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3310 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A06JN SG CYS g 44 125.827 118.850 199.930 1.00 67.48 S ATOM A06K5 SG CYS g 47 121.380 118.552 199.506 1.00 69.46 S ATOM A06RQ SG CYS g 84 124.021 116.503 202.214 1.00 71.17 S ATOM A07LG SG CYS i 19 147.517 135.394 149.729 1.00 43.84 S ATOM A07M5 SG CYS i 22 148.106 137.075 145.735 1.00 45.06 S ATOM A07OX SG CYS i 34 145.782 133.884 146.104 1.00 42.40 S ATOM A07PF SG CYS i 37 149.442 133.909 146.233 1.00 41.82 S ATOM A08VP SG CYS l 12 144.234 63.540 85.982 1.00 64.35 S ATOM A08WO SG CYS l 17 146.525 60.390 84.483 1.00 70.38 S ATOM A099K SG CYS l 74 142.963 59.980 87.336 1.00 62.34 S ATOM A09A6 SG CYS l 77 146.887 61.309 87.799 1.00 63.14 S ATOM A09MT SG CYS m 39 108.001 108.108 196.437 1.00 66.73 S ATOM A09QH SG CYS m 57 110.796 108.238 194.947 1.00 65.07 S ATOM A0CDV SG CYS w 143 69.034 99.931 109.960 1.00167.69 S ATOM A0BMI SG CYS w 19 24.314 124.409 129.279 1.00141.77 S ATOM A0BN2 SG CYS w 22 21.577 122.426 127.804 1.00143.11 S ATOM A0ILF SG CYS t 96 55.833 132.248 79.431 1.00 87.35 S ATOM A0IOK SG CYS t 110 56.085 136.573 77.611 1.00 84.00 S Time building chain proxies: 49.13, per 1000 atoms: 0.38 Number of scatterers: 130259 At special positions: 0 Unit cell: (231.105, 230.04, 249.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 131 16.00 P 3418 15.00 O 33898 8.00 N 23993 7.00 C 68812 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: 49.72 Conformation dependent library (CDL) restraints added in 6.7 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 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb=" ZN i 101 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 34 " pdb="ZN ZN i 101 " - pdb=" SG CYS i 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 ZN l 201 " - pdb=" SG CYS l 77 " pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 39 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 57 " pdb=" ZN t 201 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 110 " pdb="ZN ZN t 201 " - pdb=" SG CYS t 96 " pdb=" ZN w 601 " pdb="ZN ZN w 601 " - pdb=" SG CYS w 143 " pdb=" ZN w 602 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 19 " pdb="ZN ZN w 602 " - pdb=" SG CYS w 22 " Number of angles added : 12 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13572 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 80 sheets defined 33.6% alpha, 14.2% beta 974 base pairs and 1584 stacking pairs defined. Time for finding SS restraints: 37.78 Creating SS restraints... 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 'C' and resid 114 through 118 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.986A pdb=" N ALA C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.908A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 Processing helix chain 'C' and resid 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 38 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.505A pdb=" N VAL D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.602A pdb=" N GLU D 157 " --> pdb=" O THR D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.729A pdb=" N ALA D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.796A pdb=" N LEU D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.507A pdb=" N HIS D 243 " --> pdb=" O PRO D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.139A pdb=" N ASP D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.858A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 35 removed outlier: 3.667A pdb=" N THR E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 42 removed outlier: 3.752A pdb=" N LEU E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 85 removed outlier: 3.806A pdb=" N ALA E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.143A pdb=" N VAL E 138 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 4.013A pdb=" N LYS E 153 " --> pdb=" O ASN E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 Processing helix chain 'F' and resid 64 through 84 removed outlier: 3.792A pdb=" N ARG F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 150 through 165 removed outlier: 3.676A pdb=" N GLN F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 4.268A pdb=" N VAL G 135 " --> pdb=" O LYS G 131 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 152 removed outlier: 4.572A pdb=" N THR G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 161 removed outlier: 3.552A pdb=" N SER G 160 " --> pdb=" O LYS G 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 69 removed outlier: 3.827A pdb=" N GLN H 59 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS H 63 " --> pdb=" O GLN H 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 83 through 96 removed outlier: 3.587A pdb=" N LEU H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 116 Processing helix chain 'H' and resid 135 through 145 Processing helix chain 'H' and resid 165 through 174 removed outlier: 3.752A pdb=" N LYS H 172 " --> pdb=" O ALA H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.648A pdb=" N LEU H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 220 removed outlier: 3.638A pdb=" N ALA H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 239 through 247 removed outlier: 3.669A pdb=" N ALA H 244 " --> pdb=" O ASN H 240 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 26 removed outlier: 3.715A pdb=" N SER J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR J 21 " --> pdb=" O ARG J 17 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 39 Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.988A pdb=" N TYR J 53 " --> pdb=" O ASN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.614A pdb=" N GLY J 68 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.519A pdb=" N TYR J 80 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 Processing helix chain 'J' and resid 119 through 122 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'J' and resid 151 through 183 removed outlier: 4.030A pdb=" N LYS J 158 " --> pdb=" O LYS J 154 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU J 165 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS J 176 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 197 removed outlier: 3.865A pdb=" N LEU J 193 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 28 No H-bonds generated for 'chain 'K' and resid 26 through 28' Processing helix chain 'K' and resid 29 through 46 removed outlier: 4.052A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.776A pdb=" N TYR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 179 removed outlier: 3.609A pdb=" N ARG K 174 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.895A pdb=" N LYS K 185 " --> pdb=" O GLY K 181 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG K 186 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.895A pdb=" N ALA L 130 " --> pdb=" O TRP L 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 88 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.524A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.613A pdb=" N LYS M 125 " --> pdb=" O MET M 121 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN M 126 " --> pdb=" O VAL M 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.746A pdb=" N ASP N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLN N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 131 through 142 removed outlier: 3.682A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 11 Processing helix chain 'O' and resid 16 through 32 removed outlier: 4.406A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP O 28 " --> pdb=" O ARG O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 52 removed outlier: 4.139A pdb=" N ARG O 50 " --> pdb=" O ASP O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 108 removed outlier: 3.604A pdb=" N ARG O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 148 through 157 removed outlier: 3.711A pdb=" N ILE O 151 " --> pdb=" O TYR O 148 " (cutoff:3.500A) Proline residue: O 154 - end of helix Processing helix chain 'O' and resid 158 through 163 removed outlier: 3.793A pdb=" N ARG O 162 " --> pdb=" O HIS O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 173 Processing helix chain 'O' and resid 186 through 196 removed outlier: 3.520A pdb=" N TRP O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 15 removed outlier: 3.965A pdb=" N SER P 13 " --> pdb=" O SER P 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 29 through 37 removed outlier: 4.200A pdb=" N ARG P 35 " --> pdb=" O TYR P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 86 Proline residue: P 84 - end of helix No H-bonds generated for 'chain 'P' and resid 81 through 86' Processing helix chain 'P' and resid 94 through 113 removed outlier: 3.905A pdb=" N GLN P 111 " --> pdb=" O ARG P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 170 removed outlier: 3.935A pdb=" N GLY P 161 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA P 162 " --> pdb=" O ARG P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 180 removed outlier: 3.834A pdb=" N ARG P 179 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 200 removed outlier: 3.694A pdb=" N LEU P 195 " --> pdb=" O ASP P 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE P 200 " --> pdb=" O ARG P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 215 removed outlier: 4.358A pdb=" N ASP P 213 " --> pdb=" O GLU P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 223 Processing helix chain 'P' and resid 235 through 250 Processing helix chain 'P' and resid 263 through 270 removed outlier: 3.683A pdb=" N GLU P 268 " --> pdb=" O GLN P 264 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER P 269 " --> pdb=" O TYR P 265 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 39 removed outlier: 4.404A pdb=" N LEU Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.898A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 75 through 79 removed outlier: 4.302A pdb=" N ASN Q 78 " --> pdb=" O GLY Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 125 through 131 Processing helix chain 'Q' and resid 149 through 153 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 39 through 48 removed outlier: 3.557A pdb=" N LYS R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.656A pdb=" N ARG R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU R 72 " --> pdb=" O GLN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 101 removed outlier: 3.558A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 113 Processing helix chain 'R' and resid 116 through 129 removed outlier: 4.885A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 removed outlier: 3.582A pdb=" N GLN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 47 removed outlier: 3.663A pdb=" N SER S 39 " --> pdb=" O VAL S 35 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN S 46 " --> pdb=" O TRP S 42 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.681A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'T' and resid 26 through 30 Processing helix chain 'T' and resid 54 through 58 Processing helix chain 'T' and resid 99 through 104 removed outlier: 4.007A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.847A pdb=" N ARG T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 35 removed outlier: 4.213A pdb=" N GLU U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 53 removed outlier: 3.852A pdb=" N LEU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP U 53 " --> pdb=" O GLU U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 77 removed outlier: 3.882A pdb=" N GLY U 73 " --> pdb=" O THR U 70 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU U 75 " --> pdb=" O GLN U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 106 removed outlier: 4.200A pdb=" N LEU U 94 " --> pdb=" O PHE U 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN U 96 " --> pdb=" O GLN U 92 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN U 97 " --> pdb=" O GLY U 93 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 25 Processing helix chain 'V' and resid 29 through 41 Processing helix chain 'V' and resid 72 through 87 removed outlier: 3.652A pdb=" N LEU V 76 " --> pdb=" O SER V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 62 removed outlier: 3.571A pdb=" N VAL W 62 " --> pdb=" O ASP W 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 58 through 62' Processing helix chain 'W' and resid 71 through 79 removed outlier: 3.945A pdb=" N GLU W 77 " --> pdb=" O MET W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 103 removed outlier: 3.710A pdb=" N TYR W 103 " --> pdb=" O VAL W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 140 removed outlier: 3.532A pdb=" N ARG W 138 " --> pdb=" O ASP W 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 21 removed outlier: 3.637A pdb=" N TYR X 19 " --> pdb=" O ALA X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 30 removed outlier: 3.922A pdb=" N VAL X 29 " --> pdb=" O SER X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 44 Processing helix chain 'X' and resid 100 through 102 No H-bonds generated for 'chain 'X' and resid 100 through 102' Processing helix chain 'X' and resid 115 through 123 removed outlier: 3.766A pdb=" N LYS X 122 " --> pdb=" O LEU X 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 66 Processing helix chain 'Y' and resid 89 through 93 Processing helix chain 'Y' and resid 97 through 101 removed outlier: 3.673A pdb=" N PHE Y 101 " --> pdb=" O THR Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 125 removed outlier: 3.624A pdb=" N LYS Y 112 " --> pdb=" O GLU Y 108 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG Y 121 " --> pdb=" O ALA Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 removed outlier: 3.696A pdb=" N SER Y 132 " --> pdb=" O TRP Y 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 10 removed outlier: 3.640A pdb=" N LEU Z 9 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 35 removed outlier: 3.694A pdb=" N LEU Z 24 " --> pdb=" O GLN Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 42 through 68 removed outlier: 3.800A pdb=" N THR Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG Z 48 " --> pdb=" O ILE Z 44 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER Z 50 " --> pdb=" O THR Z 46 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Z 52 " --> pdb=" O ARG Z 48 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA Z 65 " --> pdb=" O GLN Z 61 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL Z 66 " --> pdb=" O GLN Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 91 Processing helix chain 'Z' and resid 101 through 109 Processing helix chain 'a' and resid 12 through 19 removed outlier: 4.084A pdb=" N ASN a 19 " --> pdb=" O LYS a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 57 removed outlier: 4.142A pdb=" N ASN a 42 " --> pdb=" O LYS a 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY a 49 " --> pdb=" O HIS a 45 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA a 57 " --> pdb=" O ALA a 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 73 removed outlier: 4.332A pdb=" N LYS b 38 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 53 " --> pdb=" O ALA b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 106 removed outlier: 3.746A pdb=" N GLN b 104 " --> pdb=" O ARG b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 128 removed outlier: 3.942A pdb=" N GLU b 125 " --> pdb=" O LYS b 121 " (cutoff:3.500A) removed outlier: 4.875A 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 149 Processing helix chain 'b' and resid 166 through 174 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 removed outlier: 3.612A pdb=" N LEU b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 241 removed outlier: 3.593A pdb=" N LEU b 239 " --> pdb=" O PHE b 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 20 Processing helix chain 'c' and resid 26 through 35 Processing helix chain 'c' and resid 49 through 63 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 43 removed outlier: 3.642A pdb=" N LYS d 38 " --> pdb=" O LYS d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 87 removed outlier: 4.261A pdb=" N MET e 87 " --> pdb=" O THR e 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 84 through 87' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.578A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 45 removed outlier: 3.558A pdb=" N LEU f 45 " --> pdb=" O GLN f 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 62 Processing helix chain 'g' and resid 81 through 104 removed outlier: 3.637A pdb=" N VAL g 85 " --> pdb=" O CYS g 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS g 86 " --> pdb=" O ALA g 82 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG g 91 " --> pdb=" O GLU g 87 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 49 removed outlier: 3.575A pdb=" N GLU h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 64 removed outlier: 3.604A pdb=" N ARG h 56 " --> pdb=" O PRO h 52 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 77 removed outlier: 3.527A pdb=" N ARG h 70 " --> pdb=" O GLU h 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS h 71 " --> pdb=" O LYS h 67 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL h 72 " --> pdb=" O ARG h 68 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 100 removed outlier: 4.150A pdb=" N ALA h 85 " --> pdb=" O THR h 81 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS h 86 " --> pdb=" O ARG h 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA h 95 " --> pdb=" O ASN h 91 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG h 98 " --> pdb=" O ILE h 94 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG h 99 " --> pdb=" O ALA h 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 54 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 75 Processing helix chain 'j' and resid 8 through 15 removed outlier: 3.585A pdb=" N THR j 15 " --> pdb=" O PHE j 11 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 69 Processing helix chain 'k' and resid 7 through 19 Processing helix chain 'k' and resid 24 through 29 removed outlier: 4.210A pdb=" N ARG k 28 " --> pdb=" O PRO k 24 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU k 29 " --> pdb=" O GLN k 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 24 through 29' Processing helix chain 'l' and resid 37 through 48 removed outlier: 4.107A pdb=" N TYR l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER l 48 " --> pdb=" O ASP l 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 15 removed outlier: 3.671A pdb=" N GLY m 12 " --> pdb=" O GLY m 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS m 13 " --> pdb=" O ILE m 10 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 25 Processing helix chain 'm' and resid 26 through 34 removed outlier: 3.588A pdb=" N ILE m 31 " --> pdb=" O LYS m 27 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 73 through 90 removed outlier: 3.833A pdb=" N ALA m 77 " --> pdb=" O THR m 73 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL m 79 " --> pdb=" O ALA m 75 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR m 82 " --> pdb=" O THR m 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 16 removed outlier: 3.827A pdb=" N PHE n 16 " --> pdb=" O GLU n 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 12 through 16' Processing helix chain 'n' and resid 31 through 40 removed outlier: 3.869A pdb=" N TYR n 35 " --> pdb=" O SER n 31 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE n 38 " --> pdb=" O PHE n 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA n 40 " --> pdb=" O SER n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 56 removed outlier: 3.630A pdb=" N GLY n 55 " --> pdb=" O THR n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 87 removed outlier: 4.107A pdb=" N HIS n 83 " --> pdb=" O GLN n 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 103 through 106 Processing helix chain 'n' and resid 124 through 134 removed outlier: 4.368A pdb=" N SER n 130 " --> pdb=" O GLU n 126 " (cutoff:3.500A) Processing helix chain 'n' and resid 166 through 178 removed outlier: 3.760A pdb=" N GLU n 171 " --> pdb=" O VAL n 167 " (cutoff:3.500A) Processing helix chain 'n' and resid 192 through 197 removed outlier: 3.512A pdb=" N MET n 197 " --> pdb=" O VAL n 193 " (cutoff:3.500A) Processing helix chain 'n' and resid 211 through 222 removed outlier: 4.169A pdb=" N VAL n 217 " --> pdb=" O PRO n 213 " (cutoff:3.500A) Processing helix chain 'z' and resid 379 through 387 removed outlier: 3.741A pdb=" N VAL z 386 " --> pdb=" O ASP z 382 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER z 387 " --> pdb=" O ARG z 383 " (cutoff:3.500A) Processing helix chain 'z' and resid 390 through 417 removed outlier: 3.807A pdb=" N ALA z 408 " --> pdb=" O LEU z 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE z 409 " --> pdb=" O GLU z 405 " (cutoff:3.500A) Processing helix chain 'w' and resid 35 through 42 Processing helix chain 'w' and resid 79 through 88 removed outlier: 4.034A pdb=" N ALA w 83 " --> pdb=" O ARG w 79 " (cutoff:3.500A) Processing helix chain 'w' and resid 90 through 94 removed outlier: 4.002A pdb=" N THR w 93 " --> pdb=" O LYS w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 106 through 109 Processing helix chain 'w' and resid 143 through 151 Processing helix chain 'w' and resid 169 through 182 removed outlier: 4.220A pdb=" N LEU w 179 " --> pdb=" O GLU w 175 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS w 180 " --> pdb=" O GLN w 176 " (cutoff:3.500A) Processing helix chain 'w' and resid 203 through 215 removed outlier: 3.994A pdb=" N ALA w 207 " --> pdb=" O GLN w 203 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 267 Processing helix chain 'w' and resid 297 through 302 Processing helix chain 'w' and resid 311 through 315 Processing helix chain 'w' and resid 381 through 387 Processing helix chain 'w' and resid 388 through 392 removed outlier: 3.797A pdb=" N TYR w 391 " --> pdb=" O ASN w 388 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 42 Processing helix chain 'v' and resid 52 through 60 Processing helix chain 'o' and resid 147 through 152 removed outlier: 3.712A pdb=" N ASP o 152 " --> pdb=" O LYS o 148 " (cutoff:3.500A) Processing helix chain 'o' and resid 152 through 173 Processing helix chain 'o' and resid 184 through 192 removed outlier: 3.840A pdb=" N TRP o 188 " --> pdb=" O ASN o 184 " (cutoff:3.500A) Processing helix chain 'o' and resid 243 through 245 No H-bonds generated for 'chain 'o' and resid 243 through 245' Processing helix chain 'o' and resid 246 through 255 removed outlier: 3.816A pdb=" N TYR o 252 " --> pdb=" O ALA o 248 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE o 253 " --> pdb=" O TRP o 249 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE o 254 " --> pdb=" O ALA o 250 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER o 255 " --> pdb=" O LYS o 251 " (cutoff:3.500A) Processing helix chain 'o' and resid 352 through 356 Processing helix chain 'o' and resid 418 through 423 removed outlier: 3.667A pdb=" N LEU o 423 " --> pdb=" O GLY o 419 " (cutoff:3.500A) Processing helix chain 'o' and resid 429 through 437 removed outlier: 3.688A pdb=" N ILE o 433 " --> pdb=" O PRO o 429 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA o 435 " --> pdb=" O TYR o 431 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR o 437 " --> pdb=" O ILE o 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 461 through 469 removed outlier: 3.748A pdb=" N ALA o 465 " --> pdb=" O LEU o 461 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG o 466 " --> pdb=" O VAL o 462 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA o 467 " --> pdb=" O ALA o 463 " (cutoff:3.500A) Processing helix chain 'o' and resid 479 through 493 removed outlier: 3.921A pdb=" N TYR o 486 " --> pdb=" O ARG o 482 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN o 493 " --> pdb=" O LYS o 489 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 15 removed outlier: 3.827A pdb=" N UNK p 11 " --> pdb=" O UNK p 7 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N UNK p 12 " --> pdb=" O UNK p 8 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N UNK p 14 " --> pdb=" O UNK p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 70 removed outlier: 4.073A pdb=" N UNK p 70 " --> pdb=" O UNK p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 97 removed outlier: 4.472A pdb=" N UNK p 96 " --> pdb=" O UNK p 92 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 113 removed outlier: 4.251A pdb=" N UNK p 113 " --> pdb=" O UNK p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 121 through 125 removed outlier: 3.729A pdb=" N UNK p 124 " --> pdb=" O UNK p 121 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N UNK p 125 " --> pdb=" O UNK p 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 121 through 125' Processing helix chain 'p' and resid 139 through 144 Processing helix chain 'p' and resid 185 through 189 removed outlier: 4.282A pdb=" N UNK p 189 " --> pdb=" O UNK p 186 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 24 removed outlier: 3.997A pdb=" N ARG q 24 " --> pdb=" O ARG q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 80 removed outlier: 3.505A pdb=" N CYS q 71 " --> pdb=" O ALA q 67 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR q 75 " --> pdb=" O CYS q 71 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET q 76 " --> pdb=" O ALA q 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR q 78 " --> pdb=" O LYS q 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 84 Processing helix chain 'q' and resid 141 through 143 No H-bonds generated for 'chain 'q' and resid 141 through 143' Processing helix chain 'q' and resid 144 through 157 removed outlier: 3.670A pdb=" N GLU q 150 " --> pdb=" O ASP q 146 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA q 155 " --> pdb=" O GLY q 151 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR q 157 " --> pdb=" O ARG q 153 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 187 removed outlier: 3.971A pdb=" N ALA q 187 " --> pdb=" O LYS q 183 " (cutoff:3.500A) Processing helix chain 'q' and resid 205 through 212 Processing helix chain 't' and resid 82 through 90 removed outlier: 3.819A pdb=" N TYR t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 71 through 77 removed outlier: 3.629A pdb=" N PHE B 63 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 58 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 48 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 60 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG B 64 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 7.563A 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: 6.305A pdb=" N ILE B 136 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG B 149 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 138 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 356 through 359 removed outlier: 6.309A pdb=" N VAL C 57 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE C 359 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR C 55 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 335 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL C 220 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 339 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE C 215 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE C 282 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS C 325 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 284 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 74 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 56 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP C 80 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS C 50 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 106 removed outlier: 5.048A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 95 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 93 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR C 103 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 91 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL C 86 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS C 163 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 88 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 98 through 106 removed outlier: 5.048A pdb=" N LEU C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 95 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 93 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR C 103 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 91 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 84 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 227 Processing sheet with id=AA7, first strand: chain 'D' and resid 15 through 21 removed outlier: 4.785A pdb=" N VAL D 8 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN D 18 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL D 6 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL D 151 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.761A pdb=" N GLU D 63 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 70 through 71 removed outlier: 7.407A pdb=" N VAL E 130 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU E 17 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR E 128 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 21 through 22 removed outlier: 3.794A pdb=" N ALA E 66 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 92 removed outlier: 6.435A pdb=" N LEU E 91 " --> pdb=" O LEU E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 6 through 11 removed outlier: 3.703A pdb=" N ALA F 56 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 21 removed outlier: 3.767A pdb=" N LYS F 21 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 132 through 135 removed outlier: 5.688A pdb=" N ARG F 91 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL F 181 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL F 93 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE F 179 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 100 through 105 Processing sheet with id=AB7, first strand: chain 'G' and resid 76 through 79 removed outlier: 3.616A pdb=" N LYS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER G 66 " --> pdb=" O TYR G 54 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR G 54 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 177 through 179 Processing sheet with id=AB9, first strand: chain 'J' and resid 101 through 103 removed outlier: 6.974A pdb=" N ILE J 32 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL J 6 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL J 35 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE J 8 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL J 117 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 7 " --> pdb=" O VAL J 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AC2, first strand: chain 'K' and resid 23 through 24 removed outlier: 6.159A pdb=" N LYS K 23 " --> pdb=" O LEU O 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AC4, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AC5, first strand: chain 'L' and resid 17 through 18 removed outlier: 3.884A pdb=" N LEU L 17 " --> pdb=" O ALA L 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 22 through 25 removed outlier: 6.849A pdb=" N MET L 59 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL L 39 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N MET L 57 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA L 99 " --> pdb=" O VAL L 79 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY L 100 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN L 24 " --> pdb=" O GLY L 100 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE L 102 " --> pdb=" O ASN L 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AC8, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AC9, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AD1, first strand: chain 'M' and resid 56 through 59 removed outlier: 8.231A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 101 through 103 removed outlier: 3.628A pdb=" N ALA N 127 " --> pdb=" O GLU N 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 36 through 39 removed outlier: 4.111A pdb=" N ILE O 61 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLN O 123 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR O 129 " --> pdb=" O VAL O 121 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN O 117 " --> pdb=" O ILE O 133 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL O 135 " --> pdb=" O VAL O 115 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL O 115 " --> pdb=" O VAL O 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 71 through 79 removed outlier: 4.989A pdb=" N ASP P 72 " --> pdb=" O THR P 68 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N THR P 68 " --> pdb=" O ASP P 72 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL P 74 " --> pdb=" O SER P 66 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER P 66 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA P 76 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP P 147 " --> pdb=" O LEU P 51 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL P 53 " --> pdb=" O ASP P 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 183 through 184 removed outlier: 3.612A pdb=" N GLU P 189 " --> pdb=" O ASP P 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 61 through 63 Processing sheet with id=AD7, first strand: chain 'Q' and resid 120 through 122 Processing sheet with id=AD8, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD9, first strand: chain 'S' and resid 30 through 31 removed outlier: 7.354A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'S' and resid 87 through 96 removed outlier: 6.832A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASP S 82 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE S 121 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 83 through 92 removed outlier: 7.506A pdb=" N SER T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL T 67 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS T 97 " --> pdb=" O ASP T 41 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 139 through 141 Processing sheet with id=AE5, first strand: chain 'U' and resid 14 through 22 removed outlier: 3.981A pdb=" N TYR U 21 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER U 144 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS U 145 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL U 119 " --> pdb=" O HIS U 145 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU U 147 " --> pdb=" O ILE U 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE U 117 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL U 149 " --> pdb=" O SER U 115 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 58 through 59 Processing sheet with id=AE7, first strand: chain 'U' and resid 128 through 130 Processing sheet with id=AE8, first strand: chain 'V' and resid 54 through 58 removed outlier: 8.236A pdb=" N TYR V 103 " --> pdb=" O THR V 14 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR V 16 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU V 105 " --> pdb=" O THR V 16 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP V 18 " --> pdb=" O LEU V 105 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N PHE V 107 " --> pdb=" O ASP V 18 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU V 102 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 42 through 43 Processing sheet with id=AF1, first strand: chain 'W' and resid 63 through 66 removed outlier: 3.525A pdb=" N GLN W 65 " --> pdb=" O GLN W 85 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS W 120 " --> pdb=" O VAL W 86 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS W 109 " --> pdb=" O ARG W 125 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 32 through 34 Processing sheet with id=AF3, first strand: chain 'X' and resid 94 through 98 removed outlier: 3.535A pdb=" N ILE X 97 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL X 85 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN X 81 " --> pdb=" O SER X 71 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS X 69 " --> pdb=" O ASP X 83 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL X 85 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N GLU X 67 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU X 55 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 70 through 76 removed outlier: 6.275A pdb=" N ALA Y 44 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE Y 25 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE Y 46 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL Y 23 " --> pdb=" O ILE Y 46 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS Y 9 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL Y 10 " --> pdb=" O THR Y 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR Y 83 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 205 through 206 removed outlier: 4.573A pdb=" N SER b 113 " --> pdb=" O ARG b 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY b 137 " --> pdb=" O PHE b 85 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 153 through 156 Processing sheet with id=AF7, first strand: chain 'c' and resid 23 through 25 removed outlier: 3.831A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 92 through 95 removed outlier: 4.795A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'e' and resid 72 through 76 Processing sheet with id=AG1, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.643A pdb=" N HIS f 13 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS f 31 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL f 27 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N SER f 19 " --> pdb=" O PRO f 25 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA f 55 " --> pdb=" O LYS f 63 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AG3, first strand: chain 'i' and resid 17 through 18 removed outlier: 3.509A pdb=" N THR i 33 " --> pdb=" O HIS i 28 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 3 through 4 removed outlier: 6.660A pdb=" N ARG j 3 " --> pdb=" O THR j 53 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL j 55 " --> pdb=" O ARG j 3 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'l' and resid 3 through 4 Processing sheet with id=AG6, first strand: chain 'l' and resid 7 through 11 removed outlier: 7.178A pdb=" N LYS l 66 " --> pdb=" O ARG l 87 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG l 87 " --> pdb=" O LYS l 66 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL l 68 " --> pdb=" O LEU l 85 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'm' and resid 47 through 49 Processing sheet with id=AG8, first strand: chain 'n' and resid 2 through 5 Processing sheet with id=AG9, first strand: chain 'n' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'n' and resid 69 through 72 removed outlier: 3.753A pdb=" N GLN n 95 " --> pdb=" O LEU n 70 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'n' and resid 108 through 110 Processing sheet with id=AH3, first strand: chain 'n' and resid 153 through 154 Processing sheet with id=AH4, first strand: chain 'w' and resid 52 through 57 Processing sheet with id=AH5, first strand: chain 'w' and resid 120 through 121 removed outlier: 3.589A pdb=" N GLY w 120 " --> pdb=" O ILE w 128 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE w 128 " --> pdb=" O GLY w 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'w' and resid 197 through 201 removed outlier: 6.451A pdb=" N THR w 158 " --> pdb=" O TYR w 244 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL w 246 " --> pdb=" O THR w 158 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN w 160 " --> pdb=" O VAL w 246 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE w 248 " --> pdb=" O GLN w 160 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG w 162 " --> pdb=" O ILE w 248 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'w' and resid 256 through 258 removed outlier: 5.436A pdb=" N CYS w 276 " --> pdb=" O MET w 286 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N MET w 286 " --> pdb=" O CYS w 276 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS w 278 " --> pdb=" O GLN w 284 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'w' and resid 353 through 354 removed outlier: 3.522A pdb=" N ASP w 322 " --> pdb=" O THR w 339 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA w 341 " --> pdb=" O VAL w 320 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL w 320 " --> pdb=" O ALA w 341 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL w 369 " --> pdb=" O PHE w 318 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET w 370 " --> pdb=" O VAL w 398 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL w 398 " --> pdb=" O MET w 370 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL w 396 " --> pdb=" O TYR w 372 " (cutoff:3.500A) 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 201 through 203 removed outlier: 6.832A pdb=" N VAL o 202 " --> pdb=" O VAL o 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'o' and resid 235 through 236 removed outlier: 6.539A pdb=" N VAL o 235 " --> pdb=" O TYR o 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'p' and resid 27 through 28 Processing sheet with id=AI5, first strand: chain 'q' and resid 35 through 37 removed outlier: 7.343A pdb=" N ILE q 134 " --> pdb=" O SER q 54 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER q 54 " --> pdb=" O ILE q 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE q 136 " --> pdb=" O LEU q 52 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE q 166 " --> pdb=" O HIS q 51 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'q' and resid 59 through 61 removed outlier: 6.586A pdb=" N ILE q 99 " --> pdb=" O PRO q 122 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY q 124 " --> pdb=" O LEU q 97 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'q' and resid 190 through 192 Processing sheet with id=AI8, first strand: chain 't' and resid 94 through 95 1711 hydrogen bonds defined for protein. 4773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2410 hydrogen bonds 3980 hydrogen bond angles 0 basepair planarities 974 basepair parallelities 1584 stacking parallelities Total time for adding SS restraints: 179.62 Time building geometry restraints manager: 54.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14093 1.31 - 1.44: 57714 1.44 - 1.57: 61158 1.57 - 1.70: 6833 1.70 - 1.83: 202 Bond restraints: 140000 Sorted by residual: bond pdb=" C1' U A2258 " pdb=" N1 U A2258 " ideal model delta sigma weight residual 1.480 1.566 -0.086 1.50e-02 4.44e+03 3.30e+01 bond pdb=" N CYS w 143 " pdb=" CA CYS w 143 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.40e-03 1.83e+04 2.38e+01 bond pdb=" C CYS m 57 " pdb=" O CYS m 57 " ideal model delta sigma weight residual 1.236 1.179 0.056 1.17e-02 7.31e+03 2.31e+01 bond pdb=" C VAL w 249 " pdb=" N PRO w 250 " ideal model delta sigma weight residual 1.331 1.363 -0.031 7.90e-03 1.60e+04 1.55e+01 bond pdb=" N THR w 151 " pdb=" CA THR w 151 " ideal model delta sigma weight residual 1.454 1.505 -0.051 1.34e-02 5.57e+03 1.45e+01 ... (remaining 139995 not shown) Histogram of bond angle deviations from ideal: 92.87 - 101.41: 1749 101.41 - 109.95: 55453 109.95 - 118.48: 72743 118.48 - 127.02: 66816 127.02 - 135.56: 9068 Bond angle restraints: 205829 Sorted by residual: angle pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 112.00 92.87 19.13 1.40e+00 5.10e-01 1.87e+02 angle pdb=" CA PRO C 18 " pdb=" N PRO C 18 " pdb=" CD PRO C 18 " ideal model delta sigma weight residual 112.00 97.52 14.48 1.40e+00 5.10e-01 1.07e+02 angle pdb=" C PRO H 159 " pdb=" CA PRO H 159 " pdb=" CB PRO H 159 " ideal model delta sigma weight residual 111.56 125.84 -14.28 1.65e+00 3.67e-01 7.49e+01 angle pdb=" N SER N 95 " pdb=" CA SER N 95 " pdb=" C SER N 95 " ideal model delta sigma weight residual 111.28 101.85 9.43 1.09e+00 8.42e-01 7.48e+01 angle pdb=" C TYR E 167 " pdb=" CA TYR E 167 " pdb=" CB TYR E 167 " ideal model delta sigma weight residual 109.83 118.18 -8.35 9.90e-01 1.02e+00 7.11e+01 ... (remaining 205824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 73903 35.79 - 71.58: 2631 71.58 - 107.37: 197 107.37 - 143.16: 15 143.16 - 178.95: 38 Dihedral angle restraints: 76784 sinusoidal: 55753 harmonic: 21031 Sorted by residual: 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 15.69 -175.69 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A2137 " pdb=" C1' U A2137 " pdb=" N1 U A2137 " pdb=" C2 U A2137 " ideal model delta sinusoidal sigma weight residual 200.00 30.54 169.46 1 1.50e+01 4.44e-03 8.46e+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 200.00 31.34 168.66 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 76781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 25524 0.123 - 0.247: 268 0.247 - 0.370: 11 0.370 - 0.494: 2 0.494 - 0.617: 1 Chirality restraints: 25806 Sorted by residual: chirality pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" C PRO H 159 " pdb=" CB PRO H 159 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CA CYS l 77 " pdb=" N CYS l 77 " pdb=" C CYS l 77 " pdb=" CB CYS l 77 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.97e+00 chirality pdb=" CA ASP w 145 " pdb=" N ASP w 145 " pdb=" C ASP w 145 " pdb=" CB ASP w 145 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 25803 not shown) Planarity restraints: 13383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 158 " 0.090 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO H 159 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 17 " 0.088 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO C 18 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO C 18 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO C 18 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS l 74 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C CYS l 74 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS l 74 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL l 75 " -0.022 2.00e-02 2.50e+03 ... (remaining 13380 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 5 1.91 - 2.66: 6288 2.66 - 3.41: 165579 3.41 - 4.15: 385982 4.15 - 4.90: 587128 Nonbonded interactions: 1144982 Sorted by model distance: nonbonded pdb=" OD1 ASP w 99 " pdb=" CD1 LEU o 178 " model vdw 1.165 3.460 nonbonded pdb=" OG SER w 56 " pdb=" SD MET w 141 " model vdw 1.368 2.800 nonbonded pdb=" O GLU o 402 " pdb=" CD1 LEU o 423 " model vdw 1.573 3.460 nonbonded pdb=" CE1 PHE w 57 " pdb=" CD1 PHE w 64 " model vdw 1.681 3.640 nonbonded pdb=" OD2 ASP g 46 " pdb=" NH2 ARG g 88 " model vdw 1.862 2.520 ... (remaining 1144977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 18.220 Check model and map are aligned: 1.430 Set scattering table: 0.850 Process input model: 428.240 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.310 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 456.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.006 0.086 140000 Z= 0.348 Angle : 0.811 19.130 205829 Z= 0.427 Chirality : 0.042 0.617 25806 Planarity : 0.005 0.123 13383 Dihedral : 15.785 178.950 63212 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.35 % Favored : 92.45 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.12 % 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: -4.44 (0.08), residues: 6956 helix: -2.93 (0.08), residues: 2114 sheet: -2.64 (0.14), residues: 962 loop : -3.11 (0.08), residues: 3880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1222 time to evaluate : 6.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 1258 average time/residue: 1.2556 time to fit residues: 2647.1621 Evaluate side-chains 874 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 850 time to evaluate : 6.062 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 24 outliers final: 8 residues processed: 24 average time/residue: 1.0584 time to fit residues: 52.0102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 881 optimal weight: 4.9990 chunk 791 optimal weight: 5.9990 chunk 439 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 533 optimal weight: 0.9990 chunk 422 optimal weight: 0.9990 chunk 818 optimal weight: 0.9980 chunk 316 optimal weight: 7.9990 chunk 497 optimal weight: 4.9990 chunk 609 optimal weight: 7.9990 chunk 948 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS D 58 HIS D 175 HIS E 43 GLN G 138 GLN H 191 ASN H 243 GLN J 64 ASN J 121 GLN J 192 GLN K 114 GLN O 156 HIS P 206 GLN R 92 GLN S 88 HIS S 154 HIS U 97 ASN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 120 GLN Y 106 GLN Y 122 HIS a 43 HIS b 80 GLN b 104 GLN c 36 GLN c 71 GLN ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN g 11 ASN g 18 ASN g 33 GLN i 20 ASN j 76 ASN k 33 ASN l 3 ASN l 23 HIS n 50 HIS z 403 GLN o 143 ASN o 399 ASN q 133 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 140000 Z= 0.216 Angle : 0.605 12.108 205829 Z= 0.307 Chirality : 0.036 0.270 25806 Planarity : 0.005 0.168 13383 Dihedral : 14.727 179.831 49112 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.09), residues: 6956 helix: -1.63 (0.10), residues: 2138 sheet: -2.04 (0.15), residues: 1013 loop : -2.49 (0.09), residues: 3805 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 962 time to evaluate : 6.874 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 S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 113 outliers final: 73 residues processed: 1019 average time/residue: 1.1238 time to fit residues: 1974.7204 Evaluate side-chains 933 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 860 time to evaluate : 6.479 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 73 outliers final: 7 residues processed: 73 average time/residue: 0.8946 time to fit residues: 132.0877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 526 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 789 optimal weight: 3.9990 chunk 645 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 949 optimal weight: 20.0000 chunk 1026 optimal weight: 10.0000 chunk 845 optimal weight: 9.9990 chunk 941 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 761 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 HIS ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN H 59 GLN H 137 ASN K 28 GLN K 114 GLN M 59 ASN R 121 HIS ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN b 80 GLN b 104 GLN c 36 GLN e 71 HIS ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 ASN g 33 GLN n 9 ASN n 83 HIS w 108 HIS ** o 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 ASN q 175 ASN q 209 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.120 140000 Z= 0.482 Angle : 0.749 14.656 205829 Z= 0.378 Chirality : 0.044 0.305 25806 Planarity : 0.006 0.157 13383 Dihedral : 15.122 179.912 49112 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.32 % Favored : 91.58 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.09), residues: 6956 helix: -1.55 (0.10), residues: 2155 sheet: -1.92 (0.14), residues: 1047 loop : -2.36 (0.09), residues: 3754 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 968 time to evaluate : 6.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 99 residues processed: 1065 average time/residue: 1.1510 time to fit residues: 2122.7825 Evaluate side-chains 989 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 890 time to evaluate : 6.094 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 99 outliers final: 7 residues processed: 99 average time/residue: 0.9093 time to fit residues: 179.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 938 optimal weight: 7.9990 chunk 714 optimal weight: 3.9990 chunk 492 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 453 optimal weight: 9.9990 chunk 637 optimal weight: 3.9990 chunk 953 optimal weight: 0.9980 chunk 1009 optimal weight: 20.0000 chunk 497 optimal weight: 2.9990 chunk 903 optimal weight: 0.6980 chunk 271 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN F 157 ASN H 45 ASN J 121 GLN K 114 GLN L 4 ASN Q 9 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 4 GLN b 80 GLN b 104 GLN b 146 GLN c 36 GLN d 80 ASN e 6 HIS e 49 ASN ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN m 32 GLN n 9 ASN w 108 HIS o 203 GLN o 373 HIS o 399 ASN q 144 ASN q 162 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 140000 Z= 0.163 Angle : 0.551 12.455 205829 Z= 0.285 Chirality : 0.035 0.290 25806 Planarity : 0.005 0.148 13383 Dihedral : 14.743 179.594 49112 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.09), residues: 6956 helix: -0.95 (0.11), residues: 2149 sheet: -1.56 (0.15), residues: 1052 loop : -2.02 (0.10), residues: 3755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1007 time to evaluate : 6.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE Y 136 " (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: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 62 residues processed: 1075 average time/residue: 1.1287 time to fit residues: 2113.8633 Evaluate side-chains 986 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 924 time to evaluate : 6.907 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 62 outliers final: 7 residues processed: 62 average time/residue: 0.9325 time to fit residues: 117.4567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 840 optimal weight: 9.9990 chunk 572 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 751 optimal weight: 10.0000 chunk 416 optimal weight: 30.0000 chunk 861 optimal weight: 4.9990 chunk 697 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 515 optimal weight: 5.9990 chunk 905 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN F 5 GLN F 157 ASN H 45 ASN L 4 ASN O 15 GLN P 206 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN d 80 ASN e 49 ASN e 52 GLN ** e 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 GLN i 48 ASN j 67 GLN ** k 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 129 GLN o 346 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.078 140000 Z= 0.496 Angle : 0.725 14.060 205829 Z= 0.364 Chirality : 0.043 0.348 25806 Planarity : 0.006 0.151 13383 Dihedral : 14.981 179.736 49112 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.75 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -2.55 (0.09), residues: 6956 helix: -1.07 (0.11), residues: 2157 sheet: -1.63 (0.15), residues: 1062 loop : -2.10 (0.10), residues: 3737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 907 time to evaluate : 7.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 111 residues processed: 1006 average time/residue: 1.2668 time to fit residues: 2230.9413 Evaluate side-chains 996 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 885 time to evaluate : 6.839 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 111 outliers final: 7 residues processed: 111 average time/residue: 0.9560 time to fit residues: 211.1479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 339 optimal weight: 2.9990 chunk 908 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 592 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 1010 optimal weight: 0.0980 chunk 838 optimal weight: 1.9990 chunk 467 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 334 optimal weight: 0.7980 chunk 530 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 GLN H 45 ASN H 137 ASN J 121 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN b 104 GLN b 146 GLN c 36 GLN d 105 GLN e 49 ASN e 88 HIS f 106 ASN h 91 ASN n 9 ASN o 346 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.094 140000 Z= 0.144 Angle : 0.539 13.724 205829 Z= 0.278 Chirality : 0.034 0.342 25806 Planarity : 0.004 0.144 13383 Dihedral : 14.705 178.978 49112 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 6956 helix: -0.63 (0.11), residues: 2153 sheet: -1.36 (0.15), residues: 1065 loop : -1.84 (0.10), residues: 3738 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 982 time to evaluate : 6.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (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: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 40 residues processed: 1027 average time/residue: 1.1689 time to fit residues: 2086.7329 Evaluate side-chains 949 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 909 time to evaluate : 6.855 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 6 residues processed: 40 average time/residue: 0.9498 time to fit residues: 79.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 973 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 575 optimal weight: 6.9990 chunk 737 optimal weight: 0.2980 chunk 571 optimal weight: 10.0000 chunk 850 optimal weight: 1.9990 chunk 564 optimal weight: 0.9980 chunk 1006 optimal weight: 0.9990 chunk 629 optimal weight: 0.0670 chunk 613 optimal weight: 1.9990 chunk 464 optimal weight: 10.0000 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 HIS F 5 GLN F 58 HIS H 45 ASN J 121 GLN P 206 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 GLN ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 106 GLN c 36 GLN d 57 GLN e 49 ASN g 33 GLN k 32 ASN l 82 GLN ** m 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 ASN ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.110 140000 Z= 0.127 Angle : 0.504 27.749 205829 Z= 0.259 Chirality : 0.032 0.399 25806 Planarity : 0.004 0.209 13383 Dihedral : 14.507 178.780 49112 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 6956 helix: -0.36 (0.11), residues: 2171 sheet: -1.10 (0.16), residues: 1057 loop : -1.68 (0.10), residues: 3728 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 974 time to evaluate : 7.003 Fit side-chains 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 S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "PHE Y 136 " (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: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 43 residues processed: 1008 average time/residue: 1.2316 time to fit residues: 2158.5437 Evaluate side-chains 947 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 904 time to evaluate : 6.866 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 43 outliers final: 6 residues processed: 43 average time/residue: 1.0540 time to fit residues: 91.3377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 622 optimal weight: 3.9990 chunk 401 optimal weight: 0.9990 chunk 600 optimal weight: 5.9990 chunk 303 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 639 optimal weight: 0.8980 chunk 685 optimal weight: 6.9990 chunk 497 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 790 optimal weight: 0.0670 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN F 5 GLN H 45 ASN H 137 ASN ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN Q 15 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 GLN c 36 GLN d 80 ASN g 33 GLN i 48 ASN l 82 GLN ** m 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.093 140000 Z= 0.139 Angle : 0.499 20.940 205829 Z= 0.256 Chirality : 0.032 0.313 25806 Planarity : 0.004 0.183 13383 Dihedral : 14.425 178.725 49112 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 6956 helix: -0.18 (0.11), residues: 2173 sheet: -1.01 (0.16), residues: 1060 loop : -1.60 (0.10), residues: 3723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 940 time to evaluate : 7.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE Y 136 " (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: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 965 average time/residue: 1.1543 time to fit residues: 1930.6689 Evaluate side-chains 939 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 908 time to evaluate : 6.226 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 6 residues processed: 31 average time/residue: 0.8936 time to fit residues: 58.4476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 915 optimal weight: 6.9990 chunk 964 optimal weight: 10.0000 chunk 879 optimal weight: 0.8980 chunk 937 optimal weight: 0.8980 chunk 963 optimal weight: 5.9990 chunk 564 optimal weight: 1.9990 chunk 408 optimal weight: 1.9990 chunk 736 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 847 optimal weight: 0.6980 chunk 886 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 GLN H 45 ASN H 137 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 GLN b 52 GLN c 36 GLN g 33 GLN g 52 GLN i 48 ASN l 82 GLN ** l 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 ASN ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 42 GLN ** o 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.084 140000 Z= 0.121 Angle : 0.486 16.865 205829 Z= 0.250 Chirality : 0.031 0.258 25806 Planarity : 0.004 0.170 13383 Dihedral : 14.325 178.681 49112 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.10), residues: 6956 helix: 0.04 (0.12), residues: 2159 sheet: -0.77 (0.16), residues: 1020 loop : -1.47 (0.10), residues: 3777 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 957 time to evaluate : 6.643 Fit side-chains 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 S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 972 average time/residue: 1.1951 time to fit residues: 2020.2199 Evaluate side-chains 920 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 899 time to evaluate : 6.967 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 6 residues processed: 21 average time/residue: 1.0070 time to fit residues: 46.9333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 934 optimal weight: 0.9990 chunk 615 optimal weight: 10.0000 chunk 991 optimal weight: 50.0000 chunk 605 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 chunk 689 optimal weight: 6.9990 chunk 1040 optimal weight: 10.0000 chunk 957 optimal weight: 5.9990 chunk 828 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 639 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN F 5 GLN G 61 ASN H 45 ASN J 121 GLN M 56 GLN M 119 GLN ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 GLN b 52 GLN g 33 GLN i 48 ASN l 82 GLN ** l 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 140000 Z= 0.193 Angle : 0.514 16.793 205829 Z= 0.263 Chirality : 0.033 0.252 25806 Planarity : 0.004 0.169 13383 Dihedral : 14.322 179.971 49112 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.79 % Favored : 94.13 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.10), residues: 6956 helix: 0.03 (0.12), residues: 2163 sheet: -0.89 (0.16), residues: 1029 loop : -1.45 (0.10), residues: 3764 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13912 Ramachandran restraints generated. 6956 Oldfield, 0 Emsley, 6956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 923 time to evaluate : 7.041 Fit side-chains 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 S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHE Y 136 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE f 107 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE k 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU n 224 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 936 average time/residue: 1.1849 time to fit residues: 1925.9683 Evaluate side-chains 929 residues out of total 5951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 909 time to evaluate : 6.918 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LYS E 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR S 172 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE W 142 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 244 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "HIS h 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU j 78 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 6 residues processed: 20 average time/residue: 0.9747 time to fit residues: 44.4858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 507 optimal weight: 2.9990 chunk 657 optimal weight: 4.9990 chunk 882 optimal weight: 0.0980 chunk 253 optimal weight: 10.0000 chunk 763 optimal weight: 2.9990 chunk 122 optimal weight: 40.0000 chunk 230 optimal weight: 40.0000 chunk 829 optimal weight: 0.7980 chunk 347 optimal weight: 0.9980 chunk 851 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 GLN H 45 ASN ** O 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 GLN b 52 GLN c 36 GLN d 80 ASN i 48 ASN l 82 GLN ** l 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 ASN ** w 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 346 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 = 0.3625 r_free = 0.3625 target = 0.119010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091651 restraints weight = 275800.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093791 restraints weight = 126764.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093936 restraints weight = 78004.346| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.082 140000 Z= 0.142 Angle : 0.494 15.316 205829 Z= 0.254 Chirality : 0.032 0.247 25806 Planarity : 0.004 0.165 13383 Dihedral : 14.295 178.752 49112 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 6956 helix: 0.15 (0.12), residues: 2155 sheet: -0.84 (0.16), residues: 1036 loop : -1.40 (0.10), residues: 3765 =============================================================================== Job complete usr+sys time: 28889.42 seconds wall clock time: 508 minutes 47.28 seconds (30527.28 seconds total)