Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 16 05:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4y_23670/07_2023/7m4y_23670_updated.pdb" } resolution = 2.5 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= 0.009 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4451 5.49 5 Mg 196 5.21 5 S 142 5.16 5 C 69553 2.51 5 N 25759 2.21 5 O 39712 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 47": "OE1" <-> "OE2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "S PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "U ASP 14": "OD1" <-> "OD2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U ASP 94": "OD1" <-> "OD2" Residue "V PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "Y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 10": "OD1" <-> "OD2" Residue "b ASP 118": "OD1" <-> "OD2" Residue "b ASP 206": "OD1" <-> "OD2" Residue "b ASP 221": "OD1" <-> "OD2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "d TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 16": "OD1" <-> "OD2" Residue "f ASP 33": "OD1" <-> "OD2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 62": "OE1" <-> "OE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n GLU 40": "OE1" <-> "OE2" Residue "n PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "p PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ASP 73": "OD1" <-> "OD2" Residue "p PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 31": "OD1" <-> "OD2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 39": "OE1" <-> "OE2" Residue "u TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 139817 Number of models: 1 Model: "" Number of chains: 80 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2730, 58566 Classifications: {'RNA': 2730} Modifications used: {'rna2p': 3, 'rna2p_pur': 253, 'rna2p_pyr': 150, 'rna3p': 12, 'rna3p_pur': 1307, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 405, 'rna3p': 2324} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 10, 'rna3p': 104} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 111, 'rna2p_pyr': 91, 'rna3p': 8, 'rna3p_pur': 752, 'rna3p_pyr': 565} Link IDs: {'rna2p': 202, 'rna3p': 1325} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 2, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 218 Unusual residues: {' MG': 138, 'YQM': 2} Classifications: {'undetermined': 140} Link IDs: {None: 139} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 94 Unusual residues: {' MG': 54, 'YQM': 1} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 707 Classifications: {'water': 707} Link IDs: {None: 706} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "a" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 283 Classifications: {'water': 283} Link IDs: {None: 282} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 46.631 130.657 137.651 1.00 16.26 S ATOM 1398 SG CYS 3 14 47.511 129.441 141.177 1.00 15.39 S ATOM 1503 SG CYS 3 27 46.189 126.963 138.628 1.00 15.24 S Time building chain proxies: 49.11, per 1000 atoms: 0.35 Number of scatterers: 139817 At special positions: 0 Unit cell: (227.264, 250.16, 274.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4451 15.00 Mg 196 11.99 F 3 9.00 O 39712 8.00 N 25759 7.00 C 69553 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: 54.93 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10102 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 174 helices and 69 sheets defined 39.9% alpha, 19.2% beta 1453 base pairs and 2146 stacking pairs defined. Time for finding SS restraints: 56.88 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.136A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 36 through 44 removed outlier: 3.922A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.323A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.908A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.842A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.793A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.192A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 5.083A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.197A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 4.922A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.655A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.947A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.110A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.426A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.651A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.363A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.463A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.101A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.783A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.985A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.953A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.943A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU I 109 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 4.182A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 4.784A pdb=" N ARG J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 108' Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.712A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.585A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.850A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.040A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.712A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.790A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.392A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.912A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 4.558A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 4.046A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.905A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.517A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.763A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.672A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.961A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.899A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.221A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 4.068A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.352A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.295A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.013A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 removed outlier: 3.618A pdb=" N GLU U 27 " --> pdb=" O ARG U 23 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.790A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.704A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.182A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.581A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.900A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.150A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 75 through 90 removed outlier: 4.977A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.871A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 4.065A pdb=" N LEU b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 127 through 132' Processing helix chain 'b' and resid 133 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 4.562A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 156 removed outlier: 4.120A pdb=" N LYS b 154 " --> pdb=" O GLY b 151 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN b 155 " --> pdb=" O GLY b 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.835A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.199A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.738A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.888A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.027A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'c' and resid 210 through 215 removed outlier: 4.126A pdb=" N VAL c 214 " --> pdb=" O GLY c 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET c 215 " --> pdb=" O MET c 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 210 through 215' Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.288A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.783A pdb=" N TYR d 67 " --> pdb=" O VAL d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.073A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.272A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.102A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.610A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.241A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.190A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.553A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 11 through 19 removed outlier: 3.672A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 11 through 19' Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 32 removed outlier: 5.488A pdb=" N GLN g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.849A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.545A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 38 removed outlier: 4.404A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 89 Processing helix chain 'i' and resid 90 through 100 Proline residue: i 94 - end of helix Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.093A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.862A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.901A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 4.279A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.734A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.563A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.125A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.724A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.030A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 33 removed outlier: 3.504A pdb=" N ILE n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.600A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.304A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.617A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.917A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.686A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.528A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.423A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.616A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.774A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 4.991A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 6.175A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 4 removed outlier: 6.608A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.131A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.885A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.749A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N SER C 170 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.267A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.182A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.593A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.782A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.866A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.592A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.927A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.810A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.284A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.182A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.943A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.487A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 6 through 9 removed outlier: 4.102A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP J 37 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP J 56 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.949A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 39 through 42 Processing sheet with id= 25, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.041A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 33 through 37 removed outlier: 4.835A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.793A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.643A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.968A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.138A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 17 through 22 removed outlier: 3.922A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 33, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.836A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'S' and resid 11 through 14 removed outlier: 4.068A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.634A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 80 through 83 removed outlier: 7.362A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 39, first strand: chain 'U' and resid 41 through 46 removed outlier: 3.666A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.626A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.034A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.533A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.312A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.279A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 28 through 31 removed outlier: 3.896A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 92 through 95 Processing sheet with id= 47, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.862A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 164 through 169 removed outlier: 6.796A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 143 through 146 removed outlier: 3.876A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.854A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.931A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 32 through 40 removed outlier: 6.506A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.123A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.721A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.372A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.766A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 3 through 9 Processing sheet with id= 58, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.924A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 60, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.948A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.315A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 28 through 35 removed outlier: 3.737A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY k 18 " --> pdb=" O ASN k 80 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.225A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.915A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 34 through 37 removed outlier: 3.679A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 8 through 12 removed outlier: 6.947A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'q' and resid 57 through 60 removed outlier: 7.908A pdb=" N GLY q 57 " --> pdb=" O ALA q 83 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA q 83 " --> pdb=" O GLY q 57 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU q 81 " --> pdb=" O VAL q 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 's' and resid 30 through 34 removed outlier: 4.375A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1864 hydrogen bonds defined for protein. 5499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3636 hydrogen bonds 5704 hydrogen bond angles 0 basepair planarities 1453 basepair parallelities 2146 stacking parallelities Total time for adding SS restraints: 318.89 Time building geometry restraints manager: 59.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 8 1.20 - 1.36: 36303 1.36 - 1.51: 72797 1.51 - 1.66: 41232 1.66 - 1.82: 254 Bond restraints: 150594 Sorted by residual: bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.575 -0.540 2.00e-02 2.50e+03 7.29e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.570 -0.535 2.00e-02 2.50e+03 7.15e+02 bond pdb=" C14 YQM a1601 " pdb=" C15 YQM a1601 " ideal model delta sigma weight residual 1.035 1.562 -0.527 2.00e-02 2.50e+03 6.94e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.551 0.400 2.00e-02 2.50e+03 4.01e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.951 1.553 0.398 2.00e-02 2.50e+03 3.96e+02 ... (remaining 150589 not shown) Histogram of bond angle deviations from ideal: 79.63 - 92.93: 2 92.93 - 106.24: 26005 106.24 - 119.54: 132114 119.54 - 132.84: 67205 132.84 - 146.15: 62 Bond angle restraints: 225388 Sorted by residual: angle pdb=" N PRO g 71 " pdb=" CD PRO g 71 " pdb=" CG PRO g 71 " ideal model delta sigma weight residual 103.20 79.63 23.57 1.50e+00 4.44e-01 2.47e+02 angle pdb=" CB GLU b 138 " pdb=" CG GLU b 138 " pdb=" CD GLU b 138 " ideal model delta sigma weight residual 112.60 133.54 -20.94 1.70e+00 3.46e-01 1.52e+02 angle pdb=" CB ARG b 141 " pdb=" CG ARG b 141 " pdb=" CD ARG b 141 " ideal model delta sigma weight residual 111.30 138.85 -27.55 2.30e+00 1.89e-01 1.43e+02 angle pdb=" CA PRO g 71 " pdb=" N PRO g 71 " pdb=" CD PRO g 71 " ideal model delta sigma weight residual 112.00 97.32 14.68 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CG ARG b 141 " pdb=" CD ARG b 141 " pdb=" NE ARG b 141 " ideal model delta sigma weight residual 112.00 131.26 -19.26 2.20e+00 2.07e-01 7.66e+01 ... (remaining 225383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 76813 35.88 - 71.75: 3158 71.75 - 107.63: 241 107.63 - 143.50: 34 143.50 - 179.38: 80 Dihedral angle restraints: 80326 sinusoidal: 64642 harmonic: 15684 Sorted by residual: dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual -160.00 18.87 -178.87 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C a1448 " pdb=" C1' C a1448 " pdb=" N1 C a1448 " pdb=" C2 C a1448 " ideal model delta sinusoidal sigma weight residual 200.00 27.85 172.15 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C A 715 " pdb=" C1' C A 715 " pdb=" N1 C A 715 " pdb=" C2 C A 715 " ideal model delta sinusoidal sigma weight residual -160.00 11.87 -171.87 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 80323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 27720 0.081 - 0.162: 1039 0.162 - 0.244: 21 0.244 - 0.325: 8 0.325 - 0.406: 6 Chirality restraints: 28794 Sorted by residual: chirality pdb=" C05 YQM A3201 " pdb=" C04 YQM A3201 " pdb=" C06 YQM A3201 " pdb=" C19 YQM A3201 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C05 YQM a1601 " pdb=" C04 YQM a1601 " pdb=" C06 YQM a1601 " pdb=" C19 YQM a1601 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.75 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 28791 not shown) Planarity restraints: 12033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.061 2.00e-02 2.50e+03 6.16e-01 8.55e+03 pdb=" C4' 7MG A2065 " 0.453 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.700 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.185 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.971 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.204 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.968 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU v 55 " 0.022 2.00e-02 2.50e+03 6.11e-01 8.40e+03 pdb=" C4' 5MU v 55 " 0.496 2.00e-02 2.50e+03 pdb=" O4' 5MU v 55 " 0.929 2.00e-02 2.50e+03 pdb=" C3' 5MU v 55 " -0.560 2.00e-02 2.50e+03 pdb=" O3' 5MU v 55 " -0.501 2.00e-02 2.50e+03 pdb=" C2' 5MU v 55 " -0.311 2.00e-02 2.50e+03 pdb=" O2' 5MU v 55 " 0.767 2.00e-02 2.50e+03 pdb=" C1' 5MU v 55 " 0.147 2.00e-02 2.50e+03 pdb=" N1 5MU v 55 " -0.988 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.040 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 2MG A2441 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.695 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.595 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.210 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.922 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.212 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.918 2.00e-02 2.50e+03 ... (remaining 12030 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 1053 2.41 - 3.03: 74837 3.03 - 3.65: 246223 3.65 - 4.28: 399905 4.28 - 4.90: 536207 Nonbonded interactions: 1258225 Sorted by model distance: nonbonded pdb=" O LEU b 137 " pdb=" OG1 THR b 140 " model vdw 1.783 2.440 nonbonded pdb="MG MG a1637 " pdb=" O HOH a1716 " model vdw 1.793 2.170 nonbonded pdb="MG MG a1651 " pdb=" O HOH a1789 " model vdw 1.803 2.170 nonbonded pdb=" O2' U a 403 " pdb=" OE1 GLU d 115 " model vdw 1.821 2.440 nonbonded pdb="MG MG a1651 " pdb=" O HOH a1721 " model vdw 1.839 2.170 ... (remaining 1258220 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.630 Construct map_model_manager: 0.130 Extract box with map and model: 34.510 Check model and map are aligned: 1.570 Set scattering table: 0.940 Process input model: 597.540 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 655.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 0.540 150594 Z= 0.416 Angle : 0.579 27.545 225388 Z= 0.305 Chirality : 0.034 0.406 28794 Planarity : 0.017 0.616 12033 Dihedral : 16.282 179.379 70224 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.49 % Favored : 97.34 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.73 % 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: 1.41 (0.11), residues: 5413 helix: 2.37 (0.12), residues: 1864 sheet: 0.65 (0.16), residues: 1027 loop : 0.02 (0.12), residues: 2522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 958 time to evaluate : 6.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 84 residues processed: 1043 average time/residue: 2.3446 time to fit residues: 3429.8271 Evaluate side-chains 979 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 895 time to evaluate : 6.044 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 77 residues processed: 8 average time/residue: 1.3100 time to fit residues: 24.2797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 822 optimal weight: 2.9990 chunk 738 optimal weight: 5.9990 chunk 409 optimal weight: 0.5980 chunk 252 optimal weight: 10.0000 chunk 497 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 763 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 464 optimal weight: 10.0000 chunk 568 optimal weight: 0.9990 chunk 884 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN 2 42 GLN C 117 GLN C 239 ASN D 47 GLN D 63 ASN E 29 GLN E 105 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN M 72 ASN O 9 GLN O 32 GLN P 56 GLN Q 86 GLN R 34 ASN S 29 GLN S 36 ASN S 58 ASN Y 24 GLN Y 48 ASN Z 4 GLN c 88 GLN g 29 HIS g 54 ASN h 18 GLN l 46 ASN o 35 GLN o 71 ASN r 36 ASN s 56 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 150594 Z= 0.246 Angle : 0.711 16.466 225388 Z= 0.376 Chirality : 0.040 0.607 28794 Planarity : 0.007 0.138 12033 Dihedral : 15.323 179.687 59488 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.06 % Rotamer Outliers : 5.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 1.11 (0.11), residues: 5413 helix: 1.98 (0.12), residues: 1867 sheet: 0.62 (0.16), residues: 1028 loop : -0.11 (0.12), residues: 2518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 923 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 229 outliers final: 144 residues processed: 1068 average time/residue: 2.2127 time to fit residues: 3355.6839 Evaluate side-chains 1039 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 895 time to evaluate : 6.056 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 101 residues processed: 46 average time/residue: 1.3992 time to fit residues: 115.3875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 491 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 736 optimal weight: 5.9990 chunk 602 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 886 optimal weight: 1.9990 chunk 957 optimal weight: 6.9990 chunk 789 optimal weight: 0.9990 chunk 878 optimal weight: 40.0000 chunk 302 optimal weight: 0.9990 chunk 710 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN 2 42 GLN C 117 GLN C 239 ASN D 47 GLN D 63 ASN D 115 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 ASN O 9 GLN O 32 GLN P 101 HIS Q 86 GLN R 34 ASN S 36 ASN S 58 ASN U 16 GLN V 35 ASN Y 24 GLN Y 48 ASN b 67 ASN d 56 GLN e 88 HIS o 35 GLN o 71 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 150594 Z= 0.286 Angle : 0.752 16.336 225388 Z= 0.397 Chirality : 0.042 0.400 28794 Planarity : 0.007 0.141 12033 Dihedral : 15.481 179.919 59488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.88 % Rotamer Outliers : 5.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.77 (0.11), residues: 5413 helix: 1.69 (0.12), residues: 1858 sheet: 0.47 (0.16), residues: 1017 loop : -0.30 (0.12), residues: 2538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 917 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 254 outliers final: 154 residues processed: 1087 average time/residue: 2.2964 time to fit residues: 3526.4117 Evaluate side-chains 1054 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 900 time to evaluate : 6.278 Switching outliers to nearest non-outliers outliers start: 154 outliers final: 113 residues processed: 45 average time/residue: 1.3743 time to fit residues: 111.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 875 optimal weight: 10.0000 chunk 666 optimal weight: 3.9990 chunk 459 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 422 optimal weight: 5.9990 chunk 595 optimal weight: 3.9990 chunk 889 optimal weight: 4.9990 chunk 941 optimal weight: 1.9990 chunk 464 optimal weight: 7.9990 chunk 842 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN 2 42 GLN C 21 HIS C 48 HIS C 117 GLN C 163 GLN C 239 ASN D 47 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN Q 86 GLN R 34 ASN S 36 ASN S 58 ASN Y 24 GLN Y 48 ASN b 67 ASN b 192 ASN h 18 GLN o 35 GLN o 37 ASN o 71 ASN p 64 GLN r 36 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 150594 Z= 0.373 Angle : 0.844 16.606 225388 Z= 0.436 Chirality : 0.046 0.435 28794 Planarity : 0.008 0.141 12033 Dihedral : 15.590 179.943 59488 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.75 % Rotamer Outliers : 5.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.48 (0.11), residues: 5413 helix: 1.38 (0.12), residues: 1862 sheet: 0.40 (0.16), residues: 1015 loop : -0.47 (0.11), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 887 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 264 outliers final: 177 residues processed: 1066 average time/residue: 2.3566 time to fit residues: 3549.4579 Evaluate side-chains 1050 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 873 time to evaluate : 6.063 Switching outliers to nearest non-outliers outliers start: 177 outliers final: 134 residues processed: 46 average time/residue: 1.4090 time to fit residues: 115.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 784 optimal weight: 10.0000 chunk 534 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 700 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 803 optimal weight: 2.9990 chunk 650 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 480 optimal weight: 9.9990 chunk 845 optimal weight: 0.6980 chunk 237 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN D 47 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN R 34 ASN S 36 ASN S 58 ASN Y 24 GLN Y 48 ASN b 67 ASN c 88 GLN c 139 GLN h 23 GLN o 35 GLN o 71 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 150594 Z= 0.420 Angle : 0.888 17.081 225388 Z= 0.455 Chirality : 0.048 0.444 28794 Planarity : 0.008 0.204 12033 Dihedral : 15.589 179.877 59488 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.31 % Favored : 96.53 % Rotamer Outliers : 5.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.26 (0.11), residues: 5413 helix: 1.16 (0.12), residues: 1863 sheet: 0.34 (0.16), residues: 993 loop : -0.58 (0.11), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 893 time to evaluate : 6.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 261 outliers final: 187 residues processed: 1076 average time/residue: 2.4388 time to fit residues: 3704.9158 Evaluate side-chains 1068 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 881 time to evaluate : 6.165 Switching outliers to nearest non-outliers outliers start: 187 outliers final: 144 residues processed: 46 average time/residue: 1.3751 time to fit residues: 115.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 316 optimal weight: 10.0000 chunk 847 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 552 optimal weight: 20.0000 chunk 232 optimal weight: 30.0000 chunk 942 optimal weight: 1.9990 chunk 782 optimal weight: 4.9990 chunk 436 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 311 optimal weight: 2.9990 chunk 494 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN Q 86 GLN R 34 ASN S 36 ASN S 58 ASN Y 24 GLN Y 48 ASN b 67 ASN c 123 GLN c 139 GLN h 18 GLN o 35 GLN o 71 ASN r 36 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 150594 Z= 0.302 Angle : 0.764 16.070 225388 Z= 0.402 Chirality : 0.043 0.407 28794 Planarity : 0.007 0.223 12033 Dihedral : 15.395 179.939 59488 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.97 % Favored : 96.86 % Rotamer Outliers : 5.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.41 (0.11), residues: 5413 helix: 1.37 (0.12), residues: 1869 sheet: 0.35 (0.16), residues: 1010 loop : -0.56 (0.11), residues: 2534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 899 time to evaluate : 6.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 258 outliers final: 194 residues processed: 1076 average time/residue: 2.3314 time to fit residues: 3548.1091 Evaluate side-chains 1082 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 888 time to evaluate : 6.146 Switching outliers to nearest non-outliers outliers start: 194 outliers final: 149 residues processed: 47 average time/residue: 1.4655 time to fit residues: 120.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 908 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 688 optimal weight: 10.0000 chunk 533 optimal weight: 4.9990 chunk 793 optimal weight: 0.0870 chunk 526 optimal weight: 5.9990 chunk 938 optimal weight: 5.9990 chunk 587 optimal weight: 4.9990 chunk 572 optimal weight: 20.0000 chunk 433 optimal weight: 0.9980 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 63 GLN O 9 GLN O 32 GLN Q 86 GLN R 34 ASN S 36 ASN S 58 ASN Y 48 ASN b 67 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 139 GLN o 28 GLN o 35 GLN o 71 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 150594 Z= 0.249 Angle : 0.715 15.925 225388 Z= 0.380 Chirality : 0.040 0.388 28794 Planarity : 0.007 0.155 12033 Dihedral : 15.278 179.995 59488 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.01 % Favored : 96.82 % Rotamer Outliers : 5.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.53 (0.11), residues: 5413 helix: 1.52 (0.12), residues: 1870 sheet: 0.40 (0.16), residues: 1015 loop : -0.53 (0.11), residues: 2528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 891 time to evaluate : 6.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 224 outliers final: 172 residues processed: 1063 average time/residue: 2.3424 time to fit residues: 3518.0986 Evaluate side-chains 1056 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 884 time to evaluate : 6.147 Switching outliers to nearest non-outliers outliers start: 172 outliers final: 143 residues processed: 30 average time/residue: 1.3424 time to fit residues: 75.4866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 580 optimal weight: 10.0000 chunk 374 optimal weight: 4.9990 chunk 560 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 596 optimal weight: 5.9990 chunk 639 optimal weight: 5.9990 chunk 464 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 737 optimal weight: 20.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN M 16 HIS M 72 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN Q 86 GLN R 34 ASN S 29 GLN S 36 ASN S 58 ASN Y 48 ASN b 67 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN d 91 ASN d 138 GLN f 58 HIS g 21 GLN h 18 GLN i 30 ASN l 46 ASN o 28 GLN o 35 GLN o 71 ASN r 36 ASN t 3 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.149 150594 Z= 0.695 Angle : 1.178 20.263 225388 Z= 0.576 Chirality : 0.062 0.499 28794 Planarity : 0.010 0.244 12033 Dihedral : 15.837 179.992 59488 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: -0.20 (0.11), residues: 5413 helix: 0.67 (0.12), residues: 1861 sheet: 0.19 (0.16), residues: 979 loop : -0.81 (0.11), residues: 2573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 878 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 249 outliers final: 188 residues processed: 1059 average time/residue: 2.2807 time to fit residues: 3421.5456 Evaluate side-chains 1059 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 871 time to evaluate : 6.179 Switching outliers to nearest non-outliers outliers start: 188 outliers final: 148 residues processed: 43 average time/residue: 1.5029 time to fit residues: 112.4044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 853 optimal weight: 0.7980 chunk 899 optimal weight: 1.9990 chunk 820 optimal weight: 2.9990 chunk 874 optimal weight: 4.9990 chunk 526 optimal weight: 4.9990 chunk 381 optimal weight: 8.9990 chunk 686 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 790 optimal weight: 2.9990 chunk 827 optimal weight: 0.7980 chunk 871 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN D 47 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 63 GLN O 9 GLN R 34 ASN S 36 ASN S 58 ASN Y 48 ASN b 67 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN d 138 GLN g 21 GLN h 23 GLN o 28 GLN o 35 GLN o 71 ASN r 36 ASN t 3 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 150594 Z= 0.176 Angle : 0.663 15.597 225388 Z= 0.358 Chirality : 0.038 0.361 28794 Planarity : 0.006 0.130 12033 Dihedral : 15.204 179.696 59488 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.46 (0.11), residues: 5413 helix: 1.49 (0.12), residues: 1871 sheet: 0.39 (0.16), residues: 1004 loop : -0.60 (0.11), residues: 2538 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 892 time to evaluate : 6.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 149 residues processed: 1045 average time/residue: 2.4055 time to fit residues: 3567.4498 Evaluate side-chains 1026 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 877 time to evaluate : 6.188 Switching outliers to nearest non-outliers outliers start: 149 outliers final: 132 residues processed: 17 average time/residue: 1.6811 time to fit residues: 52.2046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 574 optimal weight: 20.0000 chunk 925 optimal weight: 4.9990 chunk 564 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 chunk 643 optimal weight: 5.9990 chunk 970 optimal weight: 5.9990 chunk 893 optimal weight: 1.9990 chunk 772 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 596 optimal weight: 5.9990 chunk 473 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN M 72 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN R 34 ASN S 29 GLN S 36 ASN S 58 ASN Y 48 ASN b 67 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 139 GLN d 138 GLN g 21 GLN h 18 GLN m 8 ASN o 28 GLN o 35 GLN o 71 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 150594 Z= 0.323 Angle : 0.787 15.413 225388 Z= 0.410 Chirality : 0.043 0.412 28794 Planarity : 0.007 0.188 12033 Dihedral : 15.296 179.878 59488 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.27 % Favored : 96.60 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.36 (0.11), residues: 5413 helix: 1.34 (0.12), residues: 1871 sheet: 0.38 (0.16), residues: 1008 loop : -0.63 (0.11), residues: 2534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10826 Ramachandran restraints generated. 5413 Oldfield, 0 Emsley, 5413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 882 time to evaluate : 6.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 145 residues processed: 1026 average time/residue: 2.3498 time to fit residues: 3420.5915 Evaluate side-chains 1024 residues out of total 4483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 879 time to evaluate : 6.145 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 136 residues processed: 10 average time/residue: 1.2765 time to fit residues: 28.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 974 random chunks: chunk 613 optimal weight: 5.9990 chunk 823 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 712 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 773 optimal weight: 3.9990 chunk 323 optimal weight: 0.0050 chunk 794 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 117 GLN C 163 GLN C 239 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN M 72 ASN O 9 GLN Q 86 GLN R 34 ASN S 29 GLN S 36 ASN S 58 ASN Y 48 ASN b 67 ASN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 139 GLN d 138 GLN g 21 GLN h 98 GLN o 28 GLN o 35 GLN o 71 ASN r 36 ASN t 3 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138857 restraints weight = 155293.877| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 0.53 r_work: 0.3456 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.092 150594 Z= 0.357 Angle : 0.827 15.228 225388 Z= 0.428 Chirality : 0.045 0.430 28794 Planarity : 0.008 0.204 12033 Dihedral : 15.346 179.817 59488 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % 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: 0.24 (0.11), residues: 5413 helix: 1.22 (0.12), residues: 1863 sheet: 0.34 (0.16), residues: 1013 loop : -0.67 (0.11), residues: 2537 =============================================================================== Job complete usr+sys time: 46305.70 seconds wall clock time: 802 minutes 44.98 seconds (48164.98 seconds total)