Starting phenix.real_space_refine on Mon Nov 20 05:51:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/11_2023/7ryg_24739_updated.pdb" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 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 4406 5.49 5 Mg 4 5.21 5 S 142 5.16 5 C 69095 2.51 5 N 25581 2.21 5 O 38341 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 3": "OD1" <-> "OD2" Residue "0 GLU 47": "OE1" <-> "OE2" Residue "2 ASP 53": "OD1" <-> "OD2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" 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 ASP 81": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "P PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P ASP 97": "OD1" <-> "OD2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q ASP 37": "OD1" <-> "OD2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 206": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "e ASP 18": "OD1" <-> "OD2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h ASP 114": "OD1" <-> "OD2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 40": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "k ASP 75": "OD1" <-> "OD2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "o ASP 68": "OD1" <-> "OD2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "u TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 137579 Number of models: 1 Model: "" Number of chains: 55 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: 57610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2685, 57610 Classifications: {'RNA': 2685} Modifications used: {'rna2p': 3, 'rna2p_pur': 257, 'rna2p_pyr': 142, 'rna3p': 9, 'rna3p_pur': 1281, 'rna3p_pyr': 993} Link IDs: {'rna2p': 401, 'rna3p': 2283} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 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': 8, 'rna3p_pur': 56, 'rna3p_pyr': 47} Link IDs: {'rna2p': 11, 'rna3p': 103} 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': 106, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 757, 'rna3p_pyr': 572} Link IDs: {'rna2p': 190, 'rna3p': 1337} 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: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} 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': 3, 'rna3p': 2, 'rna3p_pur': 34, 'rna3p_pyr': 31} Link IDs: {'rna2p': 9, 'rna3p': 67} 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 127 Unusual residues: {' MG': 4, '80P': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 179.539 123.440 137.460 1.00 26.30 S ATOM 1398 SG CYS 3 14 178.748 125.235 140.717 1.00 25.14 S ATOM 1503 SG CYS 3 27 180.168 127.215 137.795 1.00 25.68 S Time building chain proxies: 53.83, per 1000 atoms: 0.39 Number of scatterers: 137579 At special positions: 0 Unit cell: (227.601, 251.559, 278.784, 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 4406 15.00 Mg 4 11.99 F 9 9.00 O 38341 8.00 N 25581 7.00 C 69095 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: 58.54 Conformation dependent library (CDL) restraints added in 7.2 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 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10090 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 65 sheets defined 39.5% alpha, 19.2% beta 1380 base pairs and 2135 stacking pairs defined. Time for finding SS restraints: 73.73 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.085A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.435A 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 removed outlier: 3.671A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 45 removed outlier: 3.721A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.299A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.306A 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: 5.003A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.748A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.538A 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 removed outlier: 3.855A pdb=" N MET C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.857A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.122A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.631A 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: 4.592A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.490A 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 'D' and resid 57 through 62 removed outlier: 3.611A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.508A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.230A pdb=" N TRP D 128 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 4.020A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.672A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.487A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.750A 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 5 through 21 removed outlier: 4.250A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.374A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.960A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.847A 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: 3.724A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.297A 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: 4.297A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.889A 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: 3.644A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 4.168A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.739A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.535A 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: 3.650A 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: 4.045A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.259A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.521A 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: 3.720A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.806A 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 56 removed outlier: 3.759A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.900A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.697A 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: 4.347A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.704A 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: 4.118A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.689A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.468A 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 Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.752A 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: 4.081A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.004A 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: 3.839A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.175A 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: 4.052A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.977A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.682A 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: 3.648A pdb=" N GLN S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.528A 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: 4.229A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.335A 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: 5.098A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.997A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.480A 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: 3.671A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.586A 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: 4.066A 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: 3.630A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 18 Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.868A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 3.933A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.974A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 75 through 90 removed outlier: 5.000A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.818A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 5.226A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) 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 228 removed outlier: 4.924A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.753A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.663A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.284A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.227A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.600A 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 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.346A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.559A pdb=" N LYS d 60 " --> pdb=" O GLN d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.020A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.907A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) 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: 5.080A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.150A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.566A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.284A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.671A 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: 4.373A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 removed outlier: 4.026A pdb=" N ALA f 32 " --> pdb=" O GLN f 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.621A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.066A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 4.880A 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: 4.172A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 4.764A 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 37 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: 3.682A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.606A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.782A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.491A 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 77 removed outlier: 4.059A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.478A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.195A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.640A 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 49 through 64 removed outlier: 3.708A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 3.901A 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 removed outlier: 3.634A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) 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 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.689A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.656A pdb=" N GLN n 90 " --> pdb=" O ASP n 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.874A pdb=" N ARG o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 43 removed outlier: 4.196A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.557A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.178A 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: 3.772A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.193A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.476A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.422A 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 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: 3.575A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.970A 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 38 removed outlier: 3.610A pdb=" N VAL u 32 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 removed outlier: 3.505A pdb=" N LYS u 46 " --> pdb=" O THR u 42 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 15 through 20 removed outlier: 6.147A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 5.831A 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: 6.332A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.696A 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: 5.338A 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: 3.910A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.868A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.995A 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: 5.311A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.193A 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: 4.117A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.660A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.166A 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: 6.729A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.521A 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: 4.489A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.632A pdb=" N GLY E 41 " --> pdb=" O GLN E 89 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG E 43 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG E 87 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS E 45 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA E 85 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.732A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.722A pdb=" N VAL F 66 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS F 88 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.511A 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 94 through 98 Processing sheet with id= 19, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.563A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 16 through 20 removed outlier: 4.342A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.392A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.254A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE J 86 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 122 through 125 Processing sheet with id= 25, first strand: chain 'L' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'L' and resid 63 through 67 removed outlier: 5.931A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 37 removed outlier: 6.145A pdb=" N ALA M 108 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE M 102 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET M 110 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.647A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 47 removed outlier: 6.592A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.977A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.127A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.109A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.725A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 removed outlier: 4.881A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.440A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.318A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 80 through 85 removed outlier: 7.132A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 40, first strand: chain 'U' and resid 41 through 46 removed outlier: 3.577A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG U 97 " --> pdb=" O TYR U 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS U 92 " --> pdb=" O GLN U 82 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.255A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.576A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.355A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 69 through 73 Processing sheet with id= 47, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.744A 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 170 removed outlier: 3.529A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 142 through 147 removed outlier: 3.800A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.575A 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: 3.999A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.999A 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 39 Processing sheet with id= 53, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.438A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.241A 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: 4.053A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR f 59 " --> pdb=" O GLY f 43 " (cutoff:3.500A) removed outlier: 6.562A 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: 6.103A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.942A 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: 4.555A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.673A 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 removed outlier: 3.667A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.630A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 28 through 34 removed outlier: 7.376A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 29 through 34 removed outlier: 4.364A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.813A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.655A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 8 through 12 removed outlier: 6.876A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 's' and resid 30 through 34 removed outlier: 4.636A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3466 hydrogen bonds 5500 hydrogen bond angles 0 basepair planarities 1380 basepair parallelities 2135 stacking parallelities Total time for adding SS restraints: 232.32 Time building geometry restraints manager: 63.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12641 1.31 - 1.43: 66708 1.43 - 1.56: 61034 1.56 - 1.69: 8841 1.69 - 1.82: 253 Bond restraints: 149477 Sorted by residual: bond pdb=" C4 5MU v 55 " pdb=" C5 5MU v 55 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.450 0.352 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " ideal model delta sigma weight residual 1.240 1.554 -0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " ideal model delta sigma weight residual 1.240 1.546 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C08 80P a1602 " pdb=" C09 80P a1602 " ideal model delta sigma weight residual 1.332 1.631 -0.299 2.00e-02 2.50e+03 2.23e+02 ... (remaining 149472 not shown) Histogram of bond angle deviations from ideal: 99.20 - 108.56: 48961 108.56 - 117.92: 91902 117.92 - 127.27: 73057 127.27 - 136.63: 9737 136.63 - 145.99: 4 Bond angle restraints: 223661 Sorted by residual: angle pdb=" C11 80P a1601 " pdb=" C12 80P a1601 " pdb=" C13 80P a1601 " ideal model delta sigma weight residual 142.25 116.69 25.56 3.00e+00 1.11e-01 7.26e+01 angle pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " pdb=" C13 80P a1603 " ideal model delta sigma weight residual 142.25 116.97 25.28 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " pdb=" C13 80P a1602 " ideal model delta sigma weight residual 142.25 117.24 25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C13 80P a1601 " pdb=" C12 80P a1601 " pdb=" C17 80P a1601 " ideal model delta sigma weight residual 101.90 123.63 -21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C13 80P a1603 " pdb=" C12 80P a1603 " pdb=" C17 80P a1603 " ideal model delta sigma weight residual 101.90 123.19 -21.29 3.00e+00 1.11e-01 5.04e+01 ... (remaining 223656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 76589 35.97 - 71.95: 2900 71.95 - 107.92: 242 107.92 - 143.89: 34 143.89 - 179.87: 72 Dihedral angle restraints: 79837 sinusoidal: 64171 harmonic: 15666 Sorted by residual: dihedral pdb=" O4' U a1378 " pdb=" C1' U a1378 " pdb=" N1 U a1378 " pdb=" C2 U a1378 " ideal model delta sinusoidal sigma weight residual -160.00 10.16 -170.16 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual 200.00 30.09 169.91 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C a 516 " pdb=" C1' C a 516 " pdb=" N1 C a 516 " pdb=" C2 C a 516 " ideal model delta sinusoidal sigma weight residual 200.00 30.94 169.06 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 79834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.133: 28564 1.133 - 2.265: 0 2.265 - 3.398: 0 3.398 - 4.531: 0 4.531 - 5.664: 3 Chirality restraints: 28567 Sorted by residual: chirality pdb=" C08 80P a1602 " pdb=" C07 80P a1602 " pdb=" C09 80P a1602 " pdb=" C21 80P a1602 " both_signs ideal model delta sigma weight residual False 2.49 -3.18 5.66 2.00e-01 2.50e+01 8.02e+02 chirality pdb=" C08 80P a1603 " pdb=" C07 80P a1603 " pdb=" C09 80P a1603 " pdb=" C21 80P a1603 " both_signs ideal model delta sigma weight residual False 2.49 -3.15 5.64 2.00e-01 2.50e+01 7.94e+02 chirality pdb=" C08 80P a1601 " pdb=" C07 80P a1601 " pdb=" C09 80P a1601 " pdb=" C21 80P a1601 " both_signs ideal model delta sigma weight residual False 2.49 -3.06 5.54 2.00e-01 2.50e+01 7.68e+02 ... (remaining 28564 not shown) Planarity restraints: 11978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.058 2.00e-02 2.50e+03 6.17e-01 8.58e+03 pdb=" C4' 7MG A2065 " 0.458 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.736 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.628 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.198 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.947 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.197 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.979 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " -0.046 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' 7MG a 524 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " -0.723 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " 0.608 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " -0.931 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " -0.204 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.055 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' 2MG a1204 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.620 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.962 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.221 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.897 2.00e-02 2.50e+03 ... (remaining 11975 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 292 2.42 - 3.04: 74272 3.04 - 3.66: 242227 3.66 - 4.28: 384316 4.28 - 4.90: 518435 Nonbonded interactions: 1219542 Sorted by model distance: nonbonded pdb=" O2' G A 799 " pdb=" OP1 A A 800 " model vdw 1.799 2.440 nonbonded pdb=" O37 80P a1603 " pdb="MG MG a1606 " model vdw 1.831 2.170 nonbonded pdb=" O2' A A1923 " pdb=" O5' A A1924 " model vdw 1.890 2.440 nonbonded pdb=" OP2 U a 423 " pdb=" O2' G a 424 " model vdw 1.916 2.440 nonbonded pdb=" O2' U A 533 " pdb=" OD2 ASP P 49 " model vdw 1.925 2.440 ... (remaining 1219537 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: 6.230 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: 0.110 Extract box with map and model: 30.110 Check model and map are aligned: 1.560 Set scattering table: 0.980 Process input model: 544.200 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 598.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 0.353 149477 Z= 0.357 Angle : 0.612 25.555 223661 Z= 0.311 Chirality : 0.067 5.664 28567 Planarity : 0.017 0.617 11978 Dihedral : 15.961 179.867 69747 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 2.32 % Allowed : 24.97 % Favored : 72.70 % 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: 1.15 (0.11), residues: 5407 helix: 2.18 (0.12), residues: 1862 sheet: 0.68 (0.16), residues: 1027 loop : -0.25 (0.12), residues: 2518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1089 time to evaluate : 6.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 87 residues processed: 1177 average time/residue: 2.2914 time to fit residues: 3746.2047 Evaluate side-chains 1137 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1050 time to evaluate : 5.993 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 79 residues processed: 11 average time/residue: 1.0957 time to fit residues: 28.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 5.9990 chunk 733 optimal weight: 30.0000 chunk 407 optimal weight: 0.8980 chunk 250 optimal weight: 7.9990 chunk 494 optimal weight: 0.3980 chunk 391 optimal weight: 6.9990 chunk 758 optimal weight: 0.6980 chunk 293 optimal weight: 6.9990 chunk 461 optimal weight: 0.0970 chunk 564 optimal weight: 9.9990 chunk 879 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 HIS C 185 HIS E 105 GLN I 63 GLN I 136 GLN O 9 GLN O 13 ASN O 32 GLN Q 86 GLN R 34 ASN R 62 ASN S 58 ASN W 36 HIS Z 4 GLN Z 5 GLN Z 25 ASN ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN c 28 GLN c 100 GLN c 216 ASN d 138 GLN f 87 ASN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS h 18 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN o 62 GLN p 64 GLN q 31 GLN r 36 ASN r 61 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 149477 Z= 0.136 Angle : 0.626 26.351 223661 Z= 0.329 Chirality : 0.039 2.084 28567 Planarity : 0.005 0.127 11978 Dihedral : 14.611 179.980 59028 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 5.41 % Allowed : 22.94 % Favored : 71.66 % 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: 1.30 (0.11), residues: 5407 helix: 2.30 (0.12), residues: 1875 sheet: 0.71 (0.15), residues: 1064 loop : -0.16 (0.12), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1080 time to evaluate : 5.976 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: 242 outliers final: 138 residues processed: 1226 average time/residue: 2.3239 time to fit residues: 3970.4632 Evaluate side-chains 1189 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1051 time to evaluate : 6.279 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 100 residues processed: 43 average time/residue: 1.4882 time to fit residues: 109.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 731 optimal weight: 4.9990 chunk 598 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 880 optimal weight: 1.9990 chunk 951 optimal weight: 1.9990 chunk 784 optimal weight: 0.8980 chunk 873 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 706 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN E 29 GLN E 96 ASN E 105 GLN E 162 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 136 GLN K 101 ASN O 9 GLN O 32 GLN P 71 GLN R 34 ASN S 20 GLN S 58 ASN T 9 GLN Z 4 GLN Z 25 ASN b 57 ASN b 60 ASN c 28 GLN c 100 GLN ** d 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 53 GLN i 124 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 14 HIS o 28 GLN o 37 ASN o 40 GLN o 62 GLN p 64 GLN q 31 GLN r 61 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 149477 Z= 0.334 Angle : 0.830 25.301 223661 Z= 0.422 Chirality : 0.049 2.314 28567 Planarity : 0.007 0.140 11978 Dihedral : 15.007 179.711 59028 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.68 % Favored : 97.19 % Rotamer: Outliers : 6.54 % Allowed : 22.22 % Favored : 71.23 % 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: 0.68 (0.11), residues: 5407 helix: 1.63 (0.12), residues: 1854 sheet: 0.53 (0.16), residues: 1028 loop : -0.43 (0.11), residues: 2525 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1065 time to evaluate : 6.139 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 revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 189 residues processed: 1236 average time/residue: 2.3122 time to fit residues: 3985.0142 Evaluate side-chains 1243 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1054 time to evaluate : 6.282 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 128 residues processed: 64 average time/residue: 1.4314 time to fit residues: 157.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 30.0000 chunk 662 optimal weight: 3.9990 chunk 457 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 420 optimal weight: 10.0000 chunk 591 optimal weight: 2.9990 chunk 883 optimal weight: 30.0000 chunk 935 optimal weight: 0.2980 chunk 461 optimal weight: 7.9990 chunk 837 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN D 37 GLN E 96 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN L 89 ASN O 9 GLN O 32 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 ASN T 9 GLN Z 4 GLN Z 25 ASN Z 52 GLN c 38 GLN c 100 GLN c 139 GLN d 36 ASN ** d 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN h 41 GLN h 42 GLN h 53 GLN h 98 GLN i 124 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN p 64 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 149477 Z= 0.288 Angle : 0.775 25.089 223661 Z= 0.399 Chirality : 0.046 2.156 28567 Planarity : 0.007 0.136 11978 Dihedral : 14.885 179.903 59028 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 6.81 % Allowed : 22.67 % Favored : 70.52 % 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: 0.55 (0.11), residues: 5407 helix: 1.56 (0.12), residues: 1853 sheet: 0.42 (0.16), residues: 1027 loop : -0.53 (0.11), residues: 2527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1054 time to evaluate : 6.083 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: 305 outliers final: 209 residues processed: 1238 average time/residue: 2.3452 time to fit residues: 4041.4612 Evaluate side-chains 1245 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1036 time to evaluate : 5.380 Switching outliers to nearest non-outliers outliers start: 209 outliers final: 142 residues processed: 73 average time/residue: 1.4275 time to fit residues: 175.9513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 50.0000 chunk 531 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 696 optimal weight: 40.0000 chunk 386 optimal weight: 10.0000 chunk 798 optimal weight: 2.9990 chunk 646 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 477 optimal weight: 10.0000 chunk 839 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 18 HIS L 89 ASN O 9 GLN O 13 ASN O 32 GLN Q 43 ASN S 58 ASN T 9 GLN U 16 GLN Z 4 GLN Z 25 ASN b 60 ASN b 197 ASN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN h 48 ASN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN o 40 GLN p 64 GLN r 61 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.135 149477 Z= 0.627 Angle : 1.157 25.251 223661 Z= 0.562 Chirality : 0.063 2.466 28567 Planarity : 0.010 0.151 11978 Dihedral : 15.465 179.963 59028 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 7.30 % Allowed : 23.27 % Favored : 69.42 % 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: -0.21 (0.11), residues: 5407 helix: 0.71 (0.11), residues: 1844 sheet: 0.20 (0.16), residues: 1009 loop : -0.86 (0.11), residues: 2554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1074 time to evaluate : 6.101 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: 327 outliers final: 236 residues processed: 1274 average time/residue: 2.2295 time to fit residues: 3982.0608 Evaluate side-chains 1290 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1054 time to evaluate : 6.017 Switching outliers to nearest non-outliers outliers start: 236 outliers final: 164 residues processed: 77 average time/residue: 1.3225 time to fit residues: 177.9987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 4.9990 chunk 842 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 549 optimal weight: 0.6980 chunk 230 optimal weight: 7.9990 chunk 936 optimal weight: 0.7980 chunk 777 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 309 optimal weight: 0.9990 chunk 491 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 25 GLN C 197 ASN C 260 ASN D 37 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN L 89 ASN O 9 GLN O 13 ASN O 32 GLN Q 12 HIS T 9 GLN Z 4 GLN Z 25 ASN b 197 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN p 64 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 149477 Z= 0.204 Angle : 0.706 24.451 223661 Z= 0.370 Chirality : 0.044 2.076 28567 Planarity : 0.006 0.131 11978 Dihedral : 14.815 179.934 59028 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 5.96 % Allowed : 24.61 % Favored : 69.42 % 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: 0.43 (0.11), residues: 5407 helix: 1.50 (0.12), residues: 1864 sheet: 0.40 (0.16), residues: 1026 loop : -0.66 (0.11), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1061 time to evaluate : 5.990 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: 267 outliers final: 189 residues processed: 1237 average time/residue: 2.2911 time to fit residues: 3964.5712 Evaluate side-chains 1224 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1035 time to evaluate : 6.049 Switching outliers to nearest non-outliers outliers start: 189 outliers final: 155 residues processed: 41 average time/residue: 1.3893 time to fit residues: 100.3401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 533 optimal weight: 7.9990 chunk 683 optimal weight: 30.0000 chunk 529 optimal weight: 7.9990 chunk 788 optimal weight: 1.9990 chunk 522 optimal weight: 0.0870 chunk 932 optimal weight: 3.9990 chunk 583 optimal weight: 4.9990 chunk 568 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 260 ASN K 18 HIS O 9 GLN O 13 ASN O 32 GLN Q 43 ASN T 9 GLN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN b 197 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 41 GLN h 42 GLN h 48 ASN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN p 64 GLN r 61 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 149477 Z= 0.284 Angle : 0.780 24.417 223661 Z= 0.401 Chirality : 0.047 2.217 28567 Planarity : 0.007 0.137 11978 Dihedral : 14.875 179.885 59028 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 5.79 % Allowed : 25.40 % Favored : 68.82 % 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: 0.37 (0.11), residues: 5407 helix: 1.43 (0.12), residues: 1842 sheet: 0.37 (0.16), residues: 1029 loop : -0.68 (0.11), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1035 time to evaluate : 6.058 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: 259 outliers final: 206 residues processed: 1200 average time/residue: 2.3342 time to fit residues: 3908.1565 Evaluate side-chains 1241 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1035 time to evaluate : 6.010 Switching outliers to nearest non-outliers outliers start: 206 outliers final: 151 residues processed: 60 average time/residue: 1.4085 time to fit residues: 144.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 4.9990 chunk 372 optimal weight: 0.0050 chunk 557 optimal weight: 0.9980 chunk 281 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 40.0000 chunk 593 optimal weight: 3.9990 chunk 635 optimal weight: 4.9990 chunk 461 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 733 optimal weight: 30.0000 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS O 9 GLN O 13 ASN O 32 GLN Q 43 ASN T 9 GLN Z 4 GLN Z 5 GLN Z 25 ASN b 60 ASN b 197 ASN c 100 GLN c 104 ASN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN h 48 ASN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN p 64 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 149477 Z= 0.301 Angle : 0.797 24.612 223661 Z= 0.408 Chirality : 0.047 2.222 28567 Planarity : 0.007 0.137 11978 Dihedral : 14.872 179.711 59028 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.89 % Rotamer: Outliers : 5.36 % Allowed : 25.89 % Favored : 68.75 % 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: 0.30 (0.11), residues: 5407 helix: 1.37 (0.12), residues: 1849 sheet: 0.32 (0.15), residues: 1041 loop : -0.71 (0.11), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1028 time to evaluate : 6.020 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: 240 outliers final: 194 residues processed: 1202 average time/residue: 2.3516 time to fit residues: 3947.5711 Evaluate side-chains 1215 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1021 time to evaluate : 6.171 Switching outliers to nearest non-outliers outliers start: 194 outliers final: 154 residues processed: 44 average time/residue: 1.5498 time to fit residues: 117.1721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 0.9980 chunk 893 optimal weight: 0.9980 chunk 815 optimal weight: 9.9990 chunk 869 optimal weight: 3.9990 chunk 523 optimal weight: 10.0000 chunk 378 optimal weight: 0.0070 chunk 682 optimal weight: 50.0000 chunk 266 optimal weight: 6.9990 chunk 785 optimal weight: 3.9990 chunk 822 optimal weight: 0.5980 chunk 866 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 153 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 13 ASN O 32 GLN Q 43 ASN T 9 GLN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN c 100 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN h 48 ASN h 53 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN p 64 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 149477 Z= 0.183 Angle : 0.681 24.632 223661 Z= 0.357 Chirality : 0.042 2.084 28567 Planarity : 0.006 0.131 11978 Dihedral : 14.648 179.962 59028 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 4.76 % Allowed : 26.45 % Favored : 68.80 % 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: 0.60 (0.11), residues: 5407 helix: 1.69 (0.12), residues: 1856 sheet: 0.44 (0.15), residues: 1044 loop : -0.58 (0.12), residues: 2507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1020 time to evaluate : 6.147 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 revert: symmetry clash revert: symmetry clash outliers start: 213 outliers final: 178 residues processed: 1180 average time/residue: 2.3414 time to fit residues: 3852.4691 Evaluate side-chains 1194 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1016 time to evaluate : 6.046 Switching outliers to nearest non-outliers outliers start: 178 outliers final: 153 residues processed: 29 average time/residue: 1.5317 time to fit residues: 77.0858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 7.9990 chunk 919 optimal weight: 3.9990 chunk 561 optimal weight: 9.9990 chunk 436 optimal weight: 4.9990 chunk 639 optimal weight: 3.9990 chunk 964 optimal weight: 4.9990 chunk 887 optimal weight: 1.9990 chunk 767 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 593 optimal weight: 3.9990 chunk 470 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: