Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 04:28:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvv_26817/07_2023/7uvv_26817_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.035 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4445 5.49 5 S 140 5.16 5 C 69389 2.51 5 N 25724 2.21 5 O 38595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 36": "OD1" <-> "OD2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O ASP 27": "OD1" <-> "OD2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 105": "OD1" <-> "OD2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 36": "OD1" <-> "OD2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R ASP 65": "OD1" <-> "OD2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R ASP 77": "OD1" <-> "OD2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U ASP 14": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "V ASP 15": "OD1" <-> "OD2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X ASP 5": "OD1" <-> "OD2" Residue "X GLU 12": "OE1" <-> "OE2" Residue "X GLU 13": "OE1" <-> "OE2" Residue "Y GLU 57": "OE1" <-> "OE2" Residue "Z ASP 14": "OD1" <-> "OD2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z ASP 45": "OD1" <-> "OD2" Residue "b TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 84": "OE1" <-> "OE2" Residue "b ASP 95": "OD1" <-> "OD2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b ASP 161": "OD1" <-> "OD2" Residue "b ASP 169": "OD1" <-> "OD2" Residue "b ASP 206": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c ASP 112": "OD1" <-> "OD2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d ASP 101": "OD1" <-> "OD2" Residue "d GLU 162": "OE1" <-> "OE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 204": "OE1" <-> "OE2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f GLU 99": "OE1" <-> "OE2" Residue "g GLU 11": "OE1" <-> "OE2" Residue "g PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 33": "OD1" <-> "OD2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "h GLU 74": "OE1" <-> "OE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 81": "OD1" <-> "OD2" Residue "j ASP 85": "OD1" <-> "OD2" Residue "k PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 109": "OD1" <-> "OD2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "o TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 47": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ASP 71": "OD1" <-> "OD2" Residue "p ASP 73": "OD1" <-> "OD2" Residue "p PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 16": "OD1" <-> "OD2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q GLU 64": "OE1" <-> "OE2" Residue "q GLU 81": "OE1" <-> "OE2" Residue "r ASP 27": "OD1" <-> "OD2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "s ASP 43": "OD1" <-> "OD2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s GLU 73": "OE1" <-> "OE2" Residue "t TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 43": "OD1" <-> "OD2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "u ASP 13": "OD1" <-> "OD2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 138294 Number of models: 1 Model: "" Number of chains: 56 Chain: "0" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} 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: 58438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2724, 58438 Classifications: {'RNA': 2724} Modifications used: {'rna2p': 3, 'rna2p_pur': 264, 'rna2p_pyr': 153, 'rna3p': 12, 'rna3p_pur': 1293, 'rna3p_pyr': 999} Link IDs: {'rna2p': 419, 'rna3p': 2304} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 334 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} 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: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} 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: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 620 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} 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': 115, 'rna2p_pyr': 90, 'rna3p': 8, 'rna3p_pur': 748, 'rna3p_pyr': 566} Link IDs: {'rna2p': 206, 'rna3p': 1321} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p': 3, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 15, 'rna3p': 61} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OI9': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OI9': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1364 SG CYS 3 11 46.599 109.837 140.243 1.00 61.17 S ATOM 1380 SG CYS 3 14 48.194 111.079 137.027 1.00 60.06 S ATOM 1485 SG CYS 3 27 46.435 113.404 139.443 1.00 60.29 S Time building chain proxies: 46.28, per 1000 atoms: 0.33 Number of scatterers: 138294 At special positions: 0 Unit cell: (222.176, 245.072, 275.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 140 16.00 P 4445 15.00 O 38595 8.00 N 25724 7.00 C 69389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 48.81 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10078 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 66 sheets defined 39.3% alpha, 18.9% beta 1488 base pairs and 2290 stacking pairs defined. Time for finding SS restraints: 50.93 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.119A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 31 through 36 removed outlier: 4.794A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 31 through 36' Processing helix chain '2' and resid 37 through 45 removed outlier: 5.600A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.553A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.912A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.922A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.927A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.177A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.495A 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: 4.678A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.550A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.224A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.864A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.994A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.242A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.649A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 11 removed outlier: 5.366A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.096A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.134A 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: 3.933A 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 45 Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.258A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.735A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.743A 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: 3.994A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.471A 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: 3.981A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.689A 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 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.998A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 3.951A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.642A 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: 3.892A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (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: 4.329A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.582A 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: 5.610A 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: 4.477A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.608A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (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: 4.264A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.828A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.745A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.699A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.998A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.977A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.315A 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: 4.216A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 4.133A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.803A pdb=" N ILE S 6 " --> pdb=" O ASN S 2 " (cutoff:3.500A) removed outlier: 4.387A 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: 4.177A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.554A 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: 5.191A 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: 3.766A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.343A 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: 3.702A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.426A 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: 4.152A 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: 3.791A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.916A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.037A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.030A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 4.179A 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 78 through 90 Processing helix chain 'b' and resid 105 through 126 removed outlier: 4.132A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 4.813A 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 227 removed outlier: 4.270A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.819A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.723A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.930A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.152A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.593A 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 removed outlier: 3.627A pdb=" N ALA c 133 " --> pdb=" O MET c 129 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET c 134 " --> pdb=" O PHE c 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.582A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.348A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.707A 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 154 removed outlier: 4.782A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN d 154 " --> pdb=" O GLY d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 168 removed outlier: 4.454A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.996A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.913A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.782A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 3.670A 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 removed outlier: 3.734A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 33 removed outlier: 4.280A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (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: 3.505A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.857A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.581A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 38 removed outlier: 4.878A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.927A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.705A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.967A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.534A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.982A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.607A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 75 removed outlier: 3.543A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN k 63 " --> pdb=" O PRO k 59 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.581A pdb=" N ALA k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.753A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.553A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.775A 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: 3.736A pdb=" N ALA m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 33 removed outlier: 5.209A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 52 Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.597A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.593A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.050A 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: 4.159A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.417A 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 removed outlier: 3.626A pdb=" N GLN r 54 " --> pdb=" O ARG r 50 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.913A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.613A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.578A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 3.537A pdb=" N GLU t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) Proline residue: t 56 - end of helix removed outlier: 3.786A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.818A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.650A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 6.111A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 5.820A 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 5 removed outlier: 6.656A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER 3 28 " --> pdb=" O SER 3 13 " (cutoff:3.500A) removed outlier: 8.448A 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 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.873A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.737A 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: 4.579A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 164 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.032A 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: 5.289A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.198A 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: 4.476A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.613A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.145A 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 85 removed outlier: 5.070A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.481A 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 30 removed outlier: 5.528A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 43 through 46 removed outlier: 7.010A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.068A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 65 through 70 removed outlier: 6.540A pdb=" N VAL F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TRP F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.060A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.144A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 74 through 78 removed outlier: 7.303A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.362A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 39 through 42 Processing sheet with id= 23, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.761A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.037A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.651A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.810A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.880A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.040A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.006A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 31, first strand: chain 'Q' and resid 65 through 74 removed outlier: 3.660A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN Q 87 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 33, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.376A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'T' and resid 38 through 42 removed outlier: 5.412A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 81 through 85 Processing sheet with id= 36, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 37, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= 38, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.681A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.166A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.388A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.364A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 43, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.166A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 28 through 31 removed outlier: 4.088A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.047A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (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: 3.736A 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: 3.639A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 172 through 177 removed outlier: 8.726A 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: 6.766A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.904A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.730A 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 43 removed outlier: 5.520A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 44 through 47 removed outlier: 7.057A 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: 6.645A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.682A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.660A 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: 4.226A pdb=" N LYS i 58 " --> pdb=" O GLY i 22 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 59, first strand: chain 'j' and resid 42 through 53 removed outlier: 5.322A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.210A pdb=" N SER k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.226A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.936A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.702A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 8 through 12 removed outlier: 6.958A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 's' and resid 30 through 34 removed outlier: 4.490A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1878 hydrogen bonds defined for protein. 5550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3720 hydrogen bonds 5828 hydrogen bond angles 0 basepair planarities 1488 basepair parallelities 2290 stacking parallelities Total time for adding SS restraints: 220.33 Time building geometry restraints manager: 53.38 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: 13179 1.31 - 1.44: 66693 1.44 - 1.56: 61277 1.56 - 1.69: 8889 1.69 - 1.82: 249 Bond restraints: 150287 Sorted by residual: bond pdb=" C22 OI9 a1601 " pdb=" C23 OI9 a1601 " ideal model delta sigma weight residual 2.106 1.520 0.586 2.00e-02 2.50e+03 8.60e+02 bond pdb=" C22 OI9 A3001 " pdb=" C23 OI9 A3001 " ideal model delta sigma weight residual 2.106 1.523 0.583 2.00e-02 2.50e+03 8.49e+02 bond pdb=" C22 OI9 A3001 " pdb=" C24 OI9 A3001 " ideal model delta sigma weight residual 1.022 1.504 -0.482 2.00e-02 2.50e+03 5.82e+02 bond pdb=" C22 OI9 a1601 " pdb=" C24 OI9 a1601 " ideal model delta sigma weight residual 1.022 1.495 -0.473 2.00e-02 2.50e+03 5.59e+02 bond pdb=" C25 OI9 a1601 " pdb=" N12 OI9 a1601 " ideal model delta sigma weight residual 1.748 1.321 0.427 2.00e-02 2.50e+03 4.56e+02 ... (remaining 150282 not shown) Histogram of bond angle deviations from ideal: 97.39 - 107.69: 32732 107.69 - 117.98: 109452 117.98 - 128.28: 76084 128.28 - 138.58: 6653 138.58 - 148.88: 1 Bond angle restraints: 224922 Sorted by residual: angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 148.88 -22.65 3.00e+00 1.11e-01 5.70e+01 angle pdb=" CA MET b 8 " pdb=" CB MET b 8 " pdb=" CG MET b 8 " ideal model delta sigma weight residual 114.10 128.73 -14.63 2.00e+00 2.50e-01 5.35e+01 angle pdb=" CA ARG b 9 " pdb=" CB ARG b 9 " pdb=" CG ARG b 9 " ideal model delta sigma weight residual 114.10 127.89 -13.79 2.00e+00 2.50e-01 4.76e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 127.81 -19.52 3.00e+00 1.11e-01 4.23e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C4 6MZ A2026 " ideal model delta sigma weight residual 121.46 103.49 17.97 3.00e+00 1.11e-01 3.59e+01 ... (remaining 224917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 76962 35.96 - 71.93: 2906 71.93 - 107.89: 205 107.89 - 143.85: 18 143.85 - 179.81: 62 Dihedral angle restraints: 80153 sinusoidal: 64504 harmonic: 15649 Sorted by residual: dihedral pdb=" O4' C A 434 " pdb=" C1' C A 434 " pdb=" N1 C A 434 " pdb=" C2 C A 434 " ideal model delta sinusoidal sigma weight residual 200.00 33.33 166.67 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C A 715 " pdb=" C1' C A 715 " pdb=" N1 C A 715 " pdb=" C2 C A 715 " ideal model delta sinusoidal sigma weight residual -160.00 4.81 -164.81 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U A2550 " pdb=" C1' U A2550 " pdb=" N1 U A2550 " pdb=" C2 U A2550 " ideal model delta sinusoidal sigma weight residual 200.00 39.17 160.83 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 80150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 28623 0.157 - 0.314: 132 0.314 - 0.470: 1 0.470 - 0.627: 0 0.627 - 0.784: 2 Chirality restraints: 28758 Sorted by residual: chirality pdb=" C24 OI9 a1601 " pdb=" C22 OI9 a1601 " pdb=" C27 OI9 a1601 " pdb=" O04 OI9 a1601 " both_signs ideal model delta sigma weight residual False -1.93 -2.72 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C24 OI9 A3001 " pdb=" C22 OI9 A3001 " pdb=" C27 OI9 A3001 " pdb=" O04 OI9 A3001 " both_signs ideal model delta sigma weight residual False -1.93 -2.66 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C1* PSU A2576 " pdb=" O4* PSU A2576 " pdb=" C2* PSU A2576 " pdb=" C5 PSU A2576 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 28755 not shown) Planarity restraints: 11996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " -0.073 2.00e-02 2.50e+03 6.20e-01 8.64e+03 pdb=" C4' 7MG A2065 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " -0.666 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " 0.598 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " 0.669 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " 0.166 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " -1.003 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " -0.209 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " 0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.058 2.00e-02 2.50e+03 5.90e-01 7.83e+03 pdb=" C4' 2MG a1204 " 0.430 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.622 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.601 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.618 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.187 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.966 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.222 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.893 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.018 2.00e-02 2.50e+03 5.81e-01 7.58e+03 pdb=" C4' 2MG A2441 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.714 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.553 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.231 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.878 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.211 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.898 2.00e-02 2.50e+03 ... (remaining 11993 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 564 2.57 - 3.16: 98339 3.16 - 3.74: 256692 3.74 - 4.32: 376841 4.32 - 4.90: 498256 Nonbonded interactions: 1230692 Sorted by model distance: nonbonded pdb=" O VAL D 30 " pdb=" OG SER D 188 " model vdw 1.993 2.440 nonbonded pdb=" OG SER e 159 " pdb=" OE1 GLU e 161 " model vdw 2.047 2.440 nonbonded pdb=" OG1 THR F 162 " pdb=" OD1 ASP F 164 " model vdw 2.089 2.440 nonbonded pdb=" O2' G a 207 " pdb=" O4' G a 208 " model vdw 2.114 2.440 nonbonded pdb=" O2' 4SU v 8 " pdb=" O2 C v 49 " model vdw 2.123 2.440 ... (remaining 1230687 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: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.620 Construct map_model_manager: 0.120 Extract box with map and model: 33.400 Check model and map are aligned: 1.470 Set scattering table: 0.900 Process input model: 476.090 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.400 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: 0.040 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 533.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 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 0.586 150287 Z= 0.410 Angle : 0.655 22.653 224922 Z= 0.345 Chirality : 0.039 0.784 28758 Planarity : 0.016 0.620 11996 Dihedral : 15.522 179.813 70075 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 5402 helix: 1.76 (0.12), residues: 1839 sheet: 0.77 (0.16), residues: 1022 loop : -0.56 (0.11), residues: 2541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1050 time to evaluate : 5.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 91 residues processed: 1143 average time/residue: 2.1389 time to fit residues: 3462.8363 Evaluate side-chains 1122 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1031 time to evaluate : 5.775 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 79 residues processed: 13 average time/residue: 1.3786 time to fit residues: 35.4441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 819 optimal weight: 1.9990 chunk 735 optimal weight: 20.0000 chunk 408 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 393 optimal weight: 0.8980 chunk 761 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 566 optimal weight: 8.9990 chunk 881 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 4 GLN C 198 GLN E 141 ASN G 64 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN g 142 HIS h 18 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 112 GLN p 95 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 150287 Z= 0.344 Angle : 0.673 16.513 224922 Z= 0.363 Chirality : 0.041 0.347 28758 Planarity : 0.006 0.137 11996 Dihedral : 14.206 179.510 59373 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.83 % Favored : 97.02 % Rotamer Outliers : 6.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 5402 helix: 1.90 (0.12), residues: 1836 sheet: 0.82 (0.16), residues: 1001 loop : -0.61 (0.11), residues: 2565 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1039 time to evaluate : 5.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 285 outliers final: 168 residues processed: 1201 average time/residue: 2.1629 time to fit residues: 3714.5654 Evaluate side-chains 1191 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1023 time to evaluate : 5.186 Switching outliers to nearest non-outliers outliers start: 168 outliers final: 102 residues processed: 66 average time/residue: 1.3355 time to fit residues: 152.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 490 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 733 optimal weight: 7.9990 chunk 600 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 883 optimal weight: 6.9990 chunk 954 optimal weight: 3.9990 chunk 786 optimal weight: 9.9990 chunk 876 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 708 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 4 GLN C 198 GLN E 141 ASN G 64 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN g 54 ASN h 18 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 112 GLN p 95 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 150287 Z= 0.318 Angle : 0.650 14.165 224922 Z= 0.352 Chirality : 0.040 0.344 28758 Planarity : 0.006 0.137 11996 Dihedral : 14.153 179.961 59373 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.76 % Favored : 97.09 % Rotamer Outliers : 6.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 5402 helix: 1.97 (0.12), residues: 1838 sheet: 0.81 (0.16), residues: 1003 loop : -0.61 (0.11), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1050 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 292 outliers final: 185 residues processed: 1222 average time/residue: 2.1326 time to fit residues: 3704.4626 Evaluate side-chains 1206 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1021 time to evaluate : 5.782 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 116 residues processed: 69 average time/residue: 1.3012 time to fit residues: 159.9970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 872 optimal weight: 9.9990 chunk 664 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 421 optimal weight: 0.3980 chunk 593 optimal weight: 10.0000 chunk 886 optimal weight: 3.9990 chunk 938 optimal weight: 5.9990 chunk 463 optimal weight: 1.9990 chunk 840 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 198 GLN E 141 ASN H 33 GLN J 89 ASN K 125 GLN N 35 HIS O 9 GLN Q 43 ASN Q 46 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN i 35 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 112 GLN m 8 ASN p 95 GLN r 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 150287 Z= 0.281 Angle : 0.630 13.673 224922 Z= 0.343 Chirality : 0.039 0.342 28758 Planarity : 0.006 0.135 11996 Dihedral : 14.088 179.166 59373 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.85 % Favored : 97.02 % Rotamer Outliers : 6.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.11), residues: 5402 helix: 2.04 (0.12), residues: 1839 sheet: 0.84 (0.16), residues: 986 loop : -0.59 (0.11), residues: 2577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1035 time to evaluate : 5.827 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: 274 outliers final: 182 residues processed: 1193 average time/residue: 2.1269 time to fit residues: 3619.3251 Evaluate side-chains 1193 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1011 time to evaluate : 5.807 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 122 residues processed: 60 average time/residue: 1.3354 time to fit residues: 140.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 781 optimal weight: 0.8980 chunk 532 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 698 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 800 optimal weight: 4.9990 chunk 648 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 479 optimal weight: 10.0000 chunk 842 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 19 ASN C 4 GLN C 198 GLN E 141 ASN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 13 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN h 18 GLN k 118 ASN l 112 GLN p 95 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 150287 Z= 0.388 Angle : 0.692 14.074 224922 Z= 0.371 Chirality : 0.042 0.363 28758 Planarity : 0.006 0.141 11996 Dihedral : 14.179 179.590 59373 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer Outliers : 6.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5402 helix: 1.89 (0.12), residues: 1838 sheet: 0.77 (0.16), residues: 1002 loop : -0.67 (0.11), residues: 2562 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1021 time to evaluate : 5.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 279 outliers final: 193 residues processed: 1191 average time/residue: 2.0949 time to fit residues: 3570.3606 Evaluate side-chains 1203 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1010 time to evaluate : 5.692 Switching outliers to nearest non-outliers outliers start: 193 outliers final: 127 residues processed: 66 average time/residue: 1.2975 time to fit residues: 151.2769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 315 optimal weight: 2.9990 chunk 845 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 551 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 939 optimal weight: 3.9990 chunk 779 optimal weight: 9.9990 chunk 434 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 310 optimal weight: 0.7980 chunk 493 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 4 GLN C 198 GLN E 141 ASN G 64 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN k 118 ASN l 112 GLN p 95 GLN u 43 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.110 150287 Z= 0.212 Angle : 0.617 13.685 224922 Z= 0.339 Chirality : 0.038 0.342 28758 Planarity : 0.006 0.132 11996 Dihedral : 14.119 179.634 59373 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer Outliers : 5.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 5402 helix: 2.04 (0.12), residues: 1837 sheet: 0.86 (0.16), residues: 989 loop : -0.61 (0.11), residues: 2576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1019 time to evaluate : 5.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 162 residues processed: 1169 average time/residue: 2.1581 time to fit residues: 3622.2889 Evaluate side-chains 1165 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1003 time to evaluate : 5.755 Switching outliers to nearest non-outliers outliers start: 162 outliers final: 127 residues processed: 36 average time/residue: 1.4224 time to fit residues: 89.7852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 905 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 535 optimal weight: 5.9990 chunk 686 optimal weight: 10.0000 chunk 531 optimal weight: 6.9990 chunk 790 optimal weight: 10.0000 chunk 524 optimal weight: 0.8980 chunk 935 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 570 optimal weight: 9.9990 chunk 432 optimal weight: 4.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN E 114 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN h 18 GLN l 112 GLN m 8 ASN p 36 GLN p 95 GLN u 43 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 150287 Z= 0.303 Angle : 0.642 14.227 224922 Z= 0.349 Chirality : 0.039 0.343 28758 Planarity : 0.006 0.136 11996 Dihedral : 14.084 179.268 59373 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5402 helix: 2.00 (0.12), residues: 1837 sheet: 0.77 (0.16), residues: 1001 loop : -0.63 (0.11), residues: 2564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1010 time to evaluate : 5.845 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: 221 outliers final: 171 residues processed: 1160 average time/residue: 2.1635 time to fit residues: 3600.9536 Evaluate side-chains 1174 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1003 time to evaluate : 5.715 Switching outliers to nearest non-outliers outliers start: 171 outliers final: 127 residues processed: 44 average time/residue: 1.2736 time to fit residues: 102.5618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 578 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 558 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 595 optimal weight: 10.0000 chunk 637 optimal weight: 8.9990 chunk 462 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 735 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN G 64 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN g 142 HIS i 48 GLN l 112 GLN m 8 ASN p 36 GLN p 95 GLN r 31 GLN u 43 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 150287 Z= 0.429 Angle : 0.719 15.870 224922 Z= 0.383 Chirality : 0.044 0.380 28758 Planarity : 0.007 0.143 11996 Dihedral : 14.212 179.870 59373 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.46 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5402 helix: 1.84 (0.12), residues: 1824 sheet: 0.63 (0.16), residues: 1050 loop : -0.73 (0.11), residues: 2528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1015 time to evaluate : 6.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 222 outliers final: 169 residues processed: 1171 average time/residue: 2.1471 time to fit residues: 3623.3025 Evaluate side-chains 1173 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1004 time to evaluate : 5.719 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 129 residues processed: 40 average time/residue: 1.2145 time to fit residues: 91.0434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 851 optimal weight: 1.9990 chunk 896 optimal weight: 6.9990 chunk 818 optimal weight: 10.0000 chunk 872 optimal weight: 5.9990 chunk 524 optimal weight: 9.9990 chunk 379 optimal weight: 0.9990 chunk 684 optimal weight: 50.0000 chunk 267 optimal weight: 5.9990 chunk 788 optimal weight: 10.0000 chunk 824 optimal weight: 0.7980 chunk 869 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN G 64 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN e 120 HIS h 18 GLN h 42 GLN i 48 GLN l 112 GLN m 8 ASN p 95 GLN r 31 GLN u 43 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 150287 Z= 0.244 Angle : 0.622 16.385 224922 Z= 0.340 Chirality : 0.038 0.347 28758 Planarity : 0.006 0.133 11996 Dihedral : 14.044 179.516 59373 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.11), residues: 5402 helix: 1.99 (0.12), residues: 1836 sheet: 0.77 (0.16), residues: 999 loop : -0.65 (0.11), residues: 2567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1014 time to evaluate : 5.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 171 outliers final: 141 residues processed: 1156 average time/residue: 2.0829 time to fit residues: 3460.1983 Evaluate side-chains 1145 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1004 time to evaluate : 5.753 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 129 residues processed: 12 average time/residue: 1.5704 time to fit residues: 35.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 572 optimal weight: 5.9990 chunk 922 optimal weight: 10.0000 chunk 562 optimal weight: 9.9990 chunk 437 optimal weight: 2.9990 chunk 641 optimal weight: 10.0000 chunk 967 optimal weight: 10.0000 chunk 890 optimal weight: 10.0000 chunk 770 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 595 optimal weight: 10.0000 chunk 472 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 19 ASN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN S 29 GLN X 21 GLN b 13 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN i 48 GLN l 112 GLN m 8 ASN p 95 GLN r 31 GLN u 43 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.143 150287 Z= 0.307 Angle : 0.651 16.638 224922 Z= 0.352 Chirality : 0.039 0.344 28758 Planarity : 0.006 0.137 11996 Dihedral : 14.053 179.138 59373 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 5402 helix: 1.94 (0.12), residues: 1830 sheet: 0.69 (0.16), residues: 1053 loop : -0.67 (0.11), residues: 2519 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1002 time to evaluate : 5.195 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 outliers start: 166 outliers final: 144 residues processed: 1140 average time/residue: 2.1176 time to fit residues: 3462.2885 Evaluate side-chains 1138 residues out of total 4473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 994 time to evaluate : 5.740 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 129 residues processed: 15 average time/residue: 1.3388 time to fit residues: 39.9214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 971 random chunks: chunk 611 optimal weight: 7.9990 chunk 820 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 710 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 771 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 chunk 792 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN H 33 GLN J 89 ASN K 125 GLN O 9 GLN Q 43 ASN Q 86 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 GLN X 44 GLN b 13 GLN b 85 GLN c 21 ASN c 28 GLN e 42 ASN h 18 GLN i 48 GLN l 111 ASN l 112 GLN m 8 ASN p 95 GLN u 43 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.054250 restraints weight = 263282.164| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 0.95 r_work: 0.2578 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.124 150287 Z= 0.475 Angle : 0.748 16.557 224922 Z= 0.396 Chirality : 0.045 0.401 28758 Planarity : 0.007 0.144 11996 Dihedral : 14.232 179.877 59373 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.35 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5402 helix: 1.71 (0.12), residues: 1822 sheet: 0.52 (0.16), residues: 1079 loop : -0.78 (0.11), residues: 2501 =============================================================================== Job complete usr+sys time: 48736.44 seconds wall clock time: 843 minutes 0.09 seconds (50580.09 seconds total)