Starting phenix.real_space_refine on Sat Jan 20 04:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/01_2024/8cst_26970_neut_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 sd= 1.235 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 4 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 895 5.49 5 Mg 30 5.21 5 S 240 5.16 5 C 38643 2.51 5 N 11920 2.21 5 O 14610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 23": "OE1" <-> "OE2" Residue "0 GLU 91": "OE1" <-> "OE2" Residue "0 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 148": "OE1" <-> "OE2" Residue "0 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 132": "OE1" <-> "OE2" Residue "1 ASP 140": "OD1" <-> "OD2" Residue "1 ASP 203": "OD1" <-> "OD2" Residue "1 TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 232": "OE1" <-> "OE2" Residue "1 GLU 240": "OE1" <-> "OE2" Residue "1 GLU 290": "OE1" <-> "OE2" Residue "1 GLU 306": "OE1" <-> "OE2" Residue "1 GLU 314": "OE1" <-> "OE2" Residue "3 ASP 172": "OD1" <-> "OD2" Residue "3 GLU 184": "OE1" <-> "OE2" Residue "4 ASP 66": "OD1" <-> "OD2" Residue "4 GLU 114": "OE1" <-> "OE2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 GLU 186": "OE1" <-> "OE2" Residue "4 TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 256": "OE1" <-> "OE2" Residue "4 GLU 273": "OE1" <-> "OE2" Residue "4 ASP 290": "OD1" <-> "OD2" Residue "4 GLU 310": "OE1" <-> "OE2" Residue "4 GLU 311": "OE1" <-> "OE2" Residue "4 GLU 318": "OE1" <-> "OE2" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 GLU 366": "OE1" <-> "OE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 451": "OD1" <-> "OD2" Residue "4 ASP 472": "OD1" <-> "OD2" Residue "4 GLU 479": "OE1" <-> "OE2" Residue "4 PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 560": "OE1" <-> "OE2" Residue "4 PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 609": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 ASP 201": "OD1" <-> "OD2" Residue "7 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 84": "OE1" <-> "OE2" Residue "7 GLU 105": "OE1" <-> "OE2" Residue "7 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 147": "OE1" <-> "OE2" Residue "7 ASP 191": "OD1" <-> "OD2" Residue "7 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 308": "OD1" <-> "OD2" Residue "7 GLU 318": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 105": "OD1" <-> "OD2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "M ASP 71": "OD1" <-> "OD2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 63": "OE1" <-> "OE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O GLU 210": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 74": "OE1" <-> "OE2" Residue "R TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 144": "OE1" <-> "OE2" Residue "R GLU 212": "OE1" <-> "OE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "S GLU 7": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 86": "OD1" <-> "OD2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "T TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "T GLU 117": "OE1" <-> "OE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "T GLU 158": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "U GLU 118": "OE1" <-> "OE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 145": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U GLU 156": "OE1" <-> "OE2" Residue "U GLU 174": "OE1" <-> "OE2" Residue "U GLU 178": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 140": "OD1" <-> "OD2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 149": "OD1" <-> "OD2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "V PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 199": "OE1" <-> "OE2" Residue "V GLU 200": "OE1" <-> "OE2" Residue "V ASP 272": "OD1" <-> "OD2" Residue "V GLU 278": "OE1" <-> "OE2" Residue "V ASP 318": "OD1" <-> "OD2" Residue "V GLU 368": "OE1" <-> "OE2" Residue "V GLU 398": "OE1" <-> "OE2" Residue "V TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W ASP 159": "OD1" <-> "OD2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X ASP 74": "OD1" <-> "OD2" Residue "X GLU 196": "OE1" <-> "OE2" Residue "X GLU 224": "OE1" <-> "OE2" Residue "X GLU 277": "OE1" <-> "OE2" Residue "X ASP 338": "OD1" <-> "OD2" Residue "X PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 291": "OE1" <-> "OE2" Residue "Y GLU 307": "OE1" <-> "OE2" Residue "Y GLU 312": "OE1" <-> "OE2" Residue "Y GLU 318": "OE1" <-> "OE2" Residue "Y ASP 322": "OD1" <-> "OD2" Residue "Y GLU 335": "OE1" <-> "OE2" Residue "Y PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 352": "OE1" <-> "OE2" Residue "Y TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66351 Number of models: 1 Model: "" Number of chains: 39 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2098 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "3" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 625 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "6" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "7" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3160 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 18866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 888, 18866 Classifications: {'RNA': 888} Modifications used: {'rna2p_pur': 69, 'rna2p_pyr': 72, 'rna3p': 2, 'rna3p_pur': 394, 'rna3p_pyr': 351} Link IDs: {'rna2p': 140, 'rna3p': 747} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 858 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1696 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "G" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2395 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain breaks: 1 Chain: "I" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1019 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "J" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 10, 'TRANS': 96} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1363 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "Q" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 744 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Z" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 76 Unusual residues: {' K': 4, ' MG': 28, 'NAD': 1} Classifications: {'undetermined': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12924 SG CYS 7 404 97.009 111.460 159.233 1.00 38.79 S ATOM 12445 SG CYS 7 347 99.919 106.909 155.052 1.00 31.45 S ATOM 12340 SG CYS 7 333 93.502 108.324 155.092 1.00 33.13 S ATOM 12387 SG CYS 7 339 98.439 112.384 153.730 1.00 37.02 S ATOM 49001 SG CYS O 94 111.518 163.006 97.500 1.00 48.32 S ATOM 49087 SG CYS O 105 114.488 163.485 95.180 1.00 45.48 S ATOM 49108 SG CYS O 108 113.207 166.427 97.131 1.00 48.35 S ATOM 49396 SG CYS O 143 111.044 165.000 94.343 1.00 41.78 S ATOM 50319 SG CYS P 65 124.945 74.490 53.134 1.00 55.17 S ATOM 50592 SG CYS P 100 122.373 77.380 53.832 1.00 48.44 S ATOM 37581 SG CYS E 105 125.044 80.097 49.948 1.00 74.38 S ATOM 50341 SG CYS P 68 126.517 76.475 49.175 1.00 57.46 S ATOM 46946 SG CYS M 26 90.572 173.926 75.224 1.00 41.84 S ATOM 56382 SG CYS T 149 94.062 174.256 75.932 1.00 46.82 S ATOM 56310 SG CYS T 139 93.545 175.310 69.799 1.00 43.43 S ATOM 56324 SG CYS T 141 96.326 175.343 72.355 1.00 42.28 S Time building chain proxies: 26.50, per 1000 atoms: 0.40 Number of scatterers: 66351 At special positions: 0 Unit cell: (224.082, 244.26, 220.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 8 26.01 K 4 19.00 S 240 16.00 P 895 15.00 Mg 30 11.99 O 14610 8.00 N 11920 7.00 C 38643 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: 23.72 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb=" SF4 7 501 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " Number of angles added : 6 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11046 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 244 helices and 35 sheets defined 46.6% alpha, 9.0% beta 250 base pairs and 445 stacking pairs defined. Time for finding SS restraints: 26.01 Creating SS restraints... Processing helix chain '0' and resid 10 through 25 Processing helix chain '0' and resid 30 through 33 No H-bonds generated for 'chain '0' and resid 30 through 33' Processing helix chain '0' and resid 52 through 59 removed outlier: 4.655A pdb=" N ALA 0 56 " --> pdb=" O VAL 0 52 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP 0 57 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.594A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 75 Processing helix chain '0' and resid 83 through 88 Processing helix chain '0' and resid 144 through 151 removed outlier: 5.332A pdb=" N GLU 0 148 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR 0 151 " --> pdb=" O GLU 0 148 " (cutoff:3.500A) Processing helix chain '0' and resid 168 through 180 Processing helix chain '0' and resid 207 through 209 No H-bonds generated for 'chain '0' and resid 207 through 209' Processing helix chain '1' and resid 56 through 59 Processing helix chain '1' and resid 66 through 69 No H-bonds generated for 'chain '1' and resid 66 through 69' Processing helix chain '1' and resid 103 through 107 Processing helix chain '1' and resid 116 through 129 removed outlier: 3.507A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 removed outlier: 3.751A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 169 removed outlier: 3.719A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 166 through 169' Processing helix chain '1' and resid 177 through 179 No H-bonds generated for 'chain '1' and resid 177 through 179' Processing helix chain '1' and resid 184 through 197 removed outlier: 6.790A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG 1 197 " --> pdb=" O LEU 1 193 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 233 Processing helix chain '1' and resid 238 through 242 Processing helix chain '1' and resid 245 through 247 No H-bonds generated for 'chain '1' and resid 245 through 247' Processing helix chain '1' and resid 257 through 272 Processing helix chain '1' and resid 287 through 301 Processing helix chain '1' and resid 306 through 320 Processing helix chain '3' and resid 130 through 149 Processing helix chain '3' and resid 151 through 180 removed outlier: 3.513A pdb=" N LYS 3 156 " --> pdb=" O PHE 3 152 " (cutoff:3.500A) Processing helix chain '4' and resid 69 through 77 Processing helix chain '4' and resid 100 through 123 Processing helix chain '4' and resid 125 through 127 No H-bonds generated for 'chain '4' and resid 125 through 127' Processing helix chain '4' and resid 138 through 140 No H-bonds generated for 'chain '4' and resid 138 through 140' Processing helix chain '4' and resid 154 through 162 Processing helix chain '4' and resid 166 through 178 Processing helix chain '4' and resid 185 through 198 Processing helix chain '4' and resid 243 through 250 Processing helix chain '4' and resid 256 through 268 Processing helix chain '4' and resid 272 through 284 Processing helix chain '4' and resid 291 through 303 Processing helix chain '4' and resid 309 through 325 Processing helix chain '4' and resid 332 through 363 removed outlier: 4.301A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER 4 351 " --> pdb=" O VAL 4 347 " (cutoff:3.500A) Proline residue: 4 352 - end of helix Processing helix chain '4' and resid 369 through 379 Processing helix chain '4' and resid 392 through 400 Processing helix chain '4' and resid 410 through 426 removed outlier: 4.316A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU 4 426 " --> pdb=" O CYS 4 423 " (cutoff:3.500A) Processing helix chain '4' and resid 429 through 440 Processing helix chain '4' and resid 444 through 448 Processing helix chain '4' and resid 451 through 468 Processing helix chain '4' and resid 471 through 481 Processing helix chain '4' and resid 490 through 503 Processing helix chain '4' and resid 506 through 518 removed outlier: 3.990A pdb=" N ILE 4 509 " --> pdb=" O LEU 4 506 " (cutoff:3.500A) Proline residue: 4 510 - end of helix Processing helix chain '4' and resid 525 through 536 Processing helix chain '4' and resid 542 through 560 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 589 through 602 removed outlier: 3.823A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 621 Processing helix chain '4' and resid 624 through 636 Processing helix chain '4' and resid 640 through 652 removed outlier: 3.731A pdb=" N GLU 4 643 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 657 through 666 Processing helix chain '6' and resid 44 through 49 Processing helix chain '6' and resid 91 through 108 Processing helix chain '6' and resid 115 through 120 removed outlier: 3.524A pdb=" N LEU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 169 removed outlier: 5.049A pdb=" N ALA 6 161 " --> pdb=" O GLN 6 157 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N HIS 6 162 " --> pdb=" O ARG 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 187 through 197 Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '7' and resid 65 through 74 Processing helix chain '7' and resid 81 through 96 removed outlier: 3.541A pdb=" N ASN 7 85 " --> pdb=" O PRO 7 81 " (cutoff:3.500A) Processing helix chain '7' and resid 103 through 116 Processing helix chain '7' and resid 133 through 139 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.239A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 207 Processing helix chain '7' and resid 221 through 231 Processing helix chain '7' and resid 268 through 270 No H-bonds generated for 'chain '7' and resid 268 through 270' Processing helix chain '7' and resid 274 through 287 Processing helix chain '7' and resid 300 through 314 Processing helix chain '7' and resid 417 through 420 No H-bonds generated for 'chain '7' and resid 417 through 420' Processing helix chain '7' and resid 422 through 430 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 81 through 86 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 100 through 105 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.645A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.562A pdb=" N SER B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 243 through 273 Processing helix chain 'C' and resid 21 through 24 No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 129 through 147 Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.834A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.583A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 removed outlier: 3.938A pdb=" N ARG F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 52' Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.570A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 133 through 136 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 176 through 191 removed outlier: 3.617A pdb=" N MET F 184 " --> pdb=" O ARG F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.648A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 Processing helix chain 'F' and resid 236 through 239 Processing helix chain 'G' and resid 71 through 91 Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 128 through 131 No H-bonds generated for 'chain 'G' and resid 128 through 131' Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'G' and resid 156 through 174 Processing helix chain 'G' and resid 202 through 209 Processing helix chain 'G' and resid 215 through 230 Processing helix chain 'G' and resid 235 through 244 removed outlier: 3.949A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 303 No H-bonds generated for 'chain 'G' and resid 300 through 303' Processing helix chain 'G' and resid 307 through 319 Proline residue: G 316 - end of helix Processing helix chain 'G' and resid 337 through 355 removed outlier: 4.433A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 366 Processing helix chain 'H' and resid 85 through 102 Processing helix chain 'H' and resid 150 through 162 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'I' and resid 119 through 123 Processing helix chain 'I' and resid 125 through 142 removed outlier: 3.960A pdb=" N LYS I 142 " --> pdb=" O ARG I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 168 removed outlier: 4.491A pdb=" N LEU I 159 " --> pdb=" O PRO I 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER I 160 " --> pdb=" O GLY I 157 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA I 161 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 39 Processing helix chain 'K' and resid 32 through 46 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.746A pdb=" N ARG K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 removed outlier: 3.688A pdb=" N VAL K 70 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'K' and resid 108 through 116 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 87 through 92 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 100 through 115 Processing helix chain 'L' and resid 125 through 145 removed outlier: 3.877A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 173 Processing helix chain 'L' and resid 175 through 185 Processing helix chain 'L' and resid 201 through 224 Processing helix chain 'M' and resid 70 through 78 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 101 through 123 Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 106 through 109 No H-bonds generated for 'chain 'O' and resid 106 through 109' Processing helix chain 'O' and resid 120 through 126 removed outlier: 3.775A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 140 No H-bonds generated for 'chain 'O' and resid 137 through 140' Processing helix chain 'O' and resid 144 through 159 Processing helix chain 'O' and resid 191 through 195 Processing helix chain 'O' and resid 201 through 203 No H-bonds generated for 'chain 'O' and resid 201 through 203' Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'P' and resid 77 through 83 removed outlier: 3.755A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 97 No H-bonds generated for 'chain 'P' and resid 94 through 97' Processing helix chain 'P' and resid 101 through 117 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'Q' and resid 19 through 32 Processing helix chain 'Q' and resid 35 through 41 Processing helix chain 'Q' and resid 48 through 75 Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 87 through 90 No H-bonds generated for 'chain 'R' and resid 87 through 90' Processing helix chain 'R' and resid 108 through 125 Processing helix chain 'R' and resid 146 through 148 No H-bonds generated for 'chain 'R' and resid 146 through 148' Processing helix chain 'R' and resid 186 through 196 Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 212 through 220 Processing helix chain 'R' and resid 224 through 234 Processing helix chain 'R' and resid 240 through 256 Processing helix chain 'R' and resid 259 through 262 Processing helix chain 'R' and resid 268 through 277 Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 307 Processing helix chain 'R' and resid 312 through 320 Processing helix chain 'R' and resid 324 through 334 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 21 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 4.088A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'T' and resid 8 through 11 Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 39 through 50 removed outlier: 4.913A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE T 50 " --> pdb=" O PHE T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 58 Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 110 through 123 removed outlier: 3.892A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 142 No H-bonds generated for 'chain 'T' and resid 140 through 142' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 161 through 163 No H-bonds generated for 'chain 'T' and resid 161 through 163' Processing helix chain 'U' and resid 50 through 85 Processing helix chain 'U' and resid 90 through 166 removed outlier: 3.858A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASN U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'V' and resid 38 through 41 No H-bonds generated for 'chain 'V' and resid 38 through 41' Processing helix chain 'V' and resid 50 through 62 Processing helix chain 'V' and resid 69 through 77 Processing helix chain 'V' and resid 82 through 96 removed outlier: 3.617A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 103 No H-bonds generated for 'chain 'V' and resid 101 through 103' Processing helix chain 'V' and resid 106 through 118 Processing helix chain 'V' and resid 122 through 130 Processing helix chain 'V' and resid 132 through 135 No H-bonds generated for 'chain 'V' and resid 132 through 135' Processing helix chain 'V' and resid 141 through 153 Processing helix chain 'V' and resid 157 through 170 Processing helix chain 'V' and resid 176 through 192 removed outlier: 4.078A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 214 Proline residue: V 211 - end of helix removed outlier: 3.920A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 238 Processing helix chain 'V' and resid 240 through 244 Processing helix chain 'V' and resid 255 through 268 Processing helix chain 'V' and resid 277 through 290 Processing helix chain 'V' and resid 323 through 344 Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 352 through 405 removed outlier: 5.314A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 85 Processing helix chain 'W' and resid 88 through 92 Processing helix chain 'W' and resid 131 through 133 No H-bonds generated for 'chain 'W' and resid 131 through 133' Processing helix chain 'X' and resid 56 through 58 No H-bonds generated for 'chain 'X' and resid 56 through 58' Processing helix chain 'X' and resid 61 through 63 No H-bonds generated for 'chain 'X' and resid 61 through 63' Processing helix chain 'X' and resid 72 through 78 Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.589A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 113 Processing helix chain 'X' and resid 134 through 147 Processing helix chain 'X' and resid 160 through 162 No H-bonds generated for 'chain 'X' and resid 160 through 162' Processing helix chain 'X' and resid 181 through 194 removed outlier: 3.588A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 198 through 201 No H-bonds generated for 'chain 'X' and resid 198 through 201' Processing helix chain 'X' and resid 222 through 231 Processing helix chain 'X' and resid 233 through 253 removed outlier: 5.109A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER X 251 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 267 No H-bonds generated for 'chain 'X' and resid 265 through 267' Processing helix chain 'X' and resid 284 through 286 No H-bonds generated for 'chain 'X' and resid 284 through 286' Processing helix chain 'X' and resid 288 through 297 removed outlier: 3.849A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 7.135A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 362 Processing helix chain 'X' and resid 374 through 384 Processing helix chain 'X' and resid 388 through 396 Processing helix chain 'Y' and resid 277 through 290 removed outlier: 3.673A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 307 Processing helix chain 'Y' and resid 323 through 325 No H-bonds generated for 'chain 'Y' and resid 323 through 325' Processing helix chain 'Y' and resid 328 through 332 removed outlier: 3.863A pdb=" N ILE Y 332 " --> pdb=" O HIS Y 329 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 360 removed outlier: 3.587A pdb=" N LYS Y 360 " --> pdb=" O CYS Y 356 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 382 Processing helix chain 'Z' and resid 6 through 18 removed outlier: 3.524A pdb=" N ARG Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 38 removed outlier: 3.530A pdb=" N SER Z 38 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 44 No H-bonds generated for 'chain 'Z' and resid 42 through 44' Processing helix chain 'Z' and resid 57 through 67 removed outlier: 3.587A pdb=" N MET Z 62 " --> pdb=" O TYR Z 58 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 80 through 82 Processing sheet with id= B, first strand: chain '0' and resid 163 through 165 Processing sheet with id= C, first strand: chain '0' and resid 94 through 102 removed outlier: 6.595A pdb=" N TRP 0 115 " --> pdb=" O THR 0 98 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL 0 100 " --> pdb=" O LYS 0 113 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS 0 113 " --> pdb=" O VAL 0 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 150 through 153 Processing sheet with id= E, first strand: chain '6' and resid 178 through 184 removed outlier: 3.607A pdb=" N LYS 6 126 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS 6 141 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU 6 124 " --> pdb=" O LYS 6 141 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '7' and resid 349 through 353 removed outlier: 4.221A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 393 through 395 removed outlier: 3.882A pdb=" N HIS 7 409 " --> pdb=" O CYS 7 405 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '7' and resid 327 through 331 removed outlier: 6.853A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.742A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 194 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.820A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.592A pdb=" N LYS C 49 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 165 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.588A pdb=" N ARG C 113 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.067A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.300A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= P, first strand: chain 'D' and resid 370 through 372 removed outlier: 3.523A pdb=" N ALA D 385 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.164A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= S, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.849A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 156 through 162 Processing sheet with id= U, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= V, first strand: chain 'G' and resid 269 through 276 removed outlier: 3.971A pdb=" N ASP G 327 " --> pdb=" O TYR G 286 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.086A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 114 through 119 Processing sheet with id= Y, first strand: chain 'I' and resid 106 through 111 removed outlier: 6.698A pdb=" N VAL I 99 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE I 109 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE I 97 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER I 111 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR I 95 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU I 171 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL I 149 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE I 173 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 12.411A pdb=" N VAL I 151 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N ILE I 175 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 107 through 111 removed outlier: 6.778A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.526A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.563A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.415A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.434A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.721A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AG, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.699A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.510A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 341 through 345 removed outlier: 9.058A pdb=" N TYR X 124 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE X 306 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU X 126 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER X 308 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY X 128 " --> pdb=" O SER X 308 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) 1958 hydrogen bonds defined for protein. 5514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 612 hydrogen bonds 1076 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 445 stacking parallelities Total time for adding SS restraints: 36.30 Time building geometry restraints manager: 25.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 27898 1.41 - 1.63: 41336 1.63 - 1.86: 376 1.86 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 69630 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.558 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.416 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" N7 MA6 A1584 " pdb=" C5 MA6 A1584 " ideal model delta sigma weight residual 1.356 1.517 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N7 MA6 A1583 " pdb=" C5 MA6 A1583 " ideal model delta sigma weight residual 1.356 1.516 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C5A NAD A1733 " pdb=" N7A NAD A1733 " ideal model delta sigma weight residual 1.372 1.514 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 69625 not shown) Histogram of bond angle deviations from ideal: 71.05 - 84.81: 16 84.81 - 98.58: 6 98.58 - 112.34: 41518 112.34 - 126.11: 53268 126.11 - 139.88: 3543 Bond angle restraints: 98351 Sorted by residual: angle pdb=" N PRO 4 606 " pdb=" CD PRO 4 606 " pdb=" CG PRO 4 606 " ideal model delta sigma weight residual 103.20 92.49 10.71 1.50e+00 4.44e-01 5.09e+01 angle pdb=" O1A NAD A1733 " pdb=" PA NAD A1733 " pdb=" O2A NAD A1733 " ideal model delta sigma weight residual 122.64 102.17 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" CA PRO 4 606 " pdb=" N PRO 4 606 " pdb=" CD PRO 4 606 " ideal model delta sigma weight residual 112.00 102.92 9.08 1.40e+00 5.10e-01 4.21e+01 angle pdb=" O1N NAD A1733 " pdb=" PN NAD A1733 " pdb=" O2N NAD A1733 " ideal model delta sigma weight residual 120.02 101.39 18.63 3.00e+00 1.11e-01 3.86e+01 angle pdb=" O3' G A1582 " pdb=" P MA6 A1583 " pdb=" OP1 MA6 A1583 " ideal model delta sigma weight residual 108.00 91.02 16.98 3.00e+00 1.11e-01 3.20e+01 ... (remaining 98346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 39889 35.97 - 71.93: 2100 71.93 - 107.90: 328 107.90 - 143.87: 9 143.87 - 179.83: 9 Dihedral angle restraints: 42335 sinusoidal: 25310 harmonic: 17025 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 122.03 57.97 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C5' U A1219 " pdb=" C4' U A1219 " pdb=" C3' U A1219 " pdb=" O3' U A1219 " ideal model delta sinusoidal sigma weight residual 147.00 76.64 70.36 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C4' U A1219 " pdb=" C3' U A1219 " pdb=" C2' U A1219 " pdb=" C1' U A1219 " ideal model delta sinusoidal sigma weight residual -35.00 31.33 -66.33 1 8.00e+00 1.56e-02 8.98e+01 ... (remaining 42332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.186: 11511 4.186 - 8.373: 0 8.373 - 12.559: 0 12.559 - 16.746: 0 16.746 - 20.932: 4 Chirality restraints: 11515 Sorted by residual: chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.38 -20.93 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE2 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.32 20.87 2.00e-01 2.50e+01 1.09e+04 chirality pdb="FE1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.30 -20.86 2.00e-01 2.50e+01 1.09e+04 ... (remaining 11512 not shown) Planarity restraints: 9288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' MA6 A1584 " 0.025 2.00e-02 2.50e+03 5.63e-01 7.14e+03 pdb=" C4' MA6 A1584 " 0.433 2.00e-02 2.50e+03 pdb=" O4' MA6 A1584 " 0.639 2.00e-02 2.50e+03 pdb=" C3' MA6 A1584 " -0.594 2.00e-02 2.50e+03 pdb=" O3' MA6 A1584 " -0.545 2.00e-02 2.50e+03 pdb=" C2' MA6 A1584 " -0.220 2.00e-02 2.50e+03 pdb=" O2' MA6 A1584 " 0.883 2.00e-02 2.50e+03 pdb=" C1' MA6 A1584 " 0.230 2.00e-02 2.50e+03 pdb=" N9 MA6 A1584 " -0.853 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' MA6 A1583 " 0.007 2.00e-02 2.50e+03 5.33e-01 6.39e+03 pdb=" C4' MA6 A1583 " 0.420 2.00e-02 2.50e+03 pdb=" O4' MA6 A1583 " 0.598 2.00e-02 2.50e+03 pdb=" C3' MA6 A1583 " -0.590 2.00e-02 2.50e+03 pdb=" O3' MA6 A1583 " -0.485 2.00e-02 2.50e+03 pdb=" C2' MA6 A1583 " -0.241 2.00e-02 2.50e+03 pdb=" O2' MA6 A1583 " 0.839 2.00e-02 2.50e+03 pdb=" C1' MA6 A1583 " 0.239 2.00e-02 2.50e+03 pdb=" N9 MA6 A1583 " -0.787 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU 4 639 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO 4 640 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO 4 640 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO 4 640 " 0.058 5.00e-02 4.00e+02 ... (remaining 9285 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 489 2.58 - 3.22: 59625 3.22 - 3.86: 142328 3.86 - 4.50: 196238 4.50 - 5.14: 283150 Nonbonded interactions: 681830 Sorted by model distance: nonbonded pdb=" OD2 ASP B 241 " pdb="MG MG B 301 " model vdw 1.938 2.170 nonbonded pdb=" OP1 C A 815 " pdb="MG MG A1710 " model vdw 1.939 2.170 nonbonded pdb=" OP2 A A1054 " pdb="MG MG A1724 " model vdw 1.943 2.170 nonbonded pdb=" O2' A A1013 " pdb=" O5' A A1014 " model vdw 1.944 2.440 nonbonded pdb=" OP2 A A 882 " pdb="MG MG A1711 " model vdw 1.967 2.170 ... (remaining 681825 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.640 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 189.400 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.005 0.221 69630 Z= 0.289 Angle : 0.670 20.474 98351 Z= 0.342 Chirality : 0.390 20.932 11515 Planarity : 0.010 0.563 9288 Dihedral : 19.045 179.833 31289 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.36 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.11), residues: 5723 helix: 1.57 (0.10), residues: 2792 sheet: -0.38 (0.20), residues: 565 loop : 0.27 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP 3 177 HIS 0.018 0.001 HIS I 183 PHE 0.020 0.001 PHE M 97 TYR 0.035 0.002 TYR 4 486 ARG 0.011 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 760 time to evaluate : 4.639 Fit side-chains revert: symmetry clash REVERT: 0 27 ARG cc_start: 0.7197 (mtm110) cc_final: 0.6961 (mtm-85) REVERT: 0 196 ILE cc_start: 0.8231 (mm) cc_final: 0.7930 (mp) REVERT: 3 138 MET cc_start: 0.7452 (mmm) cc_final: 0.7188 (mmm) REVERT: 6 92 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7316 (ttp80) REVERT: B 61 LYS cc_start: 0.7957 (tppt) cc_final: 0.7523 (tppt) REVERT: B 271 TYR cc_start: 0.7323 (t80) cc_final: 0.7047 (t80) REVERT: D 373 ILE cc_start: 0.8296 (mm) cc_final: 0.8040 (mp) REVERT: J 68 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7723 (ttm170) REVERT: J 114 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7414 (ptm-80) REVERT: L 72 LEU cc_start: 0.8546 (mt) cc_final: 0.8180 (tp) REVERT: L 144 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6866 (mt-10) REVERT: L 190 THR cc_start: 0.7640 (t) cc_final: 0.7290 (p) REVERT: M 59 ASN cc_start: 0.8804 (p0) cc_final: 0.8335 (p0) REVERT: N 11 ARG cc_start: 0.7217 (mmt90) cc_final: 0.6926 (mmt180) REVERT: N 23 GLN cc_start: 0.7325 (mt0) cc_final: 0.6838 (mm-40) REVERT: N 56 GLN cc_start: 0.7582 (mt0) cc_final: 0.6852 (tp40) REVERT: S 53 TYR cc_start: 0.8485 (m-80) cc_final: 0.8010 (m-80) REVERT: S 62 ASP cc_start: 0.8079 (m-30) cc_final: 0.7831 (m-30) REVERT: S 105 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6904 (mt-10) REVERT: U 97 LYS cc_start: 0.7621 (tttt) cc_final: 0.7411 (tttt) REVERT: U 126 GLN cc_start: 0.6966 (tp40) cc_final: 0.6272 (tm130) REVERT: V 169 MET cc_start: 0.7555 (mmt) cc_final: 0.7158 (mmm) REVERT: V 396 GLN cc_start: 0.6875 (tt0) cc_final: 0.6654 (tp-100) REVERT: Y 378 ASN cc_start: 0.7811 (m-40) cc_final: 0.7586 (m-40) REVERT: Z 24 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7471 (ttm170) outliers start: 0 outliers final: 2 residues processed: 760 average time/residue: 1.6373 time to fit residues: 1582.9090 Evaluate side-chains 551 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 549 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 411 ASP Chi-restraints excluded: chain I residue 145 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 553 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 335 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 514 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 382 optimal weight: 3.9990 chunk 595 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 32 GLN 1 321 ASN 3 166 GLN 4 90 GLN 4 285 ASN 4 326 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 121 ASN 6 165 HIS 7 49 HIS 7 69 ASN 7 249 GLN 7 290 HIS 7 398 HIS 7 400 HIS 7 412 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS D 369 HIS D 415 GLN E 54 HIS E 57 GLN F 72 GLN F 127 HIS F 169 GLN G 127 HIS G 288 HIS I 141 GLN ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN K 60 ASN Q 41 HIS R 221 GLN R 302 GLN R 308 HIS R 312 GLN U 79 GLN U 126 GLN U 147 GLN U 159 GLN U 186 ASN V 115 GLN V 381 GLN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS X 159 HIS ** X 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 GLN Y 290 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.287 69630 Z= 0.440 Angle : 0.871 51.228 98351 Z= 0.513 Chirality : 0.123 6.321 11515 Planarity : 0.006 0.119 9288 Dihedral : 19.249 178.380 19146 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 7.98 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: 0.90 (0.11), residues: 5723 helix: 1.32 (0.10), residues: 2787 sheet: -0.31 (0.20), residues: 574 loop : 0.10 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 3 177 HIS 0.014 0.002 HIS X 81 PHE 0.029 0.002 PHE M 97 TYR 0.027 0.002 TYR V 91 ARG 0.010 0.001 ARG S 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 568 time to evaluate : 4.775 Fit side-chains REVERT: 3 138 MET cc_start: 0.7420 (mmm) cc_final: 0.6998 (mmm) REVERT: 3 159 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: 6 92 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7163 (ttp80) REVERT: B 139 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8346 (mttp) REVERT: F 97 MET cc_start: 0.8647 (mtp) cc_final: 0.8394 (mtm) REVERT: G 170 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8443 (mm) REVERT: J 63 LEU cc_start: 0.7868 (mt) cc_final: 0.7521 (mt) REVERT: J 104 GLU cc_start: 0.6484 (tt0) cc_final: 0.6244 (tt0) REVERT: J 114 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7516 (ttp80) REVERT: L 72 LEU cc_start: 0.8544 (mt) cc_final: 0.8262 (tp) REVERT: L 190 THR cc_start: 0.7706 (t) cc_final: 0.7444 (p) REVERT: M 59 ASN cc_start: 0.8824 (p0) cc_final: 0.8298 (p0) REVERT: N 23 GLN cc_start: 0.7373 (mt0) cc_final: 0.6870 (mm-40) REVERT: N 56 GLN cc_start: 0.7545 (mt0) cc_final: 0.6685 (tp-100) REVERT: O 110 ASP cc_start: 0.7850 (t0) cc_final: 0.7633 (t0) REVERT: Q 16 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5181 (pp20) REVERT: S 62 ASP cc_start: 0.8078 (m-30) cc_final: 0.7827 (m-30) REVERT: T 99 MET cc_start: 0.8024 (tpt) cc_final: 0.7573 (tpt) REVERT: U 156 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: U 178 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: V 77 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7066 (t0) REVERT: V 169 MET cc_start: 0.7585 (mmt) cc_final: 0.7362 (tpp) REVERT: V 318 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7519 (p0) outliers start: 103 outliers final: 45 residues processed: 623 average time/residue: 1.5611 time to fit residues: 1250.0308 Evaluate side-chains 573 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 520 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 1 residue 128 ASP Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 4 residue 448 ILE Chi-restraints excluded: chain 4 residue 526 ASP Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 204 ASN Chi-restraints excluded: chain Q residue 16 GLU Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 156 GLU Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 260 LEU Chi-restraints excluded: chain V residue 277 ARG Chi-restraints excluded: chain V residue 318 ASP Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 96 LYS Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 373 THR Chi-restraints excluded: chain Y residue 382 GLU Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 495 optimal weight: 6.9990 chunk 405 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 596 optimal weight: 3.9990 chunk 644 optimal weight: 0.9990 chunk 531 optimal weight: 0.9980 chunk 591 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 478 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 166 GLN ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN I 141 GLN J 74 ASN R 308 HIS R 312 GLN U 147 GLN U 186 ASN V 381 GLN X 190 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.250 69630 Z= 0.274 Angle : 0.780 50.749 98351 Z= 0.475 Chirality : 0.123 6.383 11515 Planarity : 0.004 0.118 9288 Dihedral : 19.092 178.297 19142 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.66 % Allowed : 10.30 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 5723 helix: 1.61 (0.10), residues: 2781 sheet: -0.05 (0.20), residues: 563 loop : 0.28 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 177 HIS 0.010 0.001 HIS X 81 PHE 0.016 0.001 PHE 4 309 TYR 0.018 0.001 TYR V 91 ARG 0.008 0.000 ARG Y 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 564 time to evaluate : 4.698 Fit side-chains REVERT: 0 27 ARG cc_start: 0.7268 (mtm110) cc_final: 0.7067 (mtm-85) REVERT: 1 203 ASP cc_start: 0.6877 (t0) cc_final: 0.6523 (t0) REVERT: 3 138 MET cc_start: 0.7387 (mmm) cc_final: 0.6892 (mmm) REVERT: 3 159 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: 6 92 ARG cc_start: 0.7470 (ttm170) cc_final: 0.7153 (ttp80) REVERT: B 271 TYR cc_start: 0.7281 (t80) cc_final: 0.7059 (t80) REVERT: D 407 ASP cc_start: 0.7706 (m-30) cc_final: 0.7468 (t70) REVERT: F 196 HIS cc_start: 0.6295 (m90) cc_final: 0.5895 (m-70) REVERT: G 170 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8420 (mm) REVERT: I 115 GLU cc_start: 0.6502 (mp0) cc_final: 0.6021 (mp0) REVERT: J 59 LYS cc_start: 0.8234 (mttt) cc_final: 0.7901 (mttt) REVERT: J 63 LEU cc_start: 0.7687 (mt) cc_final: 0.7138 (mt) REVERT: J 104 GLU cc_start: 0.6632 (tt0) cc_final: 0.6284 (tt0) REVERT: J 114 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7516 (ttp80) REVERT: L 72 LEU cc_start: 0.8652 (mt) cc_final: 0.8293 (tp) REVERT: L 190 THR cc_start: 0.7697 (t) cc_final: 0.7453 (p) REVERT: L 221 LYS cc_start: 0.6871 (mmmt) cc_final: 0.6501 (pttt) REVERT: M 59 ASN cc_start: 0.8757 (p0) cc_final: 0.8269 (p0) REVERT: N 23 GLN cc_start: 0.7295 (mt0) cc_final: 0.6765 (mm-40) REVERT: N 56 GLN cc_start: 0.7541 (mt0) cc_final: 0.6750 (tp-100) REVERT: S 53 TYR cc_start: 0.8428 (m-80) cc_final: 0.7977 (m-80) REVERT: T 99 MET cc_start: 0.8001 (tpt) cc_final: 0.7610 (tpt) REVERT: U 156 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: U 178 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: V 77 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6931 (t0) REVERT: V 169 MET cc_start: 0.7555 (mmt) cc_final: 0.7352 (tpp) REVERT: V 313 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7129 (tp) REVERT: V 318 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7318 (p0) outliers start: 85 outliers final: 32 residues processed: 610 average time/residue: 1.6040 time to fit residues: 1256.4989 Evaluate side-chains 573 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 534 time to evaluate : 4.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 ASP Chi-restraints excluded: chain 1 residue 235 ASN Chi-restraints excluded: chain 1 residue 267 LEU Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 46 LYS Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 156 GLU Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 318 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 373 THR Chi-restraints excluded: chain Y residue 382 GLU Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 3.9990 chunk 448 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 400 optimal weight: 8.9990 chunk 598 optimal weight: 3.9990 chunk 634 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 567 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 141 HIS 3 166 GLN 4 201 GLN ** 4 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 411 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN I 141 GLN J 74 ASN O 223 HIS P 47 ASN R 308 HIS R 312 GLN S 107 GLN U 147 GLN V 381 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 69630 Z= 0.265 Angle : 0.767 50.674 98351 Z= 0.468 Chirality : 0.123 6.344 11515 Planarity : 0.004 0.115 9288 Dihedral : 18.951 179.836 19142 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.31 % Rotamer: Outliers : 2.07 % Allowed : 11.08 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5723 helix: 1.75 (0.10), residues: 2771 sheet: 0.11 (0.21), residues: 573 loop : 0.37 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 177 HIS 0.012 0.001 HIS X 81 PHE 0.028 0.001 PHE 4 309 TYR 0.019 0.001 TYR V 91 ARG 0.006 0.000 ARG O 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 570 time to evaluate : 4.714 Fit side-chains REVERT: 1 203 ASP cc_start: 0.6863 (t0) cc_final: 0.6546 (t0) REVERT: 3 138 MET cc_start: 0.7406 (mmm) cc_final: 0.6861 (mmm) REVERT: 3 159 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: 6 92 ARG cc_start: 0.7515 (ttm170) cc_final: 0.7295 (ttp80) REVERT: B 139 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8291 (mttp) REVERT: D 304 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7633 (mttp) REVERT: D 407 ASP cc_start: 0.7700 (m-30) cc_final: 0.7474 (t70) REVERT: F 196 HIS cc_start: 0.6258 (m90) cc_final: 0.5959 (m90) REVERT: G 170 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8358 (mm) REVERT: G 237 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6428 (mm-30) REVERT: I 115 GLU cc_start: 0.6417 (mp0) cc_final: 0.5980 (mp0) REVERT: J 59 LYS cc_start: 0.8225 (mttt) cc_final: 0.7928 (mttt) REVERT: J 63 LEU cc_start: 0.7725 (mt) cc_final: 0.7114 (mt) REVERT: J 104 GLU cc_start: 0.6624 (tt0) cc_final: 0.6360 (tt0) REVERT: J 114 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7523 (ttp80) REVERT: L 72 LEU cc_start: 0.8670 (mt) cc_final: 0.8340 (tp) REVERT: L 190 THR cc_start: 0.7695 (t) cc_final: 0.7466 (p) REVERT: L 221 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6602 (pttt) REVERT: M 59 ASN cc_start: 0.8721 (p0) cc_final: 0.8383 (p0) REVERT: N 23 GLN cc_start: 0.7232 (mt0) cc_final: 0.6764 (mm-40) REVERT: N 56 GLN cc_start: 0.7564 (mt0) cc_final: 0.6695 (tp-100) REVERT: O 61 SER cc_start: 0.8459 (p) cc_final: 0.8148 (p) REVERT: O 179 THR cc_start: 0.8351 (p) cc_final: 0.8086 (m) REVERT: Q 16 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5204 (pp20) REVERT: R 293 LEU cc_start: 0.7084 (mt) cc_final: 0.6831 (mt) REVERT: R 306 VAL cc_start: 0.7957 (p) cc_final: 0.7530 (m) REVERT: S 53 TYR cc_start: 0.8378 (m-80) cc_final: 0.7943 (m-80) REVERT: T 99 MET cc_start: 0.7985 (tpt) cc_final: 0.7588 (tpt) REVERT: U 133 GLN cc_start: 0.5725 (tt0) cc_final: 0.5512 (tm-30) REVERT: U 156 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: U 178 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: V 77 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6866 (t0) REVERT: V 169 MET cc_start: 0.7558 (mmt) cc_final: 0.7327 (tpp) REVERT: V 313 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7156 (tp) REVERT: V 318 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7224 (p0) REVERT: V 361 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6831 (tttt) REVERT: Z 39 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7359 (mt-10) outliers start: 106 outliers final: 51 residues processed: 630 average time/residue: 1.5505 time to fit residues: 1262.6185 Evaluate side-chains 608 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 545 time to evaluate : 4.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 148 GLU Chi-restraints excluded: chain 1 residue 128 ASP Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 1 residue 235 ASN Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 46 LYS Chi-restraints excluded: chain 6 residue 90 HIS Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 7 residue 87 VAL Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 204 ASN Chi-restraints excluded: chain Q residue 16 GLU Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 156 GLU Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 318 ASP Chi-restraints excluded: chain V residue 361 LYS Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 373 THR Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 chunk 261 optimal weight: 0.0970 chunk 541 optimal weight: 4.9990 chunk 438 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 323 optimal weight: 3.9990 chunk 569 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 141 HIS 3 166 GLN 4 90 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN I 141 GLN J 74 ASN P 47 ASN R 308 HIS R 312 GLN U 147 GLN V 381 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 69630 Z= 0.280 Angle : 0.771 50.707 98351 Z= 0.469 Chirality : 0.123 6.355 11515 Planarity : 0.004 0.116 9288 Dihedral : 18.908 179.901 19142 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.69 % Favored : 98.29 % Rotamer: Outliers : 2.24 % Allowed : 11.90 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.11), residues: 5723 helix: 1.74 (0.10), residues: 2775 sheet: 0.16 (0.21), residues: 566 loop : 0.38 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.012 0.001 HIS X 81 PHE 0.021 0.001 PHE 4 309 TYR 0.020 0.001 TYR V 91 ARG 0.006 0.000 ARG O 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 557 time to evaluate : 4.694 Fit side-chains REVERT: 0 27 ARG cc_start: 0.7343 (mtm110) cc_final: 0.7105 (mtm-85) REVERT: 0 32 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: 3 138 MET cc_start: 0.7402 (mmm) cc_final: 0.6856 (mmm) REVERT: 6 92 ARG cc_start: 0.7514 (ttm170) cc_final: 0.7292 (ttp80) REVERT: 7 215 MET cc_start: 0.6898 (mpm) cc_final: 0.6446 (mpm) REVERT: B 139 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8342 (mttp) REVERT: D 304 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7654 (mttp) REVERT: D 407 ASP cc_start: 0.7724 (m-30) cc_final: 0.7469 (t70) REVERT: F 196 HIS cc_start: 0.6211 (m90) cc_final: 0.6001 (m90) REVERT: G 170 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8357 (mm) REVERT: G 237 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6419 (mm-30) REVERT: J 59 LYS cc_start: 0.8239 (mttt) cc_final: 0.7932 (mttt) REVERT: J 63 LEU cc_start: 0.7640 (mt) cc_final: 0.7028 (mt) REVERT: J 68 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7038 (mtm180) REVERT: J 104 GLU cc_start: 0.6635 (tt0) cc_final: 0.6292 (tt0) REVERT: J 114 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7544 (ttp80) REVERT: K 62 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7539 (mt) REVERT: L 72 LEU cc_start: 0.8667 (mt) cc_final: 0.8351 (tp) REVERT: L 190 THR cc_start: 0.7669 (t) cc_final: 0.7447 (p) REVERT: M 59 ASN cc_start: 0.8701 (p0) cc_final: 0.8351 (p0) REVERT: N 23 GLN cc_start: 0.7259 (mt0) cc_final: 0.6742 (mm-40) REVERT: N 56 GLN cc_start: 0.7553 (mt0) cc_final: 0.6681 (tp-100) REVERT: O 61 SER cc_start: 0.8458 (p) cc_final: 0.8161 (p) REVERT: O 179 THR cc_start: 0.8320 (p) cc_final: 0.8046 (m) REVERT: R 293 LEU cc_start: 0.7092 (mt) cc_final: 0.6833 (mt) REVERT: S 53 TYR cc_start: 0.8397 (m-80) cc_final: 0.7975 (m-80) REVERT: S 123 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6736 (mtpt) REVERT: T 77 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8280 (ttp-170) REVERT: T 99 MET cc_start: 0.7985 (tpt) cc_final: 0.7553 (tpt) REVERT: U 133 GLN cc_start: 0.5725 (tt0) cc_final: 0.5478 (tm-30) REVERT: U 178 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: V 77 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6890 (t0) REVERT: V 169 MET cc_start: 0.7535 (mmt) cc_final: 0.7287 (tpp) REVERT: V 313 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7178 (tp) REVERT: V 318 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7243 (p0) REVERT: V 361 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6875 (tttt) REVERT: Z 39 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7357 (mt-10) outliers start: 115 outliers final: 54 residues processed: 626 average time/residue: 1.5782 time to fit residues: 1270.3314 Evaluate side-chains 604 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 536 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 32 GLN Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 148 GLU Chi-restraints excluded: chain 1 residue 128 ASP Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 1 residue 267 LEU Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 250 LEU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 526 ASP Chi-restraints excluded: chain 4 residue 639 LEU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 46 LYS Chi-restraints excluded: chain 6 residue 90 HIS Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 7 residue 87 VAL Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 304 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 204 ASN Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 123 LYS Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 318 ASP Chi-restraints excluded: chain V residue 361 LYS Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 373 THR Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 213 optimal weight: 20.0000 chunk 571 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 372 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 634 optimal weight: 3.9990 chunk 526 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 141 HIS 3 166 GLN 4 90 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 402 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN E 57 GLN F 146 HIS I 141 GLN P 47 ASN R 308 HIS R 312 GLN U 147 GLN V 381 GLN Y 290 ASN ** Z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 69630 Z= 0.304 Angle : 0.784 50.730 98351 Z= 0.475 Chirality : 0.123 6.363 11515 Planarity : 0.005 0.116 9288 Dihedral : 18.875 179.536 19142 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.87 % Favored : 98.11 % Rotamer: Outliers : 2.48 % Allowed : 12.68 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.11), residues: 5723 helix: 1.69 (0.10), residues: 2761 sheet: 0.14 (0.21), residues: 566 loop : 0.35 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.015 0.001 HIS X 81 PHE 0.022 0.001 PHE 4 309 TYR 0.022 0.001 TYR V 91 ARG 0.014 0.000 ARG 0 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11446 Ramachandran restraints generated. 5723 Oldfield, 0 Emsley, 5723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 567 time to evaluate : 4.739 Fit side-chains REVERT: 3 138 MET cc_start: 0.7355 (mmm) cc_final: 0.6826 (mmm) REVERT: 3 159 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 139 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: D 407 ASP cc_start: 0.7718 (m-30) cc_final: 0.7467 (t70) REVERT: F 196 HIS cc_start: 0.6194 (m90) cc_final: 0.5978 (m90) REVERT: G 170 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8347 (mm) REVERT: G 237 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6581 (mm-30) REVERT: J 59 LYS cc_start: 0.8253 (mttt) cc_final: 0.7913 (mttt) REVERT: J 63 LEU cc_start: 0.7600 (mt) cc_final: 0.6988 (mt) REVERT: J 66 PHE cc_start: 0.7590 (p90) cc_final: 0.7353 (p90) REVERT: J 68 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7103 (mtm180) REVERT: J 104 GLU cc_start: 0.6622 (tt0) cc_final: 0.6301 (tt0) REVERT: J 114 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7571 (ttp80) REVERT: K 62 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7523 (mt) REVERT: L 72 LEU cc_start: 0.8677 (mt) cc_final: 0.8346 (tp) REVERT: L 83 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5028 (mp0) REVERT: L 190 THR cc_start: 0.7662 (t) cc_final: 0.7439 (p) REVERT: M 59 ASN cc_start: 0.8749 (p0) cc_final: 0.8394 (p0) REVERT: N 23 GLN cc_start: 0.7275 (mt0) cc_final: 0.6771 (mm-40) REVERT: N 67 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7678 (ttp-110) REVERT: O 61 SER cc_start: 0.8433 (p) cc_final: 0.8124 (p) REVERT: O 179 THR cc_start: 0.8227 (p) cc_final: 0.7964 (m) REVERT: R 293 LEU cc_start: 0.7076 (mt) cc_final: 0.6833 (mt) REVERT: R 306 VAL cc_start: 0.8035 (p) cc_final: 0.7599 (m) REVERT: S 53 TYR cc_start: 0.8411 (m-80) cc_final: 0.8001 (m-80) REVERT: S 123 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6737 (mtpt) REVERT: T 99 MET cc_start: 0.7996 (tpt) cc_final: 0.7536 (tpt) REVERT: U 133 GLN cc_start: 0.5856 (tt0) cc_final: 0.5554 (tm-30) REVERT: U 178 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: V 77 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6903 (t0) REVERT: V 313 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7230 (tp) REVERT: V 361 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6895 (tttt) REVERT: Z 39 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7377 (mt-10) outliers start: 127 outliers final: 69 residues processed: 641 average time/residue: 1.5494 time to fit residues: 1285.3492 Evaluate side-chains 622 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 541 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 80 VAL Chi-restraints excluded: chain 0 residue 148 GLU Chi-restraints excluded: chain 1 residue 128 ASP Chi-restraints excluded: chain 1 residue 154 THR Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 267 LEU Chi-restraints excluded: chain 3 residue 159 GLU Chi-restraints excluded: chain 4 residue 64 THR Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 526 ASP Chi-restraints excluded: chain 4 residue 639 LEU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 46 LYS Chi-restraints excluded: chain 6 residue 90 HIS Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 7 residue 87 VAL Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 238 HIS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 59 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 204 ASN Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 154 THR Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 123 LYS Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 178 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 85 ILE Chi-restraints excluded: chain V residue 260 LEU Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 344 LEU Chi-restraints excluded: chain V residue 361 LYS Chi-restraints excluded: chain V residue 372 ILE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 373 THR Chi-restraints excluded: chain Z residue 6 GLU Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain Z residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 361 optimal weight: 5.9990 chunk 463 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 534 optimal weight: 0.7980 chunk 354 optimal weight: 10.0000 chunk 632 optimal weight: 0.7980 chunk 395 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: