Starting phenix.real_space_refine on Sun Dec 10 06:49:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_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_26970/12_2023/8cst_26970_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_26970_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cst_26970/12_2023/8cst_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 27.68, per 1000 atoms: 0.42 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: 23.87 Conformation dependent library (CDL) restraints added in 6.5 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: 24.28 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: 36.68 Time building geometry restraints manager: 26.01 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: 3.030 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: 15.610 Check model and map are aligned: 0.920 Set scattering table: 0.480 Process input model: 187.890 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.220 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.470 ------------------------------------------------------------------------------- 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 : 4.704 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 760 average time/residue: 1.6739 time to fit residues: 1621.2864 Evaluate side-chains 540 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 538 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.5627 time to fit residues: 7.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 514 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 382 optimal weight: 3.9990 chunk 595 optimal weight: 0.0980 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 4 285 ASN 4 326 GLN 6 121 ASN 6 165 HIS 7 49 HIS 7 69 ASN 7 249 GLN 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 G 127 HIS G 288 HIS I 141 GLN I 183 HIS ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN K 60 ASN Q 15 GLN Q 41 HIS R 221 GLN R 302 GLN R 308 HIS R 312 GLN U 79 GLN U 147 GLN U 159 GLN U 186 ASN V 115 GLN V 381 GLN V 396 GLN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS X 159 HIS X 190 ASN X 205 GLN Y 290 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 69630 Z= 0.340 Angle : 0.821 50.883 98351 Z= 0.491 Chirality : 0.122 6.329 11515 Planarity : 0.005 0.120 9288 Dihedral : 19.174 178.694 19142 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.89 % Allowed : 7.80 % Favored : 90.30 % 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: 1.20 (0.11), residues: 5723 helix: 1.56 (0.10), residues: 2795 sheet: -0.16 (0.21), residues: 558 loop : 0.25 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 3 177 HIS 0.010 0.001 HIS H 83 PHE 0.021 0.002 PHE G 99 TYR 0.022 0.002 TYR V 91 ARG 0.009 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 665 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 568 time to evaluate : 4.758 Fit side-chains outliers start: 97 outliers final: 38 residues processed: 618 average time/residue: 1.6087 time to fit residues: 1282.0598 Evaluate side-chains 560 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 522 time to evaluate : 6.390 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 21 residues processed: 17 average time/residue: 0.6046 time to fit residues: 24.0033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 596 optimal weight: 6.9990 chunk 644 optimal weight: 0.0770 chunk 531 optimal weight: 0.9980 chunk 591 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 166 GLN 4 90 GLN ** 4 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 290 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN F 72 GLN I 141 GLN J 74 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: 0.7624 moved from start: 0.1299 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= 0.268 Angle : 0.770 50.651 98351 Z= 0.470 Chirality : 0.123 6.355 11515 Planarity : 0.004 0.116 9288 Dihedral : 19.023 179.128 19142 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.68 % Allowed : 9.87 % Favored : 88.45 % 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: 1.43 (0.11), residues: 5723 helix: 1.73 (0.10), residues: 2792 sheet: 0.11 (0.21), residues: 554 loop : 0.34 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 3 177 HIS 0.008 0.001 HIS X 81 PHE 0.021 0.001 PHE 4 309 TYR 0.018 0.001 TYR V 91 ARG 0.007 0.000 ARG S 50 *********************** 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 644 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 558 time to evaluate : 4.735 Fit side-chains outliers start: 86 outliers final: 38 residues processed: 607 average time/residue: 1.6464 time to fit residues: 1285.5479 Evaluate side-chains 560 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 522 time to evaluate : 4.659 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 12 average time/residue: 0.6899 time to fit residues: 19.6507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 9.9990 chunk 448 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 284 optimal weight: 0.0570 chunk 400 optimal weight: 10.0000 chunk 598 optimal weight: 5.9990 chunk 634 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 567 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 overall best weight: 3.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 235 ASN 3 141 HIS 3 166 GLN 4 201 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 545 GLN 7 411 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN F 169 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1519 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= 0.351 Angle : 0.809 50.765 98351 Z= 0.486 Chirality : 0.124 6.382 11515 Planarity : 0.005 0.118 9288 Dihedral : 19.004 179.464 19142 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 2.05 % Allowed : 11.24 % Favored : 86.71 % 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: 1.27 (0.11), residues: 5723 helix: 1.58 (0.10), residues: 2776 sheet: 0.02 (0.20), residues: 576 loop : 0.31 (0.13), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 107 HIS 0.017 0.001 HIS X 81 PHE 0.022 0.002 PHE 4 309 TYR 0.024 0.002 TYR V 91 ARG 0.008 0.001 ARG 0 17 *********************** 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 648 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 543 time to evaluate : 4.737 Fit side-chains outliers start: 105 outliers final: 57 residues processed: 607 average time/residue: 1.6115 time to fit residues: 1267.4947 Evaluate side-chains 577 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 520 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 35 residues processed: 23 average time/residue: 0.6200 time to fit residues: 30.6831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 472 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 541 optimal weight: 6.9990 chunk 438 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 569 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 141 HIS 3 166 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 545 GLN 7 402 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN E 57 GLN F 146 HIS I 141 GLN J 74 ASN L 77 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.006 0.242 69630 Z= 0.386 Angle : 0.830 50.818 98351 Z= 0.495 Chirality : 0.124 6.388 11515 Planarity : 0.005 0.118 9288 Dihedral : 19.036 179.974 19142 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.08 % Favored : 97.90 % Rotamer: Outliers : 2.54 % Allowed : 12.20 % Favored : 85.27 % 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: 1.04 (0.11), residues: 5723 helix: 1.38 (0.10), residues: 2765 sheet: -0.03 (0.21), residues: 566 loop : 0.18 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 1 66 HIS 0.022 0.002 HIS X 81 PHE 0.025 0.002 PHE 4 309 TYR 0.025 0.002 TYR V 91 ARG 0.008 0.001 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 684 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 554 time to evaluate : 4.788 Fit side-chains outliers start: 130 outliers final: 69 residues processed: 632 average time/residue: 1.6421 time to fit residues: 1343.3675 Evaluate side-chains 596 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 527 time to evaluate : 4.674 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 43 residues processed: 27 average time/residue: 0.9057 time to fit residues: 43.1798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 125 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 634 optimal weight: 0.9990 chunk 526 optimal weight: 0.8980 chunk 293 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 209 optimal weight: 10.0000 chunk 333 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 3 141 HIS 3 166 GLN 4 90 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 130 HIS E 57 GLN I 141 GLN I 184 ASN J 74 ASN P 47 ASN R 312 GLN U 147 GLN Z 56 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1872 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= 0.241 Angle : 0.763 50.631 98351 Z= 0.466 Chirality : 0.122 6.321 11515 Planarity : 0.004 0.113 9288 Dihedral : 18.892 179.893 19142 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.56 % Favored : 98.43 % Rotamer: Outliers : 1.97 % Allowed : 13.23 % Favored : 84.80 % 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: 1.48 (0.11), residues: 5723 helix: 1.75 (0.10), residues: 2765 sheet: 0.22 (0.21), residues: 558 loop : 0.40 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 177 HIS 0.008 0.001 HIS X 81 PHE 0.020 0.001 PHE 4 309 TYR 0.017 0.001 TYR L 189 ARG 0.011 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 663 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 562 time to evaluate : 4.762 Fit side-chains outliers start: 101 outliers final: 55 residues processed: 630 average time/residue: 1.5715 time to fit residues: 1287.1987 Evaluate side-chains 577 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 522 time to evaluate : 4.753 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 12 average time/residue: 0.9749 time to fit residues: 23.3499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 463 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 534 optimal weight: 0.0040 chunk 354 optimal weight: 9.9990 chunk 632 optimal weight: 3.9990 chunk 395 optimal weight: 0.0770 chunk 385 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 overall best weight: 0.5954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 166 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 373 HIS ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 88 GLN B 59 ASN C 126 GLN I 184 ASN P 47 ASN U 147 GLN V 391 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2078 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= 0.238 Angle : 0.751 50.612 98351 Z= 0.460 Chirality : 0.122 6.313 11515 Planarity : 0.004 0.114 9288 Dihedral : 18.744 178.072 19142 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.43 % Favored : 98.55 % Rotamer: Outliers : 1.68 % Allowed : 14.19 % Favored : 84.14 % 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: 1.69 (0.11), residues: 5723 helix: 1.91 (0.10), residues: 2762 sheet: 0.42 (0.21), residues: 566 loop : 0.49 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.006 0.001 HIS X 81 PHE 0.020 0.001 PHE 4 309 TYR 0.017 0.001 TYR L 189 ARG 0.009 0.000 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 7 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 669 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 583 time to evaluate : 4.669 Fit side-chains outliers start: 86 outliers final: 52 residues processed: 643 average time/residue: 1.6430 time to fit residues: 1366.5657 Evaluate side-chains 589 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 537 time to evaluate : 4.645 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 40 residues processed: 12 average time/residue: 0.8104 time to fit residues: 21.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 391 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 401 optimal weight: 0.7980 chunk 430 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 496 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 166 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 374 HIS ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 175 HIS ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 130 HIS P 47 ASN P 137 ASN R 312 GLN U 147 GLN V 391 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 69630 Z= 0.305 Angle : 0.785 50.722 98351 Z= 0.474 Chirality : 0.123 6.352 11515 Planarity : 0.005 0.116 9288 Dihedral : 18.753 177.424 19142 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 1.91 % Allowed : 15.00 % Favored : 83.08 % 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: 1.56 (0.11), residues: 5723 helix: 1.78 (0.10), residues: 2761 sheet: 0.32 (0.21), residues: 568 loop : 0.46 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 177 HIS 0.015 0.001 HIS X 81 PHE 0.021 0.001 PHE 4 348 TYR 0.021 0.002 TYR V 91 ARG 0.014 0.000 ARG 0 17 *********************** REFINEMENT MACRO_CYCLE 8 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 625 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 527 time to evaluate : 4.808 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 64 residues processed: 598 average time/residue: 1.6674 time to fit residues: 1292.9968 Evaluate side-chains 577 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 513 time to evaluate : 4.865 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 55 residues processed: 10 average time/residue: 0.8345 time to fit residues: 19.5772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 575 optimal weight: 0.6980 chunk 605 optimal weight: 0.0870 chunk 552 optimal weight: 2.9990 chunk 589 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 462 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 532 optimal weight: 10.0000 chunk 557 optimal weight: 7.9990 chunk 587 optimal weight: 1.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- 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 4 257 HIS ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 417 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 ASN R 305 HIS R 312 GLN U 147 GLN V 391 GLN X 291 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 69630 Z= 0.273 Angle : 0.775 50.687 98351 Z= 0.470 Chirality : 0.122 6.340 11515 Planarity : 0.004 0.115 9288 Dihedral : 18.739 177.604 19142 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Rotamer: Outliers : 1.62 % Allowed : 15.34 % Favored : 83.04 % 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: 1.56 (0.11), residues: 5723 helix: 1.79 (0.10), residues: 2762 sheet: 0.33 (0.21), residues: 566 loop : 0.45 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.013 0.001 HIS X 81 PHE 0.018 0.001 PHE 4 348 TYR 0.021 0.001 TYR L 189 ARG 0.010 0.000 ARG S 50 *********************** REFINEMENT MACRO_CYCLE 9 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 612 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 529 time to evaluate : 4.848 Fit side-chains outliers start: 83 outliers final: 67 residues processed: 596 average time/residue: 1.6396 time to fit residues: 1272.0713 Evaluate side-chains 585 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 518 time to evaluate : 4.643 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 58 residues processed: 10 average time/residue: 0.7445 time to fit residues: 19.2639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 386 optimal weight: 3.9990 chunk 623 optimal weight: 0.7980 chunk 380 optimal weight: 0.9990 chunk 295 optimal weight: 0.6980 chunk 433 optimal weight: 2.9990 chunk 653 optimal weight: 4.9990 chunk 601 optimal weight: 0.0970 chunk 520 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 319 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 417 GLN B 59 ASN P 47 ASN R 312 GLN U 147 GLN V 391 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2278 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= 0.240 Angle : 0.756 50.618 98351 Z= 0.462 Chirality : 0.122 6.314 11515 Planarity : 0.004 0.113 9288 Dihedral : 18.665 177.333 19142 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.61 % Favored : 98.37 % Rotamer: Outliers : 1.25 % Allowed : 15.94 % Favored : 82.81 % 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: 1.74 (0.11), residues: 5723 helix: 1.93 (0.10), residues: 2769 sheet: 0.43 (0.21), residues: 556 loop : 0.55 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.008 0.001 HIS X 81 PHE 0.029 0.001 PHE 4 309 TYR 0.021 0.001 TYR L 189 ARG 0.014 0.000 ARG L 123 ********************** REFINEMENT MACRO_CYCLE 10 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 609 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 545 time to evaluate : 4.698 Fit side-chains outliers start: 64 outliers final: 51 residues processed: 605 average time/residue: 1.6299 time to fit residues: 1284.8057 Evaluate side-chains 579 residues out of total 5125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 528 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 50 residues processed: 1 average time/residue: 1.8599 time to fit residues: 8.3641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 413 optimal weight: 8.9990 chunk 554 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 479 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 521 optimal weight: 0.6980 chunk 218 optimal weight: 20.0000 chunk 535 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 141 HIS 3 166 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 417 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN P 47 ASN U 147 GLN V 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111259 restraints weight = 123596.358| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.29 r_work: 0.3332 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 69630 Z= 0.292 Angle : 0.781 50.690 98351 Z= 0.472 Chirality : 0.123 6.349 11515 Planarity : 0.004 0.116 9288 Dihedral : 18.658 176.956 19142 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 1.40 % Allowed : 16.10 % Favored : 82.50 % 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: 1.62 (0.11), residues: 5723 helix: 1.82 (0.10), residues: 2773 sheet: 0.39 (0.21), residues: 561 loop : 0.49 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 3 177 HIS 0.016 0.001 HIS X 81 PHE 0.018 0.001 PHE 4 348 TYR 0.024 0.001 TYR L 189 ARG 0.010 0.000 ARG S 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20435.78 seconds wall clock time: 356 minutes 36.06 seconds (21396.06 seconds total)