Starting phenix.real_space_refine (version: dev) on Mon Feb 27 10:54:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csu_26971/02_2023/8csu_26971_neut_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 sd= 1.227 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 Process input model Symmetric amino acids flipped 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 127": "OE1" <-> "OE2" Residue "0 GLU 148": "OE1" <-> "OE2" Residue "0 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 128": "OD1" <-> "OD2" Residue "1 GLU 144": "OE1" <-> "OE2" Residue "1 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 196": "OE1" <-> "OE2" Residue "1 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 159": "OE1" <-> "OE2" Residue "3 GLU 170": "OE1" <-> "OE2" Residue "3 ASP 172": "OD1" <-> "OD2" Residue "3 GLU 184": "OE1" <-> "OE2" Residue "4 ASP 92": "OD1" <-> "OD2" Residue "4 GLU 114": "OE1" <-> "OE2" Residue "4 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 146": "OE1" <-> "OE2" Residue "4 GLU 154": "OE1" <-> "OE2" Residue "4 GLU 253": "OE1" <-> "OE2" Residue "4 GLU 281": "OE1" <-> "OE2" Residue "4 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 299": "OE1" <-> "OE2" Residue "4 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 399": "OE1" <-> "OE2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 409": "OD1" <-> "OD2" Residue "4 ASP 443": "OD1" <-> "OD2" Residue "4 PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 479": "OE1" <-> "OE2" Residue "4 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 518": "OE1" <-> "OE2" Residue "4 ASP 538": "OD1" <-> "OD2" Residue "4 ASP 616": "OD1" <-> "OD2" Residue "5 ASP 45": "OD1" <-> "OD2" Residue "5 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 61": "OE1" <-> "OE2" Residue "5 GLU 123": "OE1" <-> "OE2" Residue "5 GLU 130": "OE1" <-> "OE2" Residue "5 GLU 270": "OE1" <-> "OE2" Residue "5 GLU 275": "OE1" <-> "OE2" Residue "5 GLU 324": "OE1" <-> "OE2" Residue "5 GLU 325": "OE1" <-> "OE2" Residue "6 GLU 123": "OE1" <-> "OE2" Residue "6 GLU 147": "OE1" <-> "OE2" Residue "6 GLU 153": "OE1" <-> "OE2" Residue "6 GLU 192": "OE1" <-> "OE2" Residue "7 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 84": "OE1" <-> "OE2" Residue "7 GLU 105": "OE1" <-> "OE2" Residue "7 TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 218": "OD1" <-> "OD2" Residue "7 GLU 236": "OE1" <-> "OE2" Residue "7 ASP 276": "OD1" <-> "OD2" Residue "7 GLU 296": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 211": "OE1" <-> "OE2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 263": "OD1" <-> "OD2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G ASP 299": "OD1" <-> "OD2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G GLU 378": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "K TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "L ASP 176": "OD1" <-> "OD2" Residue "L GLU 179": "OE1" <-> "OE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "O GLU 54": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O ASP 197": "OD1" <-> "OD2" Residue "O GLU 210": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R GLU 73": "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 149": "OE1" <-> "OE2" Residue "R GLU 212": "OE1" <-> "OE2" Residue "R GLU 213": "OE1" <-> "OE2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R ASP 292": "OD1" <-> "OD2" Residue "R TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S ASP 86": "OD1" <-> "OD2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S ASP 113": "OD1" <-> "OD2" Residue "T ASP 25": "OD1" <-> "OD2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "T GLU 138": "OE1" <-> "OE2" Residue "T GLU 158": "OE1" <-> "OE2" Residue "U ASP 49": "OD1" <-> "OD2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 92": "OE1" <-> "OE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "U GLU 112": "OE1" <-> "OE2" Residue "U GLU 118": "OE1" <-> "OE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U GLU 144": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U GLU 171": "OE1" <-> "OE2" Residue "U GLU 174": "OE1" <-> "OE2" Residue "U GLU 178": "OE1" <-> "OE2" Residue "U GLU 194": "OE1" <-> "OE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 149": "OD1" <-> "OD2" Residue "V GLU 171": "OE1" <-> "OE2" Residue "V PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 281": "OD1" <-> "OD2" Residue "V GLU 315": "OE1" <-> "OE2" Residue "V ASP 318": "OD1" <-> "OD2" Residue "V GLU 348": "OE1" <-> "OE2" Residue "V GLU 376": "OE1" <-> "OE2" Residue "V GLU 403": "OE1" <-> "OE2" Residue "W GLU 78": "OE1" <-> "OE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W GLU 128": "OE1" <-> "OE2" Residue "W TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 146": "OD1" <-> "OD2" Residue "W GLU 164": "OE1" <-> "OE2" Residue "X ASP 55": "OD1" <-> "OD2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X ASP 74": "OD1" <-> "OD2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 206": "OE1" <-> "OE2" Residue "X TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 263": "OD1" <-> "OD2" Residue "X GLU 375": "OE1" <-> "OE2" Residue "X GLU 379": "OE1" <-> "OE2" Residue "Y PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 312": "OE1" <-> "OE2" Residue "Y PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 374": "OE1" <-> "OE2" Residue "Y GLU 382": "OE1" <-> "OE2" Residue "Z TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 60": "OE1" <-> "OE2" Residue "Z PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 68661 Number of models: 1 Model: "" Number of chains: 40 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: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 395 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: "5" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2568 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 23, 'TRANS': 295} 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: 3276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3276 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 381} Chain: "A" Number of atoms: 18715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 18715 Classifications: {'RNA': 881} Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 72, 'rna3p_pur': 387, 'rna3p_pyr': 348} Link IDs: {'rna2p': 146, 'rna3p': 734} Chain breaks: 6 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: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} 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: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 73 Unusual residues: {' K': 5, ' MG': 24, 'NAD': 1} Classifications: {'undetermined': 30} Link IDs: {None: 29} 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 15378 SG CYS 7 404 98.090 112.664 152.558 1.00 48.60 S ATOM 14899 SG CYS 7 347 102.426 108.308 149.441 1.00 40.02 S ATOM 14794 SG CYS 7 333 96.548 110.079 147.226 1.00 41.21 S ATOM 14841 SG CYS 7 339 101.378 113.824 147.540 1.00 46.78 S ATOM 51314 SG CYS O 94 112.962 155.439 94.666 1.00 41.44 S ATOM 51400 SG CYS O 105 115.771 155.877 92.353 1.00 37.52 S ATOM 51421 SG CYS O 108 114.725 158.877 94.233 1.00 39.10 S ATOM 51709 SG CYS O 143 112.404 157.481 91.478 1.00 34.10 S ATOM 52632 SG CYS P 65 124.184 66.124 49.851 1.00 52.93 S ATOM 52905 SG CYS P 100 121.595 68.912 50.659 1.00 47.85 S ATOM 39884 SG CYS E 105 124.160 71.752 46.550 1.00 76.63 S ATOM 52654 SG CYS P 68 125.554 68.208 45.763 1.00 54.68 S ATOM 49259 SG CYS M 26 91.401 166.688 72.834 1.00 36.97 S ATOM 58695 SG CYS T 149 94.804 166.766 73.760 1.00 41.48 S ATOM 58623 SG CYS T 139 94.084 167.810 67.382 1.00 39.73 S ATOM 58637 SG CYS T 141 96.886 167.745 70.016 1.00 38.86 S Time building chain proxies: 28.19, per 1000 atoms: 0.41 Number of scatterers: 68661 At special positions: 0 Unit cell: (223.02, 236.826, 215.586, 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 5 19.00 S 250 16.00 P 888 15.00 Mg 26 11.99 O 15018 8.00 N 12316 7.00 C 40149 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: 23.45 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " 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 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb=" SF4 7 501 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " Number of angles added : 6 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 260 helices and 36 sheets defined 46.3% alpha, 9.2% beta 239 base pairs and 429 stacking pairs defined. Time for finding SS restraints: 20.54 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: 4.534A pdb=" N ALA 0 56 " --> pdb=" O VAL 0 52 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP 0 57 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.457A 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: 3.572A pdb=" N GLU 0 147 " --> pdb=" O LYS 0 144 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU 0 148 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.936A 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 '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 106 No H-bonds generated for 'chain '1' and resid 103 through 106' Processing helix chain '1' and resid 116 through 129 removed outlier: 3.697A pdb=" N LYS 1 127 " --> pdb=" O CYS 1 123 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 Processing helix chain '1' and resid 166 through 169 removed outlier: 3.849A 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: 6.637A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.106A 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 240 through 242 No H-bonds generated for 'chain '1' and resid 240 through 242' 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 154 through 180 removed outlier: 3.523A pdb=" N TRP 3 177 " --> pdb=" O LEU 3 173 " (cutoff:3.500A) Processing helix chain '4' and resid 69 through 77 Processing helix chain '4' and resid 93 through 95 No H-bonds generated for 'chain '4' and resid 93 through 95' 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 362 removed outlier: 4.166A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.060A 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 391 through 400 removed outlier: 3.513A pdb=" N TYR 4 394 " --> pdb=" O PHE 4 391 " (cutoff:3.500A) Processing helix chain '4' and resid 412 through 426 removed outlier: 4.607A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.830A 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 502 Processing helix chain '4' and resid 506 through 518 Proline residue: 4 510 - end of helix Processing helix chain '4' and resid 521 through 523 No H-bonds generated for 'chain '4' and resid 521 through 523' 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 586 Processing helix chain '4' and resid 589 through 602 removed outlier: 3.510A pdb=" N ARG 4 600 " --> pdb=" O LEU 4 596 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 621 Processing helix chain '4' and resid 624 through 637 removed outlier: 3.673A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 640 through 652 removed outlier: 3.816A pdb=" N GLU 4 643 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP 4 652 " --> pdb=" O VAL 4 649 " (cutoff:3.500A) Processing helix chain '4' and resid 657 through 666 Processing helix chain '5' and resid 18 through 24 Processing helix chain '5' and resid 41 through 50 Processing helix chain '5' and resid 68 through 75 Processing helix chain '5' and resid 91 through 100 Processing helix chain '5' and resid 123 through 125 No H-bonds generated for 'chain '5' and resid 123 through 125' Processing helix chain '5' and resid 147 through 160 Processing helix chain '5' and resid 163 through 167 removed outlier: 3.950A pdb=" N TYR 5 167 " --> pdb=" O PRO 5 164 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 184 Processing helix chain '5' and resid 195 through 201 Processing helix chain '5' and resid 214 through 216 No H-bonds generated for 'chain '5' and resid 214 through 216' Processing helix chain '5' and resid 242 through 253 Processing helix chain '5' and resid 260 through 267 removed outlier: 4.377A pdb=" N MET 5 266 " --> pdb=" O ARG 5 262 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU 5 267 " --> pdb=" O GLY 5 263 " (cutoff:3.500A) Processing helix chain '5' and resid 273 through 284 Processing helix chain '5' and resid 292 through 294 No H-bonds generated for 'chain '5' and resid 292 through 294' Processing helix chain '5' and resid 297 through 313 Processing helix chain '5' and resid 322 through 327 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 Processing helix chain '6' and resid 146 through 169 removed outlier: 5.177A pdb=" N ALA 6 161 " --> pdb=" O GLN 6 157 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N HIS 6 162 " --> pdb=" O ARG 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 199 removed outlier: 4.195A pdb=" N LEU 6 190 " --> pdb=" O GLY 6 186 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL 6 199 " --> pdb=" O GLN 6 195 " (cutoff:3.500A) 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 75 Processing helix chain '7' and resid 81 through 96 Processing helix chain '7' and resid 103 through 119 Processing helix chain '7' and resid 127 through 139 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.294A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.641A 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 286 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: 3.678A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.538A pdb=" N SER B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 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: 3.912A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) 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: 4.714A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.887A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.558A pdb=" N CYS F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 191 Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.630A 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 234 through 237 Processing helix chain 'G' and resid 71 through 92 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 242 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 320 Proline residue: G 316 - end of helix removed outlier: 3.725A pdb=" N VAL G 320 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 355 removed outlier: 4.373A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.582A 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: 3.996A pdb=" N LYS I 142 " --> pdb=" O ARG I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 167 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 58 removed outlier: 3.814A pdb=" N ARG K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 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: 3.806A 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 120 through 126 removed outlier: 3.913A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.738A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.318A 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 78 removed outlier: 3.999A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS Q 78 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) 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 335 removed outlier: 4.727A pdb=" N GLU R 335 " --> pdb=" O ALA R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 22 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 3.969A 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: 5.195A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.883A 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 164 No H-bonds generated for 'chain 'T' and resid 161 through 164' Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'U' and resid 50 through 86 Processing helix chain 'U' and resid 89 through 166 removed outlier: 3.560A pdb=" N ALA U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.661A 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 32 through 35 No H-bonds generated for 'chain 'V' and resid 32 through 35' 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 78 Processing helix chain 'V' and resid 82 through 96 removed outlier: 3.551A 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: 4.214A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 212 Proline residue: V 211 - end of helix 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 343 Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 352 through 404 removed outlier: 5.482A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.627A 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: 3.769A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.701A 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 148 removed outlier: 3.614A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) 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: 3.736A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.714A 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: 5.147A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 4.282A 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: 3.899A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 7.057A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.632A 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 397 removed outlier: 3.917A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 290 removed outlier: 3.748A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.552A 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 Processing helix chain 'Y' and resid 335 through 337 No H-bonds generated for 'chain 'Y' and resid 335 through 337' Processing helix chain 'Y' and resid 346 through 360 removed outlier: 3.681A 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 19 removed outlier: 3.521A pdb=" N ARG Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 30 through 38 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 46 through 49 No H-bonds generated for 'chain 'Z' and resid 46 through 49' Processing helix chain 'Z' and resid 57 through 67 removed outlier: 3.604A 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: 6.740A pdb=" N TRP 0 115 " --> pdb=" O THR 0 98 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL 0 100 " --> pdb=" O LYS 0 113 " (cutoff:3.500A) removed outlier: 6.720A 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 '5' and resid 204 through 212 removed outlier: 6.854A pdb=" N VAL 5 227 " --> pdb=" O ILE 5 209 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR 5 211 " --> pdb=" O VAL 5 225 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL 5 225 " --> pdb=" O THR 5 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR 5 58 " --> pdb=" O HIS 5 137 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE 5 139 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR 5 60 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU 5 80 " --> pdb=" O VAL 5 59 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU 5 61 " --> pdb=" O GLU 5 80 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU 5 82 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '6' and resid 178 through 184 removed outlier: 3.516A pdb=" N LYS 6 126 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS 6 141 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU 6 124 " --> pdb=" O LYS 6 141 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 349 through 353 removed outlier: 4.399A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU 7 213 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP 7 191 " --> pdb=" O GLU 7 213 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET 7 215 " --> pdb=" O ASP 7 191 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '7' and resid 393 through 395 Processing sheet with id= I, first strand: chain '7' and resid 327 through 331 removed outlier: 6.633A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.738A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.860A 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: 7.974A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.805A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 49 through 51 Processing sheet with id= M, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.529A pdb=" N ARG C 113 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.038A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.351A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= Q, first strand: chain 'D' and resid 370 through 372 removed outlier: 3.684A pdb=" N ALA D 385 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.534A pdb=" N GLY E 43 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= T, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.872A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 156 through 162 Processing sheet with id= V, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= W, first strand: chain 'G' and resid 269 through 276 Processing sheet with id= X, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.059A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 114 through 119 Processing sheet with id= Z, first strand: chain 'I' and resid 106 through 111 removed outlier: 6.668A pdb=" N VAL I 99 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE I 109 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE I 97 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER I 111 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR I 95 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU I 171 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL I 149 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE I 173 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 12.300A pdb=" N VAL I 151 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N ILE I 175 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.939A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.536A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU M 65 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.616A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.452A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.542A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.729A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.856A 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= AG, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AH, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.651A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.502A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'X' and resid 341 through 345 removed outlier: 9.017A pdb=" N TYR X 124 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE X 306 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU X 126 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER X 308 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N GLY X 128 " --> pdb=" O SER X 308 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) 2038 hydrogen bonds defined for protein. 5763 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 586 hydrogen bonds 1044 hydrogen bond angles 0 basepair planarities 239 basepair parallelities 429 stacking parallelities Total time for adding SS restraints: 37.62 Time building geometry restraints manager: 25.58 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: 28888 1.41 - 1.64: 42680 1.64 - 1.86: 390 1.86 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 71978 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 1.417 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C5A NAD A1730 " pdb=" N7A NAD A1730 " ideal model delta sigma weight residual 1.372 1.516 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C7N NAD A1730 " pdb=" N7N NAD A1730 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 71973 not shown) Histogram of bond angle deviations from ideal: 71.88 - 85.50: 16 85.50 - 99.12: 2 99.12 - 112.74: 44351 112.74 - 126.36: 53718 126.36 - 139.98: 3418 Bond angle restraints: 101505 Sorted by residual: angle pdb=" O1A NAD A1730 " pdb=" PA NAD A1730 " pdb=" O2A NAD A1730 " ideal model delta sigma weight residual 122.64 101.36 21.28 3.00e+00 1.11e-01 5.03e+01 angle pdb=" O1N NAD A1730 " pdb=" PN NAD A1730 " pdb=" O2N NAD A1730 " ideal model delta sigma weight residual 120.02 101.40 18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" C4A NAD A1730 " pdb=" N9A NAD A1730 " pdb=" C8A NAD A1730 " ideal model delta sigma weight residual 106.11 120.05 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C PHE 5 90 " pdb=" N ILE 5 91 " pdb=" CA ILE 5 91 " ideal model delta sigma weight residual 120.24 123.11 -2.87 6.30e-01 2.52e+00 2.08e+01 angle pdb=" C VAL 4 508 " pdb=" N ILE 4 509 " pdb=" CA ILE 4 509 " ideal model delta sigma weight residual 120.24 122.95 -2.71 6.30e-01 2.52e+00 1.85e+01 ... (remaining 101500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 40460 35.85 - 71.69: 1156 71.69 - 107.54: 120 107.54 - 143.38: 12 143.38 - 179.23: 8 Dihedral angle restraints: 41756 sinusoidal: 23830 harmonic: 17926 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 180.00 118.20 61.80 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual 200.00 30.40 169.60 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U A1526 " pdb=" C1' U A1526 " pdb=" N1 U A1526 " pdb=" C2 U A1526 " ideal model delta sinusoidal sigma weight residual 200.00 39.86 160.14 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 41753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.205: 11875 4.205 - 8.410: 0 8.410 - 12.615: 0 12.615 - 16.819: 0 16.819 - 21.024: 4 Chirality restraints: 11879 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 10.47 -21.02 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.42 20.98 2.00e-01 2.50e+01 1.10e+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 10.34 -20.89 2.00e-01 2.50e+01 1.09e+04 ... (remaining 11876 not shown) Planarity restraints: 9726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 4 605 " -0.090 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO 4 606 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO 4 606 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO 4 606 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 72 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO J 73 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO J 73 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 73 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 396 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO D 397 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 397 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 397 " -0.035 5.00e-02 4.00e+02 ... (remaining 9723 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 667 2.60 - 3.23: 64136 3.23 - 3.87: 146056 3.87 - 4.50: 200126 4.50 - 5.14: 289721 Nonbonded interactions: 700706 Sorted by model distance: nonbonded pdb=" O2' A A1013 " pdb=" O5' A A1014 " model vdw 1.964 2.440 nonbonded pdb=" OP2 A A 940 " pdb="MG MG A1712 " model vdw 1.965 2.170 nonbonded pdb=" OP2 A A1054 " pdb="MG MG A1713 " model vdw 1.970 2.170 nonbonded pdb=" OP1 C A1429 " pdb=" O2' U A1432 " model vdw 1.977 2.440 nonbonded pdb=" OG1 THR X 135 " pdb="MG MG X 502 " model vdw 1.992 2.170 ... (remaining 700701 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 Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 5 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 888 5.49 5 Mg 26 5.21 5 S 250 5.16 5 C 40149 2.51 5 N 12316 2.21 5 O 15018 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.660 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: 0.050 Extract box with map and model: 17.330 Check model and map are aligned: 0.740 Process input model: 184.500 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.480 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 210.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.004 0.221 71978 Z= 0.235 Angle : 0.638 21.281 101505 Z= 0.329 Chirality : 0.386 21.024 11879 Planarity : 0.005 0.134 9726 Dihedral : 15.540 179.229 30124 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.16 (0.11), residues: 6032 helix: 1.61 (0.10), residues: 2899 sheet: -0.35 (0.20), residues: 616 loop : 0.19 (0.13), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 895 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 895 average time/residue: 0.7258 time to fit residues: 1074.0141 Evaluate side-chains 663 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 578 optimal weight: 2.9990 chunk 519 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 350 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 536 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 chunk 622 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 32 GLN 0 111 HIS 1 231 HIS 4 355 GLN 4 545 GLN 5 109 HIS 5 208 HIS 5 229 HIS 6 165 HIS 7 72 GLN 7 398 HIS 7 400 HIS B 64 ASN C 126 GLN D 196 ASN D 415 GLN E 58 HIS F 146 HIS F 196 HIS G 127 HIS G 242 GLN I 163 HIS I 178 ASN I 183 HIS L 110 GLN O 225 GLN P 78 GLN Q 53 GLN ** R 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 308 HIS R 320 GLN ** T 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 110 ASN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 GLN X 159 HIS X 291 HIS X 292 ASN Y 295 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.258 71978 Z= 0.414 Angle : 0.846 50.458 101505 Z= 0.495 Chirality : 0.127 6.632 11879 Planarity : 0.005 0.084 9726 Dihedral : 13.608 177.959 17344 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 6032 helix: 1.30 (0.10), residues: 2906 sheet: -0.31 (0.19), residues: 629 loop : 0.12 (0.13), residues: 2497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 672 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 52 residues processed: 711 average time/residue: 0.7081 time to fit residues: 835.6859 Evaluate side-chains 668 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 616 time to evaluate : 4.992 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.5080 time to fit residues: 56.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 345 optimal weight: 0.1980 chunk 193 optimal weight: 10.0000 chunk 517 optimal weight: 0.4980 chunk 423 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 623 optimal weight: 0.0030 chunk 673 optimal weight: 7.9990 chunk 554 optimal weight: 6.9990 chunk 617 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 499 optimal weight: 7.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 GLN 5 171 GLN 5 208 HIS 7 60 HIS C 126 GLN I 163 HIS I 178 ASN J 74 ASN O 111 HIS R 290 GLN T 37 HIS Y 295 GLN Z 55 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.246 71978 Z= 0.274 Angle : 0.761 50.606 101505 Z= 0.460 Chirality : 0.122 6.371 11879 Planarity : 0.004 0.084 9726 Dihedral : 13.469 179.199 17344 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.11), residues: 6032 helix: 1.53 (0.10), residues: 2907 sheet: -0.13 (0.20), residues: 627 loop : 0.22 (0.13), residues: 2498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 662 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 688 average time/residue: 0.7260 time to fit residues: 831.6870 Evaluate side-chains 636 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 616 time to evaluate : 5.009 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5114 time to fit residues: 26.0257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 615 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 chunk 323 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 418 optimal weight: 8.9990 chunk 625 optimal weight: 5.9990 chunk 662 optimal weight: 0.9990 chunk 326 optimal weight: 10.0000 chunk 592 optimal weight: 1.9990 chunk 178 optimal weight: 0.3980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 163 HIS J 74 ASN O 111 HIS R 299 ASN T 37 HIS V 261 GLN W 135 GLN Y 285 GLN Y 295 GLN Y 372 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.243 71978 Z= 0.254 Angle : 0.744 50.631 101505 Z= 0.452 Chirality : 0.121 6.342 11879 Planarity : 0.004 0.083 9726 Dihedral : 13.319 178.334 17344 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.33 (0.11), residues: 6032 helix: 1.67 (0.10), residues: 2905 sheet: 0.05 (0.20), residues: 628 loop : 0.30 (0.13), residues: 2499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 671 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 693 average time/residue: 0.7332 time to fit residues: 845.2412 Evaluate side-chains 639 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 623 time to evaluate : 5.028 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5260 time to fit residues: 22.3848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 551 optimal weight: 1.9990 chunk 375 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 492 optimal weight: 7.9990 chunk 273 optimal weight: 40.0000 chunk 565 optimal weight: 10.0000 chunk 457 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 338 optimal weight: 0.0370 chunk 594 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 GLN H 109 HIS I 163 HIS J 74 ASN L 110 GLN O 111 HIS S 66 HIS T 37 HIS U 83 HIS U 161 GLN W 135 GLN X 190 ASN Y 285 GLN Y 295 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.241 71978 Z= 0.278 Angle : 0.754 50.666 101505 Z= 0.456 Chirality : 0.121 6.347 11879 Planarity : 0.004 0.066 9726 Dihedral : 13.242 178.430 17344 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.36 (0.11), residues: 6032 helix: 1.69 (0.10), residues: 2898 sheet: 0.13 (0.20), residues: 623 loop : 0.30 (0.13), residues: 2511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 653 time to evaluate : 5.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 680 average time/residue: 0.7192 time to fit residues: 815.2227 Evaluate side-chains 639 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 618 time to evaluate : 4.996 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5047 time to fit residues: 26.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 222 optimal weight: 10.0000 chunk 596 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 388 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 662 optimal weight: 0.7980 chunk 550 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 347 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 255 ASN 4 355 GLN F 224 HIS I 163 HIS J 74 ASN O 111 HIS T 37 HIS W 135 GLN X 190 ASN Y 285 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.241 71978 Z= 0.252 Angle : 0.738 50.619 101505 Z= 0.449 Chirality : 0.121 6.329 11879 Planarity : 0.004 0.061 9726 Dihedral : 13.164 177.949 17344 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.49 (0.11), residues: 6032 helix: 1.80 (0.10), residues: 2896 sheet: 0.24 (0.20), residues: 633 loop : 0.35 (0.13), residues: 2503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 658 time to evaluate : 5.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 684 average time/residue: 0.7278 time to fit residues: 829.9027 Evaluate side-chains 647 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 631 time to evaluate : 5.033 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5134 time to fit residues: 22.3314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 638 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 377 optimal weight: 4.9990 chunk 483 optimal weight: 8.9990 chunk 374 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 chunk 660 optimal weight: 5.9990 chunk 413 optimal weight: 9.9990 chunk 402 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 GLN 5 235 GLN F 169 GLN I 163 HIS O 111 HIS R 88 GLN T 37 HIS W 135 GLN X 190 ASN Y 285 GLN Y 303 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.240 71978 Z= 0.394 Angle : 0.815 50.884 101505 Z= 0.482 Chirality : 0.122 6.352 11879 Planarity : 0.005 0.061 9726 Dihedral : 13.322 179.686 17344 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.10 (0.11), residues: 6032 helix: 1.45 (0.10), residues: 2887 sheet: 0.14 (0.20), residues: 627 loop : 0.18 (0.13), residues: 2518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 623 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 646 average time/residue: 0.7232 time to fit residues: 780.9246 Evaluate side-chains 625 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 605 time to evaluate : 5.040 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5108 time to fit residues: 26.1178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 408 optimal weight: 0.4980 chunk 263 optimal weight: 10.0000 chunk 394 optimal weight: 0.2980 chunk 198 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 127 optimal weight: 0.2980 chunk 419 optimal weight: 6.9990 chunk 449 optimal weight: 7.9990 chunk 326 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 518 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 GLN C 126 GLN I 98 GLN I 184 ASN O 111 HIS O 152 GLN Q 79 ASN ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS X 190 ASN X 292 ASN Y 285 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.250 71978 Z= 0.244 Angle : 0.744 50.567 101505 Z= 0.452 Chirality : 0.121 6.315 11879 Planarity : 0.004 0.065 9726 Dihedral : 13.188 178.907 17344 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.11), residues: 6032 helix: 1.70 (0.10), residues: 2894 sheet: 0.35 (0.21), residues: 617 loop : 0.28 (0.13), residues: 2521 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 649 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 659 average time/residue: 0.7395 time to fit residues: 812.1191 Evaluate side-chains 632 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 627 time to evaluate : 5.027 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5219 time to fit residues: 11.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 600 optimal weight: 7.9990 chunk 632 optimal weight: 1.9990 chunk 577 optimal weight: 5.9990 chunk 615 optimal weight: 7.9990 chunk 370 optimal weight: 0.2980 chunk 268 optimal weight: 20.0000 chunk 483 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 555 optimal weight: 0.2980 chunk 581 optimal weight: 4.9990 chunk 613 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 453 HIS 4 540 HIS 5 251 ASN L 110 GLN N 23 GLN O 111 HIS O 152 GLN Q 79 ASN ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.248 71978 Z= 0.242 Angle : 0.735 50.551 101505 Z= 0.447 Chirality : 0.120 6.299 11879 Planarity : 0.004 0.064 9726 Dihedral : 13.030 177.436 17344 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.54 (0.11), residues: 6032 helix: 1.83 (0.10), residues: 2889 sheet: 0.45 (0.21), residues: 617 loop : 0.33 (0.13), residues: 2526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 645 time to evaluate : 5.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 654 average time/residue: 0.7302 time to fit residues: 796.2911 Evaluate side-chains 633 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 628 time to evaluate : 5.000 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6841 time to fit residues: 12.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 404 optimal weight: 0.7980 chunk 650 optimal weight: 7.9990 chunk 397 optimal weight: 5.9990 chunk 308 optimal weight: 0.1980 chunk 452 optimal weight: 2.9990 chunk 682 optimal weight: 0.9980 chunk 628 optimal weight: 9.9990 chunk 543 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 333 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 453 HIS I 98 GLN L 110 GLN N 23 GLN O 111 HIS O 152 GLN Q 79 ASN ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.250 71978 Z= 0.238 Angle : 0.734 50.560 101505 Z= 0.447 Chirality : 0.120 6.297 11879 Planarity : 0.004 0.068 9726 Dihedral : 12.967 177.369 17344 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.61 (0.11), residues: 6032 helix: 1.88 (0.10), residues: 2887 sheet: 0.54 (0.21), residues: 615 loop : 0.36 (0.13), residues: 2530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12064 Ramachandran restraints generated. 6032 Oldfield, 0 Emsley, 6032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 645 time to evaluate : 5.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 649 average time/residue: 0.7790 time to fit residues: 844.3677 Evaluate side-chains 634 residues out of total 5401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 5.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 431 optimal weight: 10.0000 chunk 578 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 501 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 151 optimal weight: 8.9990 chunk 544 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 558 optimal weight: 0.0040 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 453 HIS 7 49 HIS N 23 GLN O 111 HIS O 152 GLN Q 79 ASN ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.138153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111409 restraints weight = 132028.196| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.50 r_work: 0.3316 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.242 71978 Z= 0.330 Angle : 0.783 50.680 101505 Z= 0.467 Chirality : 0.121 6.339 11879 Planarity : 0.004 0.072 9726 Dihedral : 13.048 178.690 17344 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.33 (0.11), residues: 6032 helix: 1.62 (0.10), residues: 2891 sheet: 0.37 (0.21), residues: 618 loop : 0.27 (0.13), residues: 2523 =============================================================================== Job complete usr+sys time: 15095.01 seconds wall clock time: 266 minutes 29.18 seconds (15989.18 seconds total)