Starting phenix.real_space_refine (version: dev) on Mon Feb 27 21:49:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2023/8csr_26968_updated.pdb" } resolution = 2.54 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= 0.034 sd= 1.307 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 39": "OE1" <-> "OE2" Residue "0 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 177": "OE1" <-> "OE2" Residue "0 ASP 183": "OD1" <-> "OD2" Residue "1 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 128": "OD1" <-> "OD2" Residue "1 TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 92": "OD1" <-> "OD2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 GLU 366": "OE1" <-> "OE2" Residue "4 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 413": "OD1" <-> "OD2" Residue "4 TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 479": "OE1" <-> "OE2" Residue "5 GLU 61": "OE1" <-> "OE2" Residue "5 GLU 123": "OE1" <-> "OE2" Residue "5 ASP 162": "OD1" <-> "OD2" Residue "5 GLU 179": "OE1" <-> "OE2" Residue "5 TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 324": "OE1" <-> "OE2" Residue "6 GLU 116": "OE1" <-> "OE2" Residue "6 PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 147": "OE1" <-> "OE2" Residue "7 GLU 152": "OE1" <-> "OE2" Residue "7 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 191": "OD1" <-> "OD2" Residue "7 ASP 311": "OD1" <-> "OD2" Residue "7 GLU 366": "OE1" <-> "OE2" Residue "7 GLU 380": "OE1" <-> "OE2" Residue "8 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 184": "OE1" <-> "OE2" Residue "8 ASP 234": "OD1" <-> "OD2" Residue "8 GLU 243": "OE1" <-> "OE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "G ASP 299": "OD1" <-> "OD2" Residue "G TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J ASP 131": "OD1" <-> "OD2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 65": "OD1" <-> "OD2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 171": "OE1" <-> "OE2" Residue "O ASP 197": "OD1" <-> "OD2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P ASP 126": "OD1" <-> "OD2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "R TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 144": "OE1" <-> "OE2" Residue "R TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 200": "OE1" <-> "OE2" Residue "R ASP 287": "OD1" <-> "OD2" Residue "R ASP 296": "OD1" <-> "OD2" Residue "R ASP 310": "OD1" <-> "OD2" Residue "R PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 101": "OE1" <-> "OE2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S GLU 120": "OE1" <-> "OE2" Residue "T ASP 25": "OD1" <-> "OD2" Residue "T PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 81": "OD1" <-> "OD2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" Residue "U GLU 77": "OE1" <-> "OE2" Residue "U ASP 98": "OD1" <-> "OD2" Residue "U GLU 130": "OE1" <-> "OE2" Residue "U GLU 145": "OE1" <-> "OE2" Residue "U GLU 174": "OE1" <-> "OE2" Residue "U ASP 182": "OD1" <-> "OD2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V ASP 140": "OD1" <-> "OD2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 281": "OD1" <-> "OD2" Residue "V GLU 315": "OE1" <-> "OE2" Residue "V GLU 362": "OE1" <-> "OE2" Residue "W PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 111": "OD1" <-> "OD2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "W ASP 159": "OD1" <-> "OD2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 335": "OD1" <-> "OD2" Residue "Y GLU 307": "OE1" <-> "OE2" Residue "Y GLU 371": "OE1" <-> "OE2" Residue "Z PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 69868 Number of models: 1 Model: "" Number of chains: 42 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: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 370} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "A" Number of atoms: 18103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 18103 Classifications: {'RNA': 853} Modifications used: {'rna2p_pur': 72, 'rna2p_pyr': 70, 'rna3p_pur': 369, 'rna3p_pyr': 342} Link IDs: {'rna2p': 142, 'rna3p': 710} Chain breaks: 7 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: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 296 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 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: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1032 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 78 Unusual residues: {' K': 5, ' MG': 29, 'NAD': 1} Classifications: {'undetermined': 35} Link IDs: {None: 34} 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} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15281 SG CYS 7 404 99.337 110.448 155.095 1.00 21.61 S ATOM 14802 SG CYS 7 347 103.548 106.157 151.868 1.00 33.65 S ATOM 14697 SG CYS 7 333 97.701 108.246 149.643 1.00 33.65 S ATOM 14744 SG CYS 7 339 102.851 111.667 149.873 1.00 22.31 S ATOM 52597 SG CYS O 94 114.604 154.274 96.076 1.00 33.35 S ATOM 52683 SG CYS O 105 117.312 154.723 93.600 1.00 30.33 S ATOM 52704 SG CYS O 108 116.268 157.728 95.504 1.00 33.70 S ATOM 52992 SG CYS O 143 113.819 156.215 92.920 1.00 27.63 S ATOM 53915 SG CYS P 65 124.894 65.287 50.727 1.00 44.36 S ATOM 54188 SG CYS P 100 122.292 68.029 51.443 1.00 39.26 S ATOM 41718 SG CYS E 105 124.498 69.800 46.609 1.00 66.97 S ATOM 53937 SG CYS P 68 126.831 67.048 46.459 1.00 46.08 S ATOM 50542 SG CYS M 26 92.897 165.851 74.463 1.00 29.96 S ATOM 59978 SG CYS T 149 96.305 165.835 75.402 1.00 33.06 S ATOM 59906 SG CYS T 139 95.579 167.184 68.963 1.00 31.31 S ATOM 59920 SG CYS T 141 98.314 166.742 71.425 1.00 31.18 S Time building chain proxies: 30.74, per 1000 atoms: 0.44 Number of scatterers: 69868 At special positions: 0 Unit cell: (216.648, 236.826, 216.648, 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 262 16.00 P 860 15.00 Mg 31 11.99 O 15176 8.00 N 12518 7.00 C 41007 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: 26.25 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " 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 100 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " 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="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 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 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 270 helices and 39 sheets defined 46.5% alpha, 9.5% beta 234 base pairs and 422 stacking pairs defined. Time for finding SS restraints: 22.04 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 60 removed outlier: 5.133A pdb=" N ALA 0 56 " --> pdb=" O ARG 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 64 through 70 removed outlier: 4.785A pdb=" N ARG 0 70 " --> pdb=" O GLN 0 66 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 75 Processing helix chain '0' and resid 83 through 88 Processing helix chain '0' and resid 144 through 151 removed outlier: 5.085A pdb=" N GLU 0 148 " --> pdb=" O HIS 0 145 " (cutoff:3.500A) removed outlier: 3.815A 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 107 Processing helix chain '1' and resid 116 through 129 removed outlier: 5.050A pdb=" N ASP 1 128 " --> pdb=" O GLU 1 124 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE 1 129 " --> pdb=" O ALA 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 146 removed outlier: 4.000A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 169 removed outlier: 3.881A 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: 7.393A pdb=" N GLU 1 196 " --> pdb=" O LYS 1 192 " (cutoff:3.500A) removed outlier: 7.037A 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 239 through 241 No H-bonds generated for 'chain '1' and resid 239 through 241' 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 Processing helix chain '4' and resid 69 through 77 Processing helix chain '4' and resid 100 through 123 Processing helix chain '4' and resid 125 through 127 No H-bonds generated for 'chain '4' and resid 125 through 127' Processing helix chain '4' and resid 138 through 140 No H-bonds generated for 'chain '4' and resid 138 through 140' Processing helix chain '4' and resid 154 through 163 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: 4.032A pdb=" N ARG 4 344 " --> pdb=" O LYS 4 340 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE 4 345 " --> pdb=" O CYS 4 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS 4 346 " --> pdb=" O LEU 4 342 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 343 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE 4 348 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 4 349 " --> pdb=" O PHE 4 345 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG 4 350 " --> pdb=" O HIS 4 346 " (cutoff:3.500A) removed outlier: 5.015A 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 Processing helix chain '4' and resid 410 through 426 removed outlier: 4.251A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE 4 416 " --> pdb=" O ASP 4 413 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN 4 417 " --> pdb=" O LYS 4 414 " (cutoff:3.500A) removed outlier: 3.528A 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 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 601 removed outlier: 3.850A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) removed outlier: 3.504A 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: 3.512A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 640 through 652 removed outlier: 3.674A pdb=" N GLU 4 643 " --> pdb=" O PRO 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 657 through 666 Processing helix chain '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 88 through 100 Proline residue: 5 92 - end of helix 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 144 through 160 removed outlier: 4.171A pdb=" N THR 5 148 " --> pdb=" O PHE 5 144 " (cutoff:3.500A) Proline residue: 5 149 - end of helix Processing helix chain '5' and resid 163 through 166 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: 4.229A pdb=" N MET 5 266 " --> pdb=" O ARG 5 262 " (cutoff:3.500A) removed outlier: 4.200A 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 312 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 removed outlier: 3.549A pdb=" N LEU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 169 removed outlier: 4.958A pdb=" N ALA 6 161 " --> pdb=" O GLN 6 157 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N HIS 6 162 " --> pdb=" O ARG 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 199 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 95 Processing helix chain '7' and resid 103 through 117 Processing helix chain '7' and resid 132 through 139 Processing helix chain '7' and resid 152 through 180 removed outlier: 6.256A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 198 through 207 removed outlier: 3.536A pdb=" N ILE 7 206 " --> pdb=" O ALA 7 202 " (cutoff:3.500A) 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 '8' and resid 87 through 98 Processing helix chain '8' and resid 102 through 107 Processing helix chain '8' and resid 117 through 138 removed outlier: 3.772A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 140 through 144 Processing helix chain '8' and resid 155 through 162 Processing helix chain '8' and resid 168 through 188 Processing helix chain '8' and resid 204 through 218 removed outlier: 3.601A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 242 through 250 Processing helix chain '8' and resid 252 through 255 No H-bonds generated for 'chain '8' and resid 252 through 255' Processing helix chain '8' and resid 272 through 287 Proline residue: 8 276 - end of helix removed outlier: 4.053A pdb=" N GLU 8 279 " --> pdb=" O PRO 8 276 " (cutoff:3.500A) Proline residue: 8 280 - end of helix removed outlier: 4.066A pdb=" N ALA 8 287 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 309 through 321 removed outlier: 4.627A pdb=" N HIS 8 313 " --> pdb=" O GLY 8 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS 8 314 " --> pdb=" O HIS 8 311 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU 8 316 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN 8 319 " --> pdb=" O LEU 8 316 " (cutoff:3.500A) Processing helix chain '8' and resid 326 through 334 Processing helix chain '8' and resid 353 through 361 Processing helix chain '8' and resid 363 through 368 removed outlier: 4.095A pdb=" N SER 8 368 " --> pdb=" O GLN 8 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 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: 3.542A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 3.587A pdb=" N SER B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.462A 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: 3.792A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 318 through 327 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 408 through 415 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 72 through 84 removed outlier: 4.638A pdb=" N GLU E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 51 No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.627A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 104 through 127 Processing helix chain 'F' and resid 133 through 136 Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.519A 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: 3.705A 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 235 through 239 removed outlier: 3.645A pdb=" N HIS F 238 " --> pdb=" O ALA F 235 " (cutoff:3.500A) 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 244 removed outlier: 3.968A pdb=" N PHE G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 303 No H-bonds generated for 'chain 'G' and resid 300 through 303' Processing helix chain 'G' and resid 307 through 320 Proline residue: G 316 - end of helix removed outlier: 3.634A pdb=" N VAL G 320 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 355 removed outlier: 4.611A pdb=" N SER G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.682A 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: 3.971A 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 49 through 57 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 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' 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: 3.873A 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 184 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 removed outlier: 4.156A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) No H-bonds generated for '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: 3.910A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 4.072A 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: 3.554A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 4.242A 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 116 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: 4.103A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) removed outlier: 5.201A 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 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' 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 261 No H-bonds generated for 'chain 'R' and resid 259 through 261' Processing helix chain 'R' and resid 268 through 277 Processing helix chain 'R' and resid 282 through 290 Processing helix chain 'R' and resid 294 through 307 Processing helix chain 'R' and resid 312 through 320 Processing helix chain 'R' and resid 324 through 334 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'S' and resid 12 through 22 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 66 through 77 removed outlier: 4.059A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'T' and resid 8 through 11 Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 39 through 50 removed outlier: 4.904A pdb=" N GLY T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 3.849A 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: 3.994A 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 87 Processing helix chain 'U' and resid 89 through 166 removed outlier: 4.212A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) removed outlier: 4.727A 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 77 Processing helix chain 'V' and resid 82 through 96 removed outlier: 3.508A 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: 4.117A pdb=" N LYS V 192 " --> pdb=" O HIS V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 214 Proline residue: V 211 - end of helix removed outlier: 3.948A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 218 through 238 Processing helix chain 'V' and resid 240 through 244 Processing helix chain 'V' and resid 255 through 268 Processing helix chain 'V' and resid 277 through 290 Processing helix chain 'V' and resid 327 through 343 Processing helix chain 'V' and resid 352 through 405 removed outlier: 5.479A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.633A 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: 3.799A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.705A 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: 3.651A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 161 Processing helix chain 'X' and resid 181 through 194 removed outlier: 3.848A 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: 4.902A pdb=" N THR X 237 " --> pdb=" O ARG X 234 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP X 238 " --> pdb=" O ASN X 235 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY X 241 " --> pdb=" O ASP X 238 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE X 242 " --> pdb=" O ALA X 239 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS X 248 " --> pdb=" O LYS X 245 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN X 250 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 4.333A 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: 3.854A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 325 through 337 removed outlier: 7.397A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 350 through 362 Processing helix chain 'X' and resid 374 through 384 Processing helix chain 'X' and resid 388 through 396 Processing helix chain 'Y' and resid 277 through 290 removed outlier: 3.512A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN Y 290 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 306 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: 3.556A 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 Processing helix chain 'Z' and resid 30 through 38 removed outlier: 4.046A pdb=" N VAL Z 33 " --> pdb=" O SER Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 68 removed outlier: 3.580A pdb=" N LEU Z 61 " --> pdb=" O THR Z 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE Z 67 " --> pdb=" O GLN Z 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU Z 68 " --> pdb=" O THR Z 64 " (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: 6.701A pdb=" N TRP 0 115 " --> pdb=" O THR 0 98 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL 0 100 " --> pdb=" O LYS 0 113 " (cutoff:3.500A) removed outlier: 6.755A 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: 6.882A pdb=" N VAL 5 227 " --> pdb=" O ILE 5 209 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR 5 211 " --> pdb=" O VAL 5 225 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL 5 225 " --> pdb=" O THR 5 211 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR 5 58 " --> pdb=" O HIS 5 137 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE 5 139 " --> pdb=" O TYR 5 58 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR 5 60 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU 5 80 " --> pdb=" O VAL 5 59 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU 5 61 " --> pdb=" O GLU 5 80 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU 5 82 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '6' and resid 179 through 184 removed outlier: 6.085A pdb=" N CYS 6 136 " --> pdb=" O VAL 6 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL 6 182 " --> pdb=" O CYS 6 136 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA 6 138 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP 6 184 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP 6 140 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS 6 126 " --> pdb=" O TYR 6 139 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYS 6 141 " --> pdb=" O LEU 6 124 " (cutoff:3.500A) removed outlier: 6.540A 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: 4.528A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (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: 6.678A pdb=" N ILE 7 373 " --> pdb=" O PHE 7 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '8' and resid 369 through 371 removed outlier: 6.027A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU 8 65 " --> pdb=" O VAL 8 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA 8 149 " --> pdb=" O LEU 8 65 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE 8 67 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY 8 151 " --> pdb=" O PHE 8 67 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER 8 296 " --> pdb=" O ALA 8 149 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY 8 151 " --> pdb=" O SER 8 296 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR 8 298 " --> pdb=" O GLY 8 151 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '8' and resid 257 through 262 removed outlier: 6.758A pdb=" N LEU 8 197 " --> pdb=" O ARG 8 258 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR 8 260 " --> pdb=" O SER 8 195 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER 8 195 " --> pdb=" O THR 8 260 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET 8 262 " --> pdb=" O MET 8 193 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET 8 193 " --> pdb=" O MET 8 262 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER 8 239 " --> pdb=" O VAL 8 227 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL 8 227 " --> pdb=" O SER 8 239 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.685A pdb=" N LEU B 192 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 145 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 194 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE B 195 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 220 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR B 234 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 223 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 236 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 106 through 110 removed outlier: 6.850A pdb=" N ILE B 115 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER B 109 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N HIS B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 110 through 113 Processing sheet with id= O, first strand: chain 'C' and resid 122 through 124 removed outlier: 5.962A pdb=" N GLN C 156 " --> pdb=" O VAL C 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= Q, first strand: chain 'D' and resid 254 through 261 removed outlier: 6.356A pdb=" N ALA D 246 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE D 222 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLY D 248 " --> pdb=" O THR D 220 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N THR D 220 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 294 through 298 Processing sheet with id= S, first strand: chain 'D' and resid 370 through 372 removed outlier: 3.588A pdb=" N ALA D 385 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU D 372 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 383 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 43 through 46 removed outlier: 6.066A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= V, first strand: chain 'E' and resid 35 through 41 removed outlier: 6.777A pdb=" N ASP E 67 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU E 39 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E 65 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 156 through 162 removed outlier: 3.627A pdb=" N VAL F 170 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 197 through 199 Processing sheet with id= Y, first strand: chain 'G' and resid 269 through 276 Processing sheet with id= Z, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.041A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU H 72 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR H 175 " --> pdb=" O LYS H 74 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU H 76 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR H 173 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL H 78 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU H 171 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL H 80 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA H 169 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 114 through 119 Processing sheet with id= AB, first strand: chain 'I' and resid 106 through 111 removed outlier: 6.678A pdb=" N VAL I 99 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE I 109 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE I 97 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER I 111 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR I 95 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU I 171 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL I 149 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE I 173 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 12.342A pdb=" N VAL I 151 " --> pdb=" O ILE I 173 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N ILE I 175 " --> pdb=" O VAL I 151 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 107 through 111 removed outlier: 6.806A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.498A pdb=" N ALA M 36 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN M 50 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU M 65 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 12 through 16 removed outlier: 8.640A pdb=" N LYS N 78 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE N 50 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU N 80 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS N 52 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG N 29 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL N 17 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 63 through 65 removed outlier: 6.442A pdb=" N LEU N 65 " --> pdb=" O ILE N 84 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE N 84 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 156 through 159 removed outlier: 6.613A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.680A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 189 through 191 Processing sheet with id= AJ, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.578A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY W 171 " --> pdb=" O ARG W 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG W 143 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU W 169 " --> pdb=" O ARG W 143 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.469A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'X' and resid 341 through 345 removed outlier: 9.035A pdb=" N TYR X 124 " --> pdb=" O GLY X 304 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE X 306 " --> pdb=" O TYR X 124 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU X 126 " --> pdb=" O ILE X 306 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER X 308 " --> pdb=" O LEU X 126 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLY X 128 " --> pdb=" O SER X 308 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU X 151 " --> pdb=" O LEU X 259 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA X 261 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU X 153 " --> pdb=" O ALA X 261 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP X 263 " --> pdb=" O LEU X 153 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE X 155 " --> pdb=" O ASP X 263 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 168 through 170 2105 hydrogen bonds defined for protein. 5865 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 578 hydrogen bonds 1040 hydrogen bond angles 0 basepair planarities 234 basepair parallelities 422 stacking parallelities Total time for adding SS restraints: 38.27 Time building geometry restraints manager: 28.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 28522 1.39 - 1.62: 44144 1.62 - 1.85: 409 1.85 - 2.08: 0 2.08 - 2.32: 20 Bond restraints: 73095 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=" CG PRO Y 346 " pdb=" CD PRO Y 346 " ideal model delta sigma weight residual 1.503 1.162 0.341 3.40e-02 8.65e+02 1.00e+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 6.97e+01 bond pdb=" C5A NAD A1735 " pdb=" N7A NAD A1735 " ideal model delta sigma weight residual 1.372 1.513 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.96e+01 ... (remaining 73090 not shown) Histogram of bond angle deviations from ideal: 71.64 - 85.25: 16 85.25 - 98.85: 11 98.85 - 112.45: 43641 112.45 - 126.06: 55728 126.06 - 139.66: 3467 Bond angle restraints: 102863 Sorted by residual: angle pdb=" N PRO Y 346 " pdb=" CD PRO Y 346 " pdb=" CG PRO Y 346 " ideal model delta sigma weight residual 103.20 87.07 16.13 1.50e+00 4.44e-01 1.16e+02 angle pdb=" N PRO G 96 " pdb=" CD PRO G 96 " pdb=" CG PRO G 96 " ideal model delta sigma weight residual 103.20 87.79 15.41 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO Y 346 " pdb=" N PRO Y 346 " pdb=" CD PRO Y 346 " ideal model delta sigma weight residual 112.00 98.15 13.85 1.40e+00 5.10e-01 9.79e+01 angle pdb=" CA PRO G 96 " pdb=" CB PRO G 96 " pdb=" CG PRO G 96 " ideal model delta sigma weight residual 104.50 89.45 15.05 1.90e+00 2.77e-01 6.27e+01 angle pdb=" O1A NAD A1735 " pdb=" PA NAD A1735 " pdb=" O2A NAD A1735 " ideal model delta sigma weight residual 122.64 101.82 20.82 3.00e+00 1.11e-01 4.81e+01 ... (remaining 102858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 41293 34.81 - 69.62: 1048 69.62 - 104.43: 125 104.43 - 139.24: 11 139.24 - 174.06: 7 Dihedral angle restraints: 42484 sinusoidal: 23897 harmonic: 18587 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 180.00 111.16 68.84 0 5.00e+00 4.00e-02 1.90e+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 40.15 159.85 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' C A1233 " pdb=" C1' C A1233 " pdb=" N1 C A1233 " pdb=" C2 C A1233 " ideal model delta sinusoidal sigma weight residual 200.00 46.11 153.89 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 42481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.198: 12009 4.198 - 8.396: 0 8.396 - 12.594: 0 12.594 - 16.792: 0 16.792 - 20.990: 4 Chirality restraints: 12013 Sorted by residual: 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 10.44 -20.99 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.38 -20.94 2.00e-01 2.50e+01 1.10e+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 -10.34 20.90 2.00e-01 2.50e+01 1.09e+04 ... (remaining 12010 not shown) Planarity restraints: 10016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 72 " 0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO J 73 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO J 73 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 73 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Y 345 " 0.069 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO Y 346 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO Y 346 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO Y 346 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 375 " 0.031 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP Y 375 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 375 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 375 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 375 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 375 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 375 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 375 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 375 " 0.015 2.00e-02 2.50e+03 ... (remaining 10013 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.56: 485 2.56 - 3.20: 61333 3.20 - 3.85: 147899 3.85 - 4.49: 206744 4.49 - 5.14: 300218 Nonbonded interactions: 716679 Sorted by model distance: nonbonded pdb="MG MG A1720 " pdb=" O HOH A1808 " model vdw 1.910 2.170 nonbonded pdb="MG MG A1720 " pdb=" O HOH A1823 " model vdw 1.922 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1716 " model vdw 1.925 2.170 nonbonded pdb="MG MG A1709 " pdb=" O HOH A1811 " model vdw 1.925 2.170 nonbonded pdb=" OP1 A A 816 " pdb="MG MG A1717 " model vdw 1.930 2.170 ... (remaining 716674 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 860 5.49 5 Mg 31 5.21 5 S 262 5.16 5 C 41007 2.51 5 N 12518 2.21 5 O 15176 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 18.000 Check model and map are aligned: 0.810 Process input model: 195.040 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.520 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 0.341 73095 Z= 0.296 Angle : 0.654 20.815 102863 Z= 0.344 Chirality : 0.384 20.990 12013 Planarity : 0.005 0.095 10016 Dihedral : 14.518 174.056 30426 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.02 % 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: 1.19 (0.11), residues: 6259 helix: 1.54 (0.09), residues: 2975 sheet: -0.16 (0.19), residues: 662 loop : 0.32 (0.12), residues: 2622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1053 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1053 average time/residue: 1.7969 time to fit residues: 2393.5342 Evaluate side-chains 682 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 5.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 595 optimal weight: 10.0000 chunk 534 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 360 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 552 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 640 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 192 ASN 4 90 GLN 4 346 HIS 5 235 GLN 5 316 GLN 6 43 ASN 6 115 GLN 6 165 HIS 6 175 ASN 6 187 ASN 7 39 ASN 7 60 HIS 7 69 ASN ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 209 GLN 7 290 HIS ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 398 HIS 7 400 HIS 8 111 GLN 8 145 ASN 8 222 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 302 HIS 8 313 HIS ** 8 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 69 HIS B 74 ASN B 124 HIS C 60 HIS C 115 ASN D 415 GLN D 424 ASN E 57 GLN E 58 HIS F 146 HIS H 51 HIS H 109 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS I 141 GLN I 183 HIS I 184 ASN K 113 HIS K 119 GLN L 169 ASN O 103 ASN O 225 GLN R 86 ASN R 221 GLN R 308 HIS R 350 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN U 110 GLN U 133 GLN V 188 HIS V 377 GLN ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 159 HIS X 176 GLN X 363 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.222 73095 Z= 0.419 Angle : 0.867 50.699 102863 Z= 0.506 Chirality : 0.126 6.591 12013 Planarity : 0.006 0.067 10016 Dihedral : 13.062 175.258 17249 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.91 (0.10), residues: 6259 helix: 1.23 (0.09), residues: 3010 sheet: 0.04 (0.20), residues: 644 loop : 0.15 (0.12), residues: 2605 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 721 time to evaluate : 5.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 46 residues processed: 793 average time/residue: 1.7439 time to fit residues: 1773.4607 Evaluate side-chains 701 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 655 time to evaluate : 5.373 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 27 residues processed: 19 average time/residue: 0.6678 time to fit residues: 28.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 355 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 532 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 641 optimal weight: 1.9990 chunk 692 optimal weight: 0.6980 chunk 571 optimal weight: 0.4980 chunk 636 optimal weight: 0.6980 chunk 218 optimal weight: 0.9990 chunk 514 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 192 ASN 4 189 ASN 4 540 HIS 5 316 GLN 6 43 ASN 7 144 HIS 8 70 GLN 8 313 HIS ** 8 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 74 ASN C 60 HIS C 115 ASN E 57 GLN F 169 GLN F 196 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS I 184 ASN O 225 GLN R 86 ASN S 47 GLN S 61 GLN T 35 ASN U 139 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 285 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.240 73095 Z= 0.229 Angle : 0.758 50.658 102863 Z= 0.458 Chirality : 0.121 6.405 12013 Planarity : 0.004 0.059 10016 Dihedral : 12.942 175.759 17249 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.41 (0.11), residues: 6259 helix: 1.70 (0.09), residues: 2976 sheet: 0.25 (0.20), residues: 635 loop : 0.36 (0.12), residues: 2648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 707 time to evaluate : 5.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 48 residues processed: 768 average time/residue: 1.7178 time to fit residues: 1704.2445 Evaluate side-chains 697 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 649 time to evaluate : 5.456 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 33 residues processed: 15 average time/residue: 0.7853 time to fit residues: 26.2688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 633 optimal weight: 1.9990 chunk 482 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 643 optimal weight: 2.9990 chunk 681 optimal weight: 6.9990 chunk 336 optimal weight: 2.9990 chunk 610 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 4 562 GLN 5 171 GLN 5 316 GLN 6 43 ASN 6 183 GLN 8 70 GLN ** 8 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 60 HIS C 115 ASN D 424 ASN E 57 GLN H 109 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN S 47 GLN S 61 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.239 73095 Z= 0.307 Angle : 0.786 50.758 102863 Z= 0.469 Chirality : 0.122 6.483 12013 Planarity : 0.004 0.054 10016 Dihedral : 12.864 175.696 17249 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.31 (0.10), residues: 6259 helix: 1.58 (0.09), residues: 2980 sheet: 0.35 (0.20), residues: 626 loop : 0.32 (0.12), residues: 2653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 670 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 59 residues processed: 754 average time/residue: 1.7024 time to fit residues: 1661.4568 Evaluate side-chains 702 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 643 time to evaluate : 5.458 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 37 residues processed: 22 average time/residue: 0.9151 time to fit residues: 37.7184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 567 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 507 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 581 optimal weight: 0.2980 chunk 471 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 0.6980 chunk 611 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 5 316 GLN 6 43 ASN 6 183 GLN ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 61 GLN 8 70 GLN 8 121 GLN 8 229 ASN ** 8 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN O 207 GLN R 86 ASN S 47 GLN S 61 GLN U 83 HIS ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.238 73095 Z= 0.301 Angle : 0.783 50.734 102863 Z= 0.468 Chirality : 0.122 6.456 12013 Planarity : 0.004 0.049 10016 Dihedral : 12.848 175.491 17249 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 6259 helix: 1.55 (0.09), residues: 2969 sheet: 0.32 (0.20), residues: 643 loop : 0.30 (0.12), residues: 2647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 675 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 64 residues processed: 750 average time/residue: 1.7317 time to fit residues: 1678.6206 Evaluate side-chains 702 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 638 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 41 residues processed: 24 average time/residue: 0.8825 time to fit residues: 39.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 229 optimal weight: 10.0000 chunk 613 optimal weight: 0.5980 chunk 134 optimal weight: 6.9990 chunk 400 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 682 optimal weight: 0.8980 chunk 566 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 4 189 ASN 4 257 HIS 5 316 GLN 6 43 ASN 8 70 GLN 8 121 GLN 8 380 HIS B 64 ASN B 74 ASN C 60 HIS C 115 ASN E 57 GLN F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN N 23 GLN O 207 GLN R 86 ASN S 47 GLN S 61 GLN T 122 GLN U 83 HIS ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.239 73095 Z= 0.234 Angle : 0.747 50.663 102863 Z= 0.453 Chirality : 0.120 6.387 12013 Planarity : 0.004 0.050 10016 Dihedral : 12.711 176.068 17249 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.52 (0.11), residues: 6259 helix: 1.76 (0.10), residues: 2974 sheet: 0.46 (0.20), residues: 639 loop : 0.42 (0.12), residues: 2646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 675 time to evaluate : 5.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 54 residues processed: 745 average time/residue: 1.7364 time to fit residues: 1675.1660 Evaluate side-chains 699 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 645 time to evaluate : 5.465 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 42 residues processed: 13 average time/residue: 0.7964 time to fit residues: 23.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 657 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 498 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 574 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 679 optimal weight: 5.9990 chunk 425 optimal weight: 7.9990 chunk 414 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 1 231 HIS 5 316 GLN 6 43 ASN 8 70 GLN 8 121 GLN B 64 ASN B 74 ASN C 60 HIS F 196 HIS H 161 GLN H 183 HIS N 23 GLN O 207 GLN O 225 GLN R 86 ASN S 47 GLN S 61 GLN T 122 GLN U 83 HIS X 140 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.240 73095 Z= 0.239 Angle : 0.750 50.667 102863 Z= 0.453 Chirality : 0.120 6.397 12013 Planarity : 0.004 0.045 10016 Dihedral : 12.599 175.916 17249 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.59 (0.11), residues: 6259 helix: 1.80 (0.10), residues: 2965 sheet: 0.46 (0.20), residues: 643 loop : 0.48 (0.12), residues: 2651 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 665 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 63 residues processed: 732 average time/residue: 1.7548 time to fit residues: 1661.4750 Evaluate side-chains 713 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 650 time to evaluate : 5.479 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 46 residues processed: 17 average time/residue: 0.9316 time to fit residues: 31.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 420 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 432 optimal weight: 1.9990 chunk 462 optimal weight: 9.9990 chunk 335 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 534 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 1 231 HIS 5 316 GLN 6 183 GLN ** 8 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 74 ASN C 60 HIS C 115 ASN C 116 GLN K 55 ASN N 23 GLN O 155 GLN O 207 GLN R 86 ASN S 47 GLN S 61 GLN U 83 HIS ** Y 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.238 73095 Z= 0.343 Angle : 0.804 50.789 102863 Z= 0.476 Chirality : 0.123 6.487 12013 Planarity : 0.004 0.042 10016 Dihedral : 12.633 175.320 17249 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 6259 helix: 1.53 (0.09), residues: 2964 sheet: 0.39 (0.20), residues: 634 loop : 0.30 (0.12), residues: 2661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 663 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 56 residues processed: 728 average time/residue: 1.7667 time to fit residues: 1662.9420 Evaluate side-chains 692 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 636 time to evaluate : 5.481 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 14 average time/residue: 1.0794 time to fit residues: 29.2056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.4358 > 50: distance: 21 - 27: 27.951 distance: 27 - 28: 22.584 distance: 28 - 29: 41.524 distance: 28 - 31: 33.494 distance: 29 - 30: 32.319 distance: 29 - 35: 10.558 distance: 31 - 32: 18.098 distance: 32 - 33: 33.002 distance: 32 - 34: 18.596 distance: 35 - 36: 18.732 distance: 35 - 41: 48.586 distance: 36 - 37: 29.142 distance: 36 - 39: 31.791 distance: 37 - 38: 37.950 distance: 37 - 42: 19.504 distance: 39 - 40: 42.732 distance: 40 - 41: 24.479 distance: 42 - 43: 30.168 distance: 43 - 44: 28.757 distance: 43 - 46: 22.082 distance: 44 - 45: 40.173 distance: 44 - 49: 18.880 distance: 46 - 47: 39.008 distance: 46 - 48: 49.518 distance: 49 - 50: 21.483 distance: 50 - 51: 39.122 distance: 50 - 53: 9.132 distance: 51 - 52: 41.835 distance: 51 - 56: 48.663 distance: 53 - 54: 26.042 distance: 53 - 55: 15.588 distance: 56 - 57: 49.850 distance: 57 - 58: 7.212 distance: 58 - 59: 39.966 distance: 58 - 60: 32.541 distance: 60 - 61: 16.390 distance: 61 - 62: 14.848 distance: 61 - 64: 45.968 distance: 62 - 63: 32.660 distance: 62 - 69: 33.395 distance: 64 - 65: 31.543 distance: 65 - 66: 51.665 distance: 66 - 67: 49.434 distance: 67 - 68: 55.407 distance: 69 - 70: 8.452 distance: 69 - 75: 23.158 distance: 70 - 71: 40.490 distance: 70 - 73: 43.523 distance: 71 - 72: 19.842 distance: 71 - 76: 39.660 distance: 73 - 74: 58.026 distance: 74 - 75: 43.255 distance: 76 - 77: 19.879 distance: 77 - 78: 10.545 distance: 77 - 80: 38.776 distance: 78 - 79: 29.912 distance: 78 - 82: 40.732 distance: 80 - 81: 41.377 distance: 82 - 83: 36.793 distance: 83 - 84: 37.105 distance: 83 - 86: 35.632 distance: 84 - 85: 35.650 distance: 84 - 87: 26.644 distance: 87 - 88: 19.983 distance: 88 - 89: 56.231 distance: 89 - 90: 23.497 distance: 89 - 91: 24.621