Starting phenix.real_space_refine on Sat Feb 17 16:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2024/8csr_26968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2024/8csr_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_2024/8csr_26968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2024/8csr_26968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2024/8csr_26968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/02_2024/8csr_26968_updated.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 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 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. 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-5238/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: 27.47, per 1000 atoms: 0.39 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: 23.88 Conformation dependent library (CDL) restraints added in 6.9 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: 26.64 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: 38.35 Time building geometry restraints manager: 26.04 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: 42592 34.81 - 69.62: 2252 69.62 - 104.43: 349 104.43 - 139.24: 11 139.24 - 174.06: 7 Dihedral angle restraints: 45211 sinusoidal: 26624 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 45208 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 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.770 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 193.700 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 18.518 174.056 33153 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 % Allowed : 0.16 % Favored : 99.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP Y 375 HIS 0.018 0.001 HIS I 183 PHE 0.043 0.002 PHE V 196 TYR 0.028 0.002 TYR V 226 ARG 0.014 0.001 ARG T 132 *********************** 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 : 5.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 183 GLN cc_start: 0.7433 (mt0) cc_final: 0.7163 (mt0) REVERT: D 361 GLN cc_start: 0.8832 (mt0) cc_final: 0.8516 (mt0) REVERT: D 424 ASN cc_start: 0.8301 (m-40) cc_final: 0.8045 (m110) REVERT: E 45 ARG cc_start: 0.8387 (ptp-170) cc_final: 0.8103 (ptp-170) REVERT: J 89 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7359 (ttp-110) REVERT: J 114 ARG cc_start: 0.8328 (ptm-80) cc_final: 0.8054 (ptt180) REVERT: L 144 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7011 (mt-10) REVERT: O 62 GLU cc_start: 0.6714 (tp30) cc_final: 0.6473 (tp30) REVERT: P 49 ASP cc_start: 0.7907 (m-30) cc_final: 0.7617 (m-30) REVERT: P 137 ASN cc_start: 0.7628 (m110) cc_final: 0.7067 (p0) REVERT: R 77 SER cc_start: 0.7968 (p) cc_final: 0.7758 (p) REVERT: S 50 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7178 (mtp85) REVERT: T 95 ASN cc_start: 0.8535 (p0) cc_final: 0.8335 (p0) REVERT: U 183 SER cc_start: 0.7854 (t) cc_final: 0.7464 (p) outliers start: 0 outliers final: 0 residues processed: 1053 average time/residue: 1.7500 time to fit residues: 2328.4128 Evaluate side-chains 685 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 5.178 ------------------------------------------------------------------------------- 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: 8.9990 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 4 540 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** 7 144 HIS 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 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** X 176 GLN X 363 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.251 73095 Z= 0.424 Angle : 0.867 51.056 102863 Z= 0.506 Chirality : 0.123 6.444 12013 Planarity : 0.006 0.069 10016 Dihedral : 19.627 175.398 19976 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.45 % Allowed : 9.08 % Favored : 88.47 % 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: 0.93 (0.10), residues: 6259 helix: 1.24 (0.09), residues: 3006 sheet: 0.07 (0.20), residues: 634 loop : 0.16 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP Y 375 HIS 0.019 0.002 HIS R 247 PHE 0.040 0.002 PHE 4 294 TYR 0.033 0.002 TYR V 91 ARG 0.009 0.001 ARG 8 96 *********************** 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 863 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 726 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 144 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5817 (pt0) REVERT: 4 650 MET cc_start: 0.5252 (mpt) cc_final: 0.4546 (ppp) REVERT: 6 106 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6942 (t70) REVERT: 7 30 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7842 (mm) REVERT: 8 272 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6882 (mtp180) REVERT: C 126 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: D 361 GLN cc_start: 0.8846 (mt0) cc_final: 0.8561 (mt0) REVERT: D 424 ASN cc_start: 0.8333 (m-40) cc_final: 0.8088 (m-40) REVERT: E 40 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: E 45 ARG cc_start: 0.8473 (ptp-170) cc_final: 0.8187 (ptp-170) REVERT: H 113 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7064 (ttp-110) REVERT: J 89 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7350 (ttp-110) REVERT: M 114 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7718 (mtt-85) REVERT: O 54 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: P 120 MET cc_start: 0.9242 (ttt) cc_final: 0.8950 (ttt) REVERT: P 137 ASN cc_start: 0.7712 (m110) cc_final: 0.7150 (p0) REVERT: Q 38 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7116 (t70) REVERT: R 77 SER cc_start: 0.8024 (p) cc_final: 0.7810 (p) REVERT: R 341 TYR cc_start: 0.7418 (t80) cc_final: 0.7052 (t80) REVERT: T 9 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8239 (tp) REVERT: T 66 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.7614 (mpp) REVERT: U 101 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: U 132 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5706 (tm-30) REVERT: U 183 SER cc_start: 0.8084 (t) cc_final: 0.7710 (p) REVERT: U 185 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7682 (tttt) REVERT: X 73 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6585 (mm-40) outliers start: 137 outliers final: 45 residues processed: 796 average time/residue: 1.7094 time to fit residues: 1742.1466 Evaluate side-chains 715 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 655 time to evaluate : 5.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 303 GLU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 441 THR Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 55 THR Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 82 THR Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 108 HIS Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain T residue 164 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 149 ASP Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 376 PHE 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: 1.9990 chunk 532 optimal weight: 5.9990 chunk 435 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 641 optimal weight: 1.9990 chunk 692 optimal weight: 0.7980 chunk 571 optimal weight: 4.9990 chunk 636 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 514 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 4 562 GLN 5 316 GLN 6 43 ASN 7 209 GLN 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 F 238 HIS H 109 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 HIS X 159 HIS Y 285 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 73095 Z= 0.268 Angle : 0.775 50.635 102863 Z= 0.465 Chirality : 0.122 6.431 12013 Planarity : 0.004 0.060 10016 Dihedral : 19.516 175.685 19976 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.22 % Allowed : 10.88 % Favored : 86.90 % 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: 1.24 (0.11), residues: 6259 helix: 1.53 (0.09), residues: 2999 sheet: 0.26 (0.20), residues: 632 loop : 0.28 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 375 HIS 0.010 0.001 HIS 8 214 PHE 0.035 0.001 PHE 4 294 TYR 0.020 0.001 TYR V 91 ARG 0.008 0.000 ARG U 134 *********************** 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: 124 poor density : 694 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 650 MET cc_start: 0.5255 (mpt) cc_final: 0.4868 (ppp) REVERT: 7 30 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (mm) REVERT: 7 178 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.7268 (tmm-80) REVERT: 7 215 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6468 (tpp) REVERT: 7 226 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7178 (tp) REVERT: 8 193 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7876 (mtm) REVERT: 8 272 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6787 (mtp180) REVERT: D 424 ASN cc_start: 0.8365 (m-40) cc_final: 0.8107 (m110) REVERT: E 40 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: I 138 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7408 (mtp180) REVERT: J 47 ARG cc_start: 0.6068 (ttt-90) cc_final: 0.5854 (ttt-90) REVERT: J 89 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7312 (ttp-110) REVERT: J 114 ARG cc_start: 0.8406 (ptm-80) cc_final: 0.8143 (ptt180) REVERT: M 114 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7705 (mtt-85) REVERT: P 120 MET cc_start: 0.9217 (ttt) cc_final: 0.8947 (ttt) REVERT: P 137 ASN cc_start: 0.7758 (m110) cc_final: 0.7237 (p0) REVERT: R 203 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8097 (mtmt) REVERT: S 50 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7336 (mtp85) REVERT: T 66 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7631 (mpp) REVERT: U 101 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: U 127 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: U 132 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5694 (tm-30) REVERT: U 183 SER cc_start: 0.8049 (t) cc_final: 0.7737 (p) REVERT: U 185 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7699 (tttt) REVERT: V 91 TYR cc_start: 0.8515 (m-80) cc_final: 0.8260 (m-80) REVERT: V 196 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6242 (t80) REVERT: W 109 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: X 73 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6578 (mm-40) REVERT: Y 285 GLN cc_start: 0.6972 (tt0) cc_final: 0.6211 (mp10) outliers start: 124 outliers final: 48 residues processed: 764 average time/residue: 1.6895 time to fit residues: 1652.7355 Evaluate side-chains 717 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 653 time to evaluate : 5.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 231 HIS Chi-restraints excluded: chain 1 residue 303 GLU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 82 THR Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 334 LEU Chi-restraints excluded: chain Y residue 376 PHE 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: 2.9990 chunk 332 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 643 optimal weight: 1.9990 chunk 681 optimal weight: 5.9990 chunk 336 optimal weight: 0.9980 chunk 610 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 5 171 GLN 5 316 GLN 6 43 ASN 6 183 GLN 8 70 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 229 ASN ** 8 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 74 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN E 57 GLN ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1935 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= 0.268 Angle : 0.767 50.690 102863 Z= 0.462 Chirality : 0.121 6.431 12013 Planarity : 0.004 0.054 10016 Dihedral : 19.420 175.988 19976 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 11.74 % Favored : 85.64 % 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: 1.35 (0.11), residues: 6259 helix: 1.62 (0.09), residues: 2978 sheet: 0.34 (0.20), residues: 642 loop : 0.32 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 375 HIS 0.016 0.001 HIS 4 288 PHE 0.040 0.001 PHE 4 294 TYR 0.022 0.001 TYR V 91 ARG 0.009 0.000 ARG O 89 *********************** 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 840 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 694 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8626 (mp) REVERT: 0 148 GLU cc_start: 0.7102 (mp0) cc_final: 0.6880 (mp0) REVERT: 4 650 MET cc_start: 0.5130 (mpt) cc_final: 0.4692 (ttp) REVERT: 5 80 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: 5 127 ARG cc_start: 0.6720 (mtp85) cc_final: 0.6488 (mtp85) REVERT: 6 106 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6917 (t70) REVERT: 6 197 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7035 (tp) REVERT: 7 30 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7755 (mm) REVERT: 7 215 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6447 (tpp) REVERT: 7 226 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7131 (tp) REVERT: 8 193 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7873 (mtm) REVERT: 8 262 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5962 (tpp) REVERT: 8 272 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: D 332 MET cc_start: 0.9002 (ttp) cc_final: 0.8698 (ttp) REVERT: D 424 ASN cc_start: 0.8338 (m-40) cc_final: 0.8067 (m110) REVERT: E 40 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: G 280 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6722 (mttm) REVERT: I 138 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: N 23 GLN cc_start: 0.8084 (mt0) cc_final: 0.7794 (tt0) REVERT: P 120 MET cc_start: 0.9200 (ttt) cc_final: 0.8890 (ttt) REVERT: P 137 ASN cc_start: 0.7805 (m110) cc_final: 0.7308 (p0) REVERT: Q 20 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7152 (tp30) REVERT: R 203 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8133 (mtmt) REVERT: S 50 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7502 (mtp85) REVERT: T 66 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: T 70 MET cc_start: 0.8496 (mtp) cc_final: 0.7999 (mtp) REVERT: T 157 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8109 (mmtp) REVERT: U 101 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: U 127 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: U 183 SER cc_start: 0.8071 (t) cc_final: 0.7777 (p) REVERT: U 185 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7690 (tttt) REVERT: V 196 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.5962 (t80) REVERT: X 73 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6586 (mm-40) REVERT: Y 259 PHE cc_start: 0.5489 (OUTLIER) cc_final: 0.4451 (t80) outliers start: 146 outliers final: 60 residues processed: 776 average time/residue: 1.6852 time to fit residues: 1681.9222 Evaluate side-chains 729 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 646 time to evaluate : 5.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 153 SER Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 231 HIS Chi-restraints excluded: chain 1 residue 303 GLU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 598 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 6 residue 197 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 102 LEU Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 334 LEU Chi-restraints excluded: chain Y residue 376 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 567 optimal weight: 10.0000 chunk 386 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 507 optimal weight: 7.9990 chunk 281 optimal weight: 10.0000 chunk 581 optimal weight: 3.9990 chunk 471 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 611 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 6 162 HIS 7 209 GLN ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 61 GLN 8 70 GLN 8 121 GLN 8 380 HIS B 64 ASN B 74 ASN B 201 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN O 207 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 HIS ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN Y 257 ASN ** Y 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.237 73095 Z= 0.450 Angle : 0.860 50.909 102863 Z= 0.502 Chirality : 0.125 6.554 12013 Planarity : 0.005 0.053 10016 Dihedral : 19.525 175.168 19976 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.01 % Allowed : 13.01 % Favored : 83.98 % 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: 0.86 (0.10), residues: 6259 helix: 1.18 (0.09), residues: 2984 sheet: 0.25 (0.20), residues: 635 loop : 0.09 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 3 177 HIS 0.013 0.002 HIS 7 400 PHE 0.040 0.002 PHE 4 294 TYR 0.034 0.002 TYR V 91 ARG 0.012 0.001 ARG G 106 *********************** 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 831 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 663 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 148 GLU cc_start: 0.7186 (mp0) cc_final: 0.6964 (mp0) REVERT: 1 119 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7221 (mm) REVERT: 1 248 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5195 (tmm) REVERT: 4 650 MET cc_start: 0.5117 (mpt) cc_final: 0.4831 (ttp) REVERT: 6 106 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6999 (t70) REVERT: 6 197 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7235 (tp) REVERT: 7 30 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (mm) REVERT: 8 193 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (mtm) REVERT: 8 272 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6922 (mtp180) REVERT: E 40 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: G 280 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6798 (mttm) REVERT: I 138 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7447 (mtp180) REVERT: K 108 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.4840 (ptp-170) REVERT: L 116 VAL cc_start: 0.8800 (m) cc_final: 0.8585 (m) REVERT: P 120 MET cc_start: 0.9255 (ttt) cc_final: 0.8958 (ttt) REVERT: P 137 ASN cc_start: 0.7815 (m110) cc_final: 0.7324 (p0) REVERT: Q 20 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: R 203 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8145 (mtmt) REVERT: T 66 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7622 (mpp) REVERT: T 70 MET cc_start: 0.8480 (mtp) cc_final: 0.8070 (mtp) REVERT: T 157 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: U 101 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: U 127 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6597 (mt-10) REVERT: U 132 GLU cc_start: 0.6037 (tm-30) cc_final: 0.5830 (tm-30) REVERT: U 183 SER cc_start: 0.8071 (t) cc_final: 0.7762 (p) REVERT: U 185 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7688 (tttt) REVERT: V 196 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.5736 (t80) REVERT: X 73 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6616 (mm-40) REVERT: Y 259 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.4578 (t80) outliers start: 168 outliers final: 76 residues processed: 764 average time/residue: 1.6826 time to fit residues: 1644.9233 Evaluate side-chains 735 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 638 time to evaluate : 5.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 231 HIS Chi-restraints excluded: chain 1 residue 248 MET Chi-restraints excluded: chain 1 residue 297 VAL Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 465 ILE Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 83 VAL Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 274 LEU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 197 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 102 LEU Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 334 LEU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 68 LEU 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: 0.9980 chunk 134 optimal weight: 0.7980 chunk 400 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 682 optimal weight: 1.9990 chunk 566 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 6 183 GLN 7 209 GLN ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 70 GLN 8 121 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 74 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 ASN K 55 ASN O 207 GLN O 225 GLN P 137 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 GLN U 83 HIS V 396 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2282 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= 0.239 Angle : 0.761 50.656 102863 Z= 0.459 Chirality : 0.121 6.383 12013 Planarity : 0.004 0.056 10016 Dihedral : 19.389 175.954 19976 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 14.21 % Favored : 83.60 % 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: 1.30 (0.11), residues: 6259 helix: 1.56 (0.09), residues: 2975 sheet: 0.37 (0.20), residues: 636 loop : 0.32 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 177 HIS 0.008 0.001 HIS 7 52 PHE 0.038 0.001 PHE 4 294 TYR 0.019 0.001 TYR H 93 ARG 0.012 0.000 ARG H 113 *********************** 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 795 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 673 time to evaluate : 5.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8608 (mp) REVERT: 0 148 GLU cc_start: 0.7114 (mp0) cc_final: 0.6866 (mp0) REVERT: 0 190 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7142 (mpt) REVERT: 1 119 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7130 (mm) REVERT: 5 80 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: 7 30 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (mm) REVERT: 8 272 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6808 (mtp180) REVERT: D 332 MET cc_start: 0.8995 (ttp) cc_final: 0.8715 (ttp) REVERT: E 40 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: G 280 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6703 (mttm) REVERT: I 138 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7329 (mtp180) REVERT: J 71 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8414 (ptmt) REVERT: K 112 ARG cc_start: 0.3791 (ptt180) cc_final: 0.3519 (ptp-170) REVERT: L 83 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: N 23 GLN cc_start: 0.8130 (tt0) cc_final: 0.7849 (tt0) REVERT: P 137 ASN cc_start: 0.7633 (m-40) cc_final: 0.7245 (p0) REVERT: S 36 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: T 66 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7541 (mpp) REVERT: T 70 MET cc_start: 0.8542 (mtp) cc_final: 0.8094 (mtp) REVERT: T 157 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (mmtp) REVERT: U 127 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6572 (mt-10) REVERT: U 183 SER cc_start: 0.8055 (t) cc_final: 0.7763 (p) REVERT: U 185 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7676 (tttt) REVERT: V 91 TYR cc_start: 0.8511 (m-80) cc_final: 0.8229 (m-80) REVERT: X 73 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6587 (mm-40) REVERT: Y 259 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4618 (t80) REVERT: Y 299 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6755 (mm-30) REVERT: Y 303 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6738 (tp-100) REVERT: Y 323 ASP cc_start: 0.5879 (t0) cc_final: 0.5259 (t0) outliers start: 122 outliers final: 49 residues processed: 738 average time/residue: 1.7333 time to fit residues: 1648.8069 Evaluate side-chains 713 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 646 time to evaluate : 5.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 190 MET Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 237 GLU Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 274 LEU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 188 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL 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: 0.9990 chunk 388 optimal weight: 0.7980 chunk 498 optimal weight: 0.9990 chunk 385 optimal weight: 0.7980 chunk 574 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 chunk 679 optimal weight: 0.8980 chunk 425 optimal weight: 1.9990 chunk 414 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 6 183 GLN 7 209 GLN 8 70 GLN 8 121 GLN B 64 ASN B 74 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN D 424 ASN F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN O 155 GLN O 207 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 GLN U 83 HIS V 396 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2351 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= 0.232 Angle : 0.752 50.609 102863 Z= 0.454 Chirality : 0.120 6.372 12013 Planarity : 0.004 0.063 10016 Dihedral : 19.292 176.252 19976 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.77 % Allowed : 15.16 % Favored : 83.06 % 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: 1.49 (0.11), residues: 6259 helix: 1.72 (0.10), residues: 2971 sheet: 0.48 (0.21), residues: 624 loop : 0.41 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 177 HIS 0.007 0.001 HIS 7 52 PHE 0.038 0.001 PHE 4 294 TYR 0.017 0.001 TYR V 91 ARG 0.016 0.000 ARG G 106 *********************** 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 780 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 681 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8560 (mp) REVERT: 0 148 GLU cc_start: 0.7067 (mp0) cc_final: 0.6844 (mp0) REVERT: 1 119 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7075 (mm) REVERT: 5 80 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: 6 106 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6893 (t70) REVERT: 7 30 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7807 (mm) REVERT: 7 215 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6443 (tpp) REVERT: 7 226 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7056 (tp) REVERT: 8 272 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6759 (mtp180) REVERT: E 40 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: G 280 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6610 (mttm) REVERT: I 138 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7426 (mtp180) REVERT: K 112 ARG cc_start: 0.3937 (ptt180) cc_final: 0.3608 (ptp-170) REVERT: L 83 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: N 23 GLN cc_start: 0.8100 (tt0) cc_final: 0.7775 (tt0) REVERT: P 54 MET cc_start: 0.8637 (ptp) cc_final: 0.8364 (ptm) REVERT: P 137 ASN cc_start: 0.7564 (m-40) cc_final: 0.7264 (p0) REVERT: S 36 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: S 50 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7547 (mtp85) REVERT: T 66 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: T 70 MET cc_start: 0.8550 (mtp) cc_final: 0.8091 (mtp) REVERT: T 119 GLU cc_start: 0.7145 (tt0) cc_final: 0.6553 (pt0) REVERT: T 157 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8098 (mmtp) REVERT: U 127 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6465 (mt-10) REVERT: U 134 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5965 (ttp-110) REVERT: U 183 SER cc_start: 0.8086 (t) cc_final: 0.7759 (p) REVERT: U 185 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7666 (tttt) REVERT: V 91 TYR cc_start: 0.8472 (m-80) cc_final: 0.8176 (m-80) REVERT: X 73 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6584 (mm-40) REVERT: Y 259 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.4563 (t80) REVERT: Y 303 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6714 (tp-100) outliers start: 99 outliers final: 40 residues processed: 737 average time/residue: 1.6755 time to fit residues: 1578.2475 Evaluate side-chains 703 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 644 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 237 GLU Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 420 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 chunk 462 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 534 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 116 GLN E 57 GLN F 196 HIS K 55 ASN O 155 GLN O 207 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** X 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 HIS Z 63 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 73095 Z= 0.317 Angle : 0.796 50.729 102863 Z= 0.473 Chirality : 0.122 6.472 12013 Planarity : 0.004 0.052 10016 Dihedral : 19.304 175.710 19976 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.02 % Allowed : 15.31 % Favored : 82.67 % 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 (0.11), residues: 6259 helix: 1.53 (0.09), residues: 2978 sheet: 0.37 (0.20), residues: 634 loop : 0.32 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 3 177 HIS 0.008 0.001 HIS 7 400 PHE 0.040 0.002 PHE 4 294 TYR 0.026 0.002 TYR V 91 ARG 0.011 0.000 ARG G 106 *********************** 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 771 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 658 time to evaluate : 5.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 148 GLU cc_start: 0.7151 (mp0) cc_final: 0.6905 (mp0) REVERT: 1 119 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7144 (mm) REVERT: 4 615 MET cc_start: 0.4162 (mmp) cc_final: 0.3897 (mmt) REVERT: 5 80 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: 6 106 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6928 (t70) REVERT: 6 183 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: 7 30 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7925 (mm) REVERT: 7 215 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6429 (tpp) REVERT: 8 193 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: 8 272 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6833 (mtp180) REVERT: E 40 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: G 280 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6731 (mttm) REVERT: I 138 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7435 (mtp180) REVERT: L 83 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: P 59 LYS cc_start: 0.7988 (tttp) cc_final: 0.7767 (tttm) REVERT: P 120 MET cc_start: 0.9237 (ttt) cc_final: 0.8889 (ttt) REVERT: P 137 ASN cc_start: 0.7551 (m-40) cc_final: 0.7238 (p0) REVERT: Q 20 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: R 203 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8178 (mtmt) REVERT: S 36 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: T 66 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: T 70 MET cc_start: 0.8511 (mtp) cc_final: 0.8045 (mtp) REVERT: T 119 GLU cc_start: 0.7174 (tt0) cc_final: 0.6608 (pt0) REVERT: T 157 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8142 (mmtp) REVERT: U 127 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: U 134 ARG cc_start: 0.6264 (mtm110) cc_final: 0.6007 (ttp-110) REVERT: U 183 SER cc_start: 0.8077 (t) cc_final: 0.7775 (p) REVERT: U 185 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7651 (tttt) REVERT: X 73 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6594 (mm-40) REVERT: Y 259 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.4649 (t80) REVERT: Y 299 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: Y 303 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6841 (tp-100) outliers start: 113 outliers final: 58 residues processed: 722 average time/residue: 1.7261 time to fit residues: 1592.1929 Evaluate side-chains 718 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 638 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 279 ASP Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 618 optimal weight: 5.9990 chunk 650 optimal weight: 0.9990 chunk 593 optimal weight: 9.9990 chunk 633 optimal weight: 6.9990 chunk 381 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 497 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 572 optimal weight: 6.9990 chunk 598 optimal weight: 0.9980 chunk 631 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 4 243 ASN 5 316 GLN ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS K 55 ASN O 207 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** Y 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 73095 Z= 0.280 Angle : 0.778 50.675 102863 Z= 0.465 Chirality : 0.122 6.431 12013 Planarity : 0.004 0.057 10016 Dihedral : 19.278 175.784 19976 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.81 % Allowed : 15.79 % Favored : 82.40 % 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: 1.33 (0.11), residues: 6259 helix: 1.57 (0.09), residues: 2971 sheet: 0.40 (0.20), residues: 634 loop : 0.36 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 304 HIS 0.007 0.001 HIS Y 372 PHE 0.040 0.001 PHE 4 294 TYR 0.022 0.001 TYR V 91 ARG 0.014 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 9 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 756 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 655 time to evaluate : 5.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8634 (mp) REVERT: 0 148 GLU cc_start: 0.7130 (mp0) cc_final: 0.6890 (mp0) REVERT: 1 119 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7117 (mm) REVERT: 1 251 TYR cc_start: 0.7340 (t80) cc_final: 0.7138 (t80) REVERT: 4 266 MET cc_start: 0.4525 (OUTLIER) cc_final: 0.3670 (tpp) REVERT: 4 270 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4603 (mmp80) REVERT: 4 394 TYR cc_start: 0.5070 (OUTLIER) cc_final: 0.4847 (m-10) REVERT: 5 80 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: 6 106 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6916 (t70) REVERT: 6 183 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: 7 30 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (mm) REVERT: 7 215 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6400 (tpp) REVERT: 8 193 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7902 (mtm) REVERT: 8 262 MET cc_start: 0.6262 (tpt) cc_final: 0.5974 (mmm) REVERT: 8 272 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6761 (mtp180) REVERT: D 332 MET cc_start: 0.9006 (ttp) cc_final: 0.8696 (ttp) REVERT: E 40 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: E 44 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: G 280 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6711 (mttm) REVERT: I 138 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7510 (mtp180) REVERT: L 83 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6597 (pm20) REVERT: P 59 LYS cc_start: 0.7978 (tttp) cc_final: 0.7770 (tttm) REVERT: P 120 MET cc_start: 0.9216 (ttt) cc_final: 0.8847 (ttt) REVERT: P 137 ASN cc_start: 0.7598 (m-40) cc_final: 0.7284 (p0) REVERT: Q 20 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: R 203 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8190 (mtmt) REVERT: S 36 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: T 66 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7476 (mpp) REVERT: T 70 MET cc_start: 0.8540 (mtp) cc_final: 0.8064 (mtp) REVERT: T 119 GLU cc_start: 0.7175 (tt0) cc_final: 0.6620 (pt0) REVERT: T 157 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8140 (mmtp) REVERT: U 127 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: U 134 ARG cc_start: 0.6252 (mtm110) cc_final: 0.5976 (ttp-110) REVERT: U 183 SER cc_start: 0.8070 (t) cc_final: 0.7773 (p) REVERT: U 185 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7693 (tttt) REVERT: X 73 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6596 (mm-40) REVERT: Y 259 PHE cc_start: 0.5639 (OUTLIER) cc_final: 0.4634 (t80) REVERT: Y 299 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6681 (mm-30) outliers start: 101 outliers final: 55 residues processed: 711 average time/residue: 1.7004 time to fit residues: 1547.0597 Evaluate side-chains 722 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 640 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 3 residue 177 TRP Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 266 MET Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 270 ARG Chi-restraints excluded: chain 4 residue 394 TYR Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 88 ARG Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 415 optimal weight: 0.9980 chunk 669 optimal weight: 0.9990 chunk 408 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 465 optimal weight: 3.9990 chunk 702 optimal weight: 2.9990 chunk 646 optimal weight: 9.9990 chunk 559 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 432 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 4 243 ASN 5 316 GLN 6 43 ASN ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 HIS J 106 GLN K 55 ASN O 207 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** Y 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 372 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.237 73095 Z= 0.318 Angle : 0.799 50.718 102863 Z= 0.474 Chirality : 0.122 6.456 12013 Planarity : 0.004 0.057 10016 Dihedral : 19.283 175.628 19976 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.68 % Allowed : 16.04 % Favored : 82.28 % 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: 1.21 (0.10), residues: 6259 helix: 1.46 (0.09), residues: 2975 sheet: 0.33 (0.20), residues: 648 loop : 0.31 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 304 HIS 0.007 0.001 HIS 7 398 PHE 0.039 0.002 PHE 4 294 TYR 0.025 0.002 TYR V 91 ARG 0.014 0.000 ARG G 106 ********************** REFINEMENT MACRO_CYCLE 10 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 736 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 642 time to evaluate : 5.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8650 (mp) REVERT: 0 148 GLU cc_start: 0.7154 (mp0) cc_final: 0.6907 (mp0) REVERT: 1 119 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7126 (mm) REVERT: 1 232 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: 1 251 TYR cc_start: 0.7450 (t80) cc_final: 0.7220 (t80) REVERT: 5 80 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: 6 47 LYS cc_start: 0.8036 (tppt) cc_final: 0.7783 (tptm) REVERT: 6 106 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6924 (t70) REVERT: 6 183 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: 6 197 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7234 (tp) REVERT: 7 30 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7952 (mm) REVERT: 7 215 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6390 (tpp) REVERT: 8 193 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7940 (mtm) REVERT: 8 262 MET cc_start: 0.6273 (tpt) cc_final: 0.5975 (mmm) REVERT: 8 272 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6778 (mtp180) REVERT: E 40 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: E 44 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: G 280 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6724 (mttm) REVERT: I 138 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7426 (mtp180) REVERT: J 89 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7544 (ttp-110) REVERT: L 83 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: P 120 MET cc_start: 0.9248 (ttt) cc_final: 0.8958 (ttt) REVERT: P 137 ASN cc_start: 0.7531 (m-40) cc_final: 0.7230 (p0) REVERT: Q 20 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: S 36 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: T 66 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.7504 (mpp) REVERT: T 70 MET cc_start: 0.8528 (mtp) cc_final: 0.8061 (mtp) REVERT: T 119 GLU cc_start: 0.7183 (tt0) cc_final: 0.6623 (pt0) REVERT: T 157 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (mmtp) REVERT: U 127 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: U 183 SER cc_start: 0.8072 (t) cc_final: 0.7779 (p) REVERT: U 185 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7690 (tttt) REVERT: X 73 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6549 (mm-40) REVERT: Y 259 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.4666 (t80) REVERT: Y 299 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: Z 31 MET cc_start: 0.4514 (ppp) cc_final: 0.3907 (ppp) outliers start: 94 outliers final: 59 residues processed: 694 average time/residue: 1.7229 time to fit residues: 1529.4801 Evaluate side-chains 713 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 629 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 97 MET Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 232 GLU Chi-restraints excluded: chain 4 residue 66 ASP Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 266 MET Chi-restraints excluded: chain 4 residue 267 VAL Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 80 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 6 residue 197 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 344 ASN Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 88 ARG Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 409 GLU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain I residue 138 ARG Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 124 SER Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 299 GLU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 444 optimal weight: 6.9990 chunk 595 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 515 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 560 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 575 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- 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 4 243 ASN 4 257 HIS 5 316 GLN 6 43 ASN 7 49 HIS B 64 ASN B 74 ASN C 60 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 HIS ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 ASN O 207 GLN O 225 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 83 HIS V 396 GLN ** Y 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122989 restraints weight = 109372.560| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.65 r_work: 0.3428 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 73095 Z= 0.232 Angle : 0.756 50.619 102863 Z= 0.455 Chirality : 0.120 6.382 12013 Planarity : 0.004 0.055 10016 Dihedral : 19.207 176.204 19976 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.45 % Allowed : 16.34 % Favored : 82.21 % 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: 1.53 (0.11), residues: 6259 helix: 1.73 (0.10), residues: 2956 sheet: 0.49 (0.20), residues: 635 loop : 0.47 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 304 HIS 0.007 0.001 HIS 7 52 PHE 0.041 0.001 PHE 4 294 TYR 0.016 0.001 TYR V 91 ARG 0.016 0.000 ARG U 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25304.60 seconds wall clock time: 440 minutes 32.45 seconds (26432.45 seconds total)